[1] "ofn"       "-oTGBM-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/GBM-TP/15078636/GBM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBM-TP/15125141/GBM-TP.mergedcluster.txt"

nPatients in clinical file=592, in cluster file=599, common to both=592
[1]  10 592
[1] "MRNA_CNMF"
[1] 3
  1   2   3   4 
154  97 156 118 
  1   2   3   4 
154  97 156 118 
[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 
165 182  90 124 
  1   2   3   4 
165 182  90 124 
[1] "MIR_CHIERARCHICAL"
[1] 3
  1   2   3 
302 129 130 
  1   2   3 
302 129 130 
[1] "CN_CNMF"
[1] 3
  1   2   3 
160 217 193 
  1   2   3 
160 217 193 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 92 110  81 
  1   2   3 
 92 110  81 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
57 61 44 49 
 1  2  3  4 
57 61 44 49 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
72 82 57 
 1  2  3 
72 82 57 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
47 70 35 
 1  2  3 
47 70 35 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
32 96 24 
 1  2  3 
32 96 24 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "DCC_UPLOAD_DATE"                       
 [7] "GENDER"                                
 [8] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
 [9] "RADIATION_THERAPY"                     
[10] "KARNOFSKY_PERFORMANCE_SCORE"           
[11] "HISTOLOGICAL_TYPE"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 592 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=378,	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=407,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              17-7-2014 26-3-2015 6-11-2014
freq.values   "1"       "590"     "1"      
freq.contrast "591"     "2"       "591"    
both >= 3     "FALSE"   "FALSE"   "FALSE"  
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'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 9:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 592 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"                        
[2] "GENDER"                                
[3] "KARNOFSKY_PERFORMANCE_SCORE"           
[4] "HISTOLOGICAL_TYPE"                     
[5] "RADIATIONS_RADIATION_REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=72, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1  16 138
  subtype2  17  80
  subtype3  27 129
  subtype4  19  99
subtype1 subtype2 subtype3 subtype4 
     154       97      156      118 
subtype1 subtype2 subtype3 subtype4 
     138       80      129       99 
$subtype1
TCGA-02-0001 TCGA-02-0003 TCGA-02-0004 TCGA-02-0009 TCGA-02-0025 TCGA-02-0027 
       11.77         4.73        11.34        10.59        42.74        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       90.58         2.83        14.14        10.52        18.31         6.87 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0075 TCGA-02-0079 TCGA-02-0086 TCGA-02-0089 
        6.02        19.73        20.84        27.25         8.81        16.96 
TCGA-02-0099 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0337 TCGA-02-0456 
        3.48        11.67        17.65        23.18        25.12         3.35 
TCGA-02-2470 TCGA-02-2486 TCGA-06-0122 TCGA-06-0124 TCGA-06-0130 TCGA-06-0139 
       12.92        20.32         6.15        20.38        12.95        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 
        0.20        10.29        11.74        17.79         8.61        12.33 
TCGA-06-0155 TCGA-06-0156 TCGA-06-0164 TCGA-06-0168 TCGA-06-0169 TCGA-06-0175 
       10.45         5.85        56.91        19.66         3.29         4.04 
TCGA-06-0176 TCGA-06-0184 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       91.00        69.90        15.42        10.42        38.96         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0210 TCGA-06-0213 TCGA-06-0397 
        5.56         0.39         7.66         7.40         0.53         9.01 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0649 
       72.36         9.57        12.62         5.75         5.75         2.10 
TCGA-06-0650 TCGA-06-0750 TCGA-06-0881 TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 
       23.57         0.92        16.57        26.76        23.93        26.79 
TCGA-06-1802 TCGA-06-2567 TCGA-06-5410 TCGA-06-5412 TCGA-06-5418 TCGA-08-0346 
       15.32         4.37         3.55         4.54         2.73         8.42 
TCGA-08-0352 TCGA-08-0360 TCGA-08-0373 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
        1.28        15.39         4.41        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0522 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        4.27        42.15        20.88        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-12-1092 TCGA-12-1093 TCGA-12-1095 TCGA-12-1096 
       20.58       127.59        21.73        15.98        15.85         9.11 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0789 TCGA-14-0817 TCGA-14-1037 
       15.12         0.95         6.21        11.24         5.39        19.30 
TCGA-14-1396 TCGA-14-1452 TCGA-14-1823 TCGA-14-1829 TCGA-14-2554 TCGA-16-1045 
        1.12         7.10        17.85         7.17        17.49        29.03 
TCGA-16-1055 TCGA-16-1060 TCGA-19-1385 TCGA-19-1389 TCGA-19-1790 TCGA-19-2623 
       10.29         9.14        10.75         4.64         5.06         7.53 
TCGA-19-5947 TCGA-19-5955 TCGA-26-1438 TCGA-26-5139 TCGA-27-1830 TCGA-27-1832 
        6.64         1.78        10.03         1.58         5.06         9.86 
TCGA-27-2524 TCGA-27-2527 TCGA-28-1745 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        7.59        14.40        11.34         8.35         7.63         8.48 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-5207 TCGA-28-5209 TCGA-28-5215 
        0.66         4.77         7.30        11.28        14.53        11.01 
TCGA-32-1977 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 
        0.10         4.67        12.69        14.86        12.23        20.78 
TCGA-32-2615 TCGA-32-2632 TCGA-32-4208 TCGA-32-4209 TCGA-32-4213 TCGA-41-3393 
       15.95         8.84        21.14        20.32        19.86         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-76-6193 TCGA-76-6282 
       11.84         0.20         2.70        17.06 

$subtype2
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0021 
       23.18        35.41        20.71        82.59        20.61        77.65 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0038 TCGA-02-0047 TCGA-02-0048 TCGA-02-0069 
       53.10        24.59        10.72        14.73         3.22        28.70 
TCGA-02-0074 TCGA-02-0104 TCGA-02-0114 TCGA-02-0116 TCGA-02-0266 TCGA-02-0271 
       10.19        65.00        99.98        48.95        17.72        14.47 
TCGA-02-0281 TCGA-02-0321 TCGA-02-0338 TCGA-02-0339 TCGA-02-2466 TCGA-02-2483 
        3.98         9.90        10.59        12.39        16.80        15.32 
TCGA-06-0174 TCGA-06-0177 TCGA-06-0241 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 
        3.22         4.18        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-06-5413 TCGA-06-5416 TCGA-06-5858 TCGA-08-0245 TCGA-08-0344 
        0.43         8.81         6.71         6.15        37.84       115.86 
TCGA-08-0353 TCGA-08-0517 TCGA-08-0524 TCGA-12-0616 TCGA-12-0692 TCGA-12-0820 
        8.42        58.68         7.27        14.73         3.65        18.48 
TCGA-12-0821 TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 TCGA-12-3650 TCGA-12-5301 
       10.62        15.65        59.77        44.02        10.95         2.04 
TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
       16.50         2.04        28.93         1.15        30.18         0.92 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-3477 TCGA-14-4157 
        0.99         1.97        17.79         7.63         3.78         3.42 
TCGA-15-1449 TCGA-16-0850 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-2624 
       13.28        16.37        25.38         3.65        12.66         0.16 
TCGA-19-5956 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-27-2521 
       22.49        14.86         5.49         8.88        18.97        10.39 
TCGA-27-2523 TCGA-28-1753 TCGA-28-5204 TCGA-28-5208 TCGA-28-5213 TCGA-28-5214 
       16.08         1.22        14.93        17.88        31.27        23.44 
TCGA-28-5216 TCGA-28-5218 TCGA-32-1973 TCGA-32-2616 TCGA-32-2634 TCGA-32-5222 
       13.64         5.16        21.07         7.36        22.78        19.23 
TCGA-41-5651 TCGA-76-4929 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
       15.12         3.65        47.93         2.53        10.78        16.70 
TCGA-76-6285 
        8.35 

$subtype3
TCGA-02-0016 TCGA-02-0023 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0083 
       87.06        20.12        26.43        25.05         5.49        22.72 
TCGA-02-0102 TCGA-02-0113 TCGA-02-0260 TCGA-02-0269 TCGA-02-0285 TCGA-02-0289 
       27.02        92.65        16.93        10.75        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0333 TCGA-02-0422 TCGA-02-0430 TCGA-02-2485 
       15.95        12.23         4.37        14.50        10.55        15.45 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0137 TCGA-06-0145 TCGA-06-0148 TCGA-06-0154 
       47.61         6.94        26.70         2.33        10.09        13.94 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0208 
        3.19        10.82         3.65        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-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-2562 
        2.70        46.19         5.65         7.17        40.41        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-5408 TCGA-06-5414 
       30.64         5.95        16.64         5.98        11.74         8.98 
TCGA-06-5415 TCGA-06-5856 TCGA-06-6390 TCGA-08-0244 TCGA-08-0246 TCGA-08-0354 
        8.55         3.75         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-08-0525 
        7.73        11.08        19.59        19.33         4.80        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0656 TCGA-12-0657 TCGA-12-0688 TCGA-12-0703 
       18.41         7.56        94.78         0.10        26.66        20.38 
TCGA-12-0707 TCGA-12-0780 TCGA-12-0826 TCGA-12-0828 TCGA-12-1090 TCGA-12-1091 
       28.41        14.86        27.78         8.94         7.59        33.21 
TCGA-12-1094 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 
       12.23         3.98        25.68        14.73        26.93        15.22 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0786 TCGA-14-0787 
       34.92        14.53        14.93         3.22        23.05         2.24 
TCGA-14-0790 TCGA-14-0866 TCGA-14-1034 TCGA-14-1402 TCGA-14-1459 TCGA-14-2555 
       13.78        26.33        15.95        32.05        12.43         7.96 
TCGA-15-0742 TCGA-15-1446 TCGA-16-1047 TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 
       13.78        19.10         4.57        14.01        21.24        13.97 
TCGA-19-0955 TCGA-19-0962 TCGA-19-0964 TCGA-19-1386 TCGA-19-1786 TCGA-19-1789 
       11.77         0.66         3.39         9.07         7.17         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 TCGA-19-2631 
        0.13         9.67         4.87         1.08         4.08         7.00 
TCGA-19-4068 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 
        4.50        17.19         8.02        18.90        12.10        14.07 
TCGA-19-5959 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       16.80        13.87         9.73         7.13         9.37         9.40 
TCGA-27-1831 TCGA-27-1833 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2526 
       16.60        24.23        21.30        14.04        11.51         2.86 
TCGA-27-2528 TCGA-28-1749 TCGA-28-1755 TCGA-28-1757 TCGA-28-1760 TCGA-28-2514 
       15.78         9.21         1.55         0.13         4.70         5.26 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1978 TCGA-32-1979 
       22.68        12.76         5.42        15.39        15.85        19.50 
TCGA-32-1991 TCGA-32-2495 TCGA-32-2638 TCGA-32-4719 TCGA-41-2572 TCGA-41-3392 
       16.93        15.02        25.18        10.85        13.35         0.99 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4931 TCGA-81-5910 TCGA-87-5896 
        4.54        17.59         3.09         9.17         1.61        26.30 

$subtype4
TCGA-02-0080 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0115 TCGA-02-0258 
       89.72        12.62        51.32        57.76        15.65        16.54 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0432 
        7.73        10.62         7.33        15.91        25.71        47.11 
TCGA-02-0439 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-06-0127 TCGA-06-0128 
        0.66        11.34         9.27        16.21         3.98        22.72 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0142 TCGA-06-0146 
       33.67        25.35        14.30        24.23         2.20        20.09 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0166 TCGA-06-0167 TCGA-06-0171 TCGA-06-0173 
       11.80         3.42         5.85        11.41        13.12         4.47 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0188 TCGA-06-0195 TCGA-06-0214 TCGA-06-0219 
       88.14        20.25        44.58         7.40        15.02         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0648 TCGA-06-0749 
       19.82        13.64        13.32        20.42         9.80         2.70 
TCGA-06-0882 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       20.78        11.84        13.61        33.90         1.08        12.49 
TCGA-06-2561 TCGA-06-2570 TCGA-06-5411 TCGA-06-5417 TCGA-06-5859 TCGA-06-6389 
       17.65        31.50         8.35         5.10         4.57         7.79 
TCGA-06-6391 TCGA-08-0345 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.48         1.74        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0359 TCGA-08-0380 TCGA-08-0385 TCGA-08-0389 TCGA-08-0520 
       65.33         3.39        14.93         2.70        15.35        10.75 
TCGA-12-0618 TCGA-12-0670 TCGA-12-0818 TCGA-12-0819 TCGA-12-0827 TCGA-12-1089 
       12.99        25.97        91.76        24.79        38.76         5.82 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1597 TCGA-12-1602 TCGA-12-3651 TCGA-14-0812 
       14.53         4.14        22.19         6.77        12.69         3.25 
TCGA-14-0813 TCGA-14-1401 TCGA-14-1451 TCGA-14-1456 TCGA-14-1458 TCGA-14-1827 
        1.35         3.75        23.11        40.96         6.67         5.88 
TCGA-14-3476 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
        0.39        50.53        53.19         3.91        17.59        26.07 
TCGA-16-0861 TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-1387 
        4.31         6.41        21.90         8.61        14.27         5.95 
TCGA-19-1388 TCGA-19-1788 TCGA-19-2629 TCGA-19-5960 TCGA-26-1442 TCGA-27-1834 
       12.95         3.68        24.23        14.96        31.33        40.54 
TCGA-27-1836 TCGA-27-2518 TCGA-27-2519 TCGA-28-1746 TCGA-28-1747 TCGA-28-1756 
       30.05        24.76        10.39         0.20         2.53         2.83 
TCGA-28-2506 TCGA-32-1976 TCGA-32-1980 TCGA-32-4210 TCGA-32-4211 TCGA-41-2571 
        6.74         0.49         1.18         3.72        12.59         0.85 
TCGA-41-2573 TCGA-41-2575 TCGA-76-4925 TCGA-76-6192 
        8.94         9.53         4.80         3.29 

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 
   10.67    14.20    13.78    12.54 
[1] "0.1 - 127.6 (10.7)" "0.2 - 115.9 (14.2)" "0.1 - 94.8 (13.8)" 
[4] "0.2 - 91.8 (12.5)" 
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 59 95
  subtype2 41 56
  subtype3 66 90
  subtype4 39 79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   95
  subtype2   41   56
  subtype3   66   90
  subtype4   39   79
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       59       41       66       39
  MALE         95       56       90       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"
D1V4, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             1                   8
  subtype2                             0                   7
  subtype3                             0                   4
  subtype4                             5                   1
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             145
  subtype2                              90
  subtype3                             152
  subtype4                             112
D1V5, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  GLIOBLASTOMA MULTIFORME (GBM)          1        0        0        5
  TREATED PRIMARY GBM                    8        7        4        1
  UNTREATED PRIMARY (DE NOVO) GBM      145       90      152      112
[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"
D1V6, binary
          cls
clus         0   1
  subtype1 106  48
  subtype2  68  29
  subtype3 116  40
  subtype4  70  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  106   48
  subtype2   68   29
  subtype3  116   40
  subtype4   70   48
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       106       68      116       70
  YES       48       29       40       48
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        12   135
  subtype2     2                         7    84
  subtype3     5                         7   139
  subtype4     2                         5   104
D1V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        2        5        2
  BLACK OR AFRICAN AMERICAN       12        7        7        5
  WHITE                          135       84      139      104
[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"
D1V8, binary
          cls
clus         0   1
  subtype1   3 131
  subtype2   5  68
  subtype3   3 135
  subtype4   1 104
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  131
  subtype2    5   68
  subtype3    3  135
  subtype4    1  104
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        5        3        1
  NOT HISPANIC OR LATINO      131       68      135      104
[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  27  80
  subtype3  16  87
  subtype4  21 141
subtype1 subtype2 subtype3 subtype4 
     153      107      103      162 
subtype1 subtype2 subtype3 subtype4 
     138       80       87      141 
$subtype1
TCGA-02-0001 TCGA-02-0003 TCGA-02-0004 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        11.34        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0015 TCGA-02-0021 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 
       20.71        20.61        77.65        53.10        42.74        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
       90.58         2.83        14.14        10.72        10.52        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
        6.87        14.73        15.09        12.59         6.54        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        8.35         9.57         6.02        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0086 TCGA-02-0102 TCGA-02-0106 
        5.49        20.84        27.25         8.81        27.02        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0116 TCGA-02-0266 TCGA-02-0271 TCGA-02-0337 
       17.65        23.18        48.95        17.72        14.47        25.12 
TCGA-02-0456 TCGA-02-2486 TCGA-06-0122 TCGA-06-0124 TCGA-06-0130 TCGA-06-0139 
        3.35        20.32         6.15        20.38        12.95        11.90 
TCGA-06-0141 TCGA-06-0143 TCGA-06-0147 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
       10.29        11.74        17.79        12.33        13.94        10.45 
TCGA-06-0164 TCGA-06-0169 TCGA-06-0175 TCGA-06-0176 TCGA-06-0184 TCGA-06-0189 
       56.91         3.29         4.04        91.00        69.90        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0206 TCGA-06-0210 
       10.42        38.96         4.67         5.56         7.66         7.40 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 TCGA-06-0645 
       10.82         9.01        72.36         9.57        12.62         5.75 
TCGA-06-0650 TCGA-06-0750 TCGA-06-0878 TCGA-06-0881 TCGA-06-1084 TCGA-06-1086 
       23.57         0.92         7.17        16.57        23.93         6.84 
TCGA-06-2562 TCGA-06-2569 TCGA-06-5410 TCGA-06-5412 TCGA-06-5418 TCGA-08-0346 
       12.56         0.43         3.55         4.54         2.73         8.42 
TCGA-08-0352 TCGA-08-0356 TCGA-08-0360 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
        1.28        31.10        15.39        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0522 TCGA-08-0525 TCGA-12-0619 TCGA-12-0620 
        4.27        42.15        20.88        15.98        34.92        10.45 
TCGA-12-0654 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0822 
        7.59        53.85         7.63         9.73        14.93        23.51 
TCGA-12-0829 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 TCGA-14-0736 TCGA-14-0781 
       20.58        15.98        12.23         9.11        15.12         0.95 
TCGA-14-0783 TCGA-14-0789 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1396 
        6.21        11.24         2.04        28.93        15.95         1.12 
TCGA-14-1452 TCGA-16-1045 TCGA-16-1060 TCGA-19-1385 TCGA-19-1389 TCGA-19-1790 
        7.10        29.03         9.14        10.75         4.64         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-26-5139 TCGA-27-1832 TCGA-27-2524 TCGA-27-2527 TCGA-28-1751 TCGA-28-1760 
        1.58         9.86         7.59        14.40         7.63         4.70 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        0.66         4.77         7.30        11.28        17.88        14.53 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-32-1977 
       31.27        23.44        11.01        13.64         5.16         0.10 
TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2638 TCGA-32-4209 
       12.69        14.86        12.23        20.78        25.18        20.32 
TCGA-76-4926 TCGA-76-6193 TCGA-76-6282 
        4.54         2.70        17.06 

$subtype2
TCGA-02-0014 TCGA-02-0026 TCGA-02-0048 TCGA-02-0069 TCGA-02-0074 TCGA-02-0080 
       82.59        24.59         3.22        28.70        10.19        89.72 
TCGA-02-0084 TCGA-02-0087 TCGA-02-0104 TCGA-02-0114 TCGA-02-0258 TCGA-02-0281 
       12.62        57.76        65.00        99.98        16.54         3.98 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-0440 TCGA-02-2466 TCGA-02-2483 
       10.59        12.39        47.11        11.34        16.80        15.32 
TCGA-02-2485 TCGA-06-0128 TCGA-06-0129 TCGA-06-0146 TCGA-06-0166 TCGA-06-0174 
       15.45        22.72        33.67        20.09         5.85         3.22 
TCGA-06-0188 TCGA-06-0241 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0648 
       44.58        48.69         4.70         3.16        35.11         9.80 
TCGA-06-0686 TCGA-06-0875 TCGA-06-1087 TCGA-06-1801 TCGA-06-1805 TCGA-06-2558 
       14.20        43.46         4.04        11.84        33.90        12.49 
TCGA-06-2559 TCGA-06-2570 TCGA-06-5416 TCGA-06-5417 TCGA-06-6389 TCGA-06-6391 
        4.93        31.50         6.71         5.10         7.79         1.48 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0385 
       37.84       115.86        12.16        29.23        65.33         2.70 
TCGA-08-0517 TCGA-08-0524 TCGA-12-0616 TCGA-12-0618 TCGA-12-0818 TCGA-12-0820 
       58.68         7.27        14.73        12.99        91.76        18.48 
TCGA-12-1099 TCGA-12-1597 TCGA-12-3646 TCGA-12-3650 TCGA-12-3651 TCGA-14-0865 
        4.14        22.19        44.02        10.95        12.69        16.50 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1821 TCGA-14-1825 
       30.18         0.92        40.96         6.67        17.79         7.63 
TCGA-14-3477 TCGA-14-4157 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 
        3.78         3.42        50.53        53.19        13.28        26.07 
TCGA-16-0850 TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 TCGA-19-1390 TCGA-19-1788 
       16.37         6.41        21.90         8.61        25.38         3.68 
TCGA-19-2624 TCGA-19-2629 TCGA-19-5956 TCGA-19-5960 TCGA-26-1442 TCGA-26-1799 
        0.16        24.23        22.49        14.96        31.33         9.37 
TCGA-26-5133 TCGA-26-5134 TCGA-27-1836 TCGA-27-1837 TCGA-27-2521 TCGA-28-1746 
       14.86         5.49        30.05        14.04        10.39         0.20 
TCGA-28-1756 TCGA-28-2514 TCGA-28-5204 TCGA-32-1976 TCGA-32-2634 TCGA-32-4208 
        2.83         5.26        14.93         0.49        22.78        21.14 
TCGA-32-4210 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 TCGA-41-5651 
        3.72        19.23         0.85         8.94         9.53        15.12 
TCGA-76-4925 TCGA-76-4932 TCGA-76-4934 TCGA-76-6191 TCGA-76-6285 
        4.80        47.93         2.53        16.70         8.35 

$subtype3
TCGA-02-0016 TCGA-02-0083 TCGA-02-0113 TCGA-02-0260 TCGA-02-0269 TCGA-02-0285 
       87.06        22.72        92.65        16.93        10.75        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0333 TCGA-02-0422 TCGA-02-0430 
       14.20        15.95        12.23         4.37        14.50        10.55 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0137 TCGA-06-0145 TCGA-06-0148 TCGA-06-0157 
       47.61         6.94        26.70         2.33        10.09         3.19 
TCGA-06-0182 TCGA-06-0187 TCGA-06-0211 TCGA-06-0402 TCGA-06-0743 TCGA-06-0744 
        3.65        27.22        11.84         0.26        26.40        46.88 
TCGA-06-0747 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 TCGA-06-2563 TCGA-06-2564 
        2.70        46.19         5.65        40.41        30.64         5.95 
TCGA-06-2565 TCGA-06-5408 TCGA-06-5414 TCGA-08-0244 TCGA-08-0246 TCGA-08-0354 
       16.64        11.74         8.98        22.68         4.18        17.95 
TCGA-08-0355 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0511 TCGA-08-0514 
       24.56        37.58        22.29        12.23         7.73        11.08 
TCGA-08-0518 TCGA-08-0529 TCGA-08-0531 TCGA-12-0656 TCGA-12-0657 TCGA-12-0688 
       19.33        18.41         7.56        94.78         0.10        26.66 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0780 TCGA-12-0821 TCGA-12-0828 TCGA-12-1091 
        3.65        20.38        14.86        10.62         8.94        33.21 
TCGA-12-1098 TCGA-12-1600 TCGA-12-3648 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
        3.98        14.73        26.93        34.92        14.53        14.93 
TCGA-12-5299 TCGA-14-0786 TCGA-14-0787 TCGA-14-0790 TCGA-14-1402 TCGA-14-1453 
        3.22        23.05         2.24        13.78        32.05         1.15 
TCGA-14-2555 TCGA-15-0742 TCGA-16-1047 TCGA-16-1056 TCGA-16-1062 TCGA-19-0964 
        7.96        13.78         4.57        14.01        21.24         3.39 
TCGA-19-1386 TCGA-19-1786 TCGA-19-2619 TCGA-19-2621 TCGA-19-2631 TCGA-19-4068 
        9.07         7.17         9.67         1.08         7.00         4.50 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5954 TCGA-26-1440 TCGA-26-1443 TCGA-27-1831 
       17.19         8.02        12.10         9.73         7.13        16.60 
TCGA-27-1833 TCGA-27-1835 TCGA-27-2523 TCGA-27-2526 TCGA-27-2528 TCGA-28-1749 
       24.23        21.30        16.08         2.86        15.78         9.21 
TCGA-28-1755 TCGA-28-1757 TCGA-28-5219 TCGA-28-6450 TCGA-32-1978 TCGA-32-1991 
        1.55         0.13        22.68         5.42        15.85        16.93 
TCGA-32-2495 TCGA-32-4719 TCGA-41-2572 TCGA-76-4927 TCGA-76-4928 TCGA-81-5910 
       15.02        10.85        13.35        17.59         3.09         1.61 
TCGA-87-5896 
       26.30 

$subtype4
TCGA-02-0023 TCGA-02-0085 TCGA-02-0089 TCGA-02-0099 TCGA-02-0115 TCGA-02-0321 
       20.12        51.32        16.96         3.48        15.65         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0439 
        7.73        10.62         7.33        15.91        25.71         0.66 
TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 TCGA-06-0127 TCGA-06-0132 TCGA-06-0133 
        9.27        16.21        12.92         3.98        25.35        14.30 
TCGA-06-0138 TCGA-06-0140 TCGA-06-0142 TCGA-06-0149 TCGA-06-0156 TCGA-06-0158 
       24.23         0.20         2.20         8.61         5.85        10.82 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0167 TCGA-06-0168 TCGA-06-0171 TCGA-06-0173 
       11.80         3.42        11.41        19.66        13.12         4.47 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 TCGA-06-0195 TCGA-06-0201 
        4.18        88.14        20.25        73.84         7.40         0.39 
TCGA-06-0208 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
        8.42         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0646 TCGA-06-0649 TCGA-06-0745 
       13.64        13.32        20.42         5.75         2.10         7.86 
TCGA-06-0749 TCGA-06-0882 TCGA-06-0939 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 
        2.70        20.78        26.76        26.79        15.32        13.61 
TCGA-06-2557 TCGA-06-2561 TCGA-06-2566 TCGA-06-2567 TCGA-06-5411 TCGA-06-5413 
        1.08        17.65         5.98         4.37         8.35         8.81 
TCGA-06-5415 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6390 TCGA-08-0345 
        8.55         3.75         6.15         4.57         5.39         1.74 
TCGA-08-0347 TCGA-08-0349 TCGA-08-0353 TCGA-08-0359 TCGA-08-0373 TCGA-08-0380 
       25.71         9.80         8.42         3.39         4.41        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0516 TCGA-08-0520 TCGA-08-0521 TCGA-12-0670 
       18.02        15.35        19.59        10.75         4.80        25.97 
TCGA-12-0707 TCGA-12-0773 TCGA-12-0819 TCGA-12-0826 TCGA-12-0827 TCGA-12-1088 
       28.41        43.23        24.79        27.78        38.76       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1095 TCGA-12-1097 TCGA-12-1598 
        5.82         7.59        21.73        15.85        14.53        15.65 
TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3649 TCGA-12-5301 TCGA-14-0812 
       25.68         6.77        59.77        15.22         2.04         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 TCGA-14-1037 TCGA-14-1401 TCGA-14-1451 
        1.35         5.39        26.33        19.30         3.75        23.11 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1827 TCGA-14-1829 
       12.43         0.99         1.97        17.85         5.88         7.17 
TCGA-14-2554 TCGA-14-3476 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 
       17.49         0.39        19.10         3.91        17.59         4.31 
TCGA-16-1055 TCGA-16-1063 TCGA-19-0955 TCGA-19-0962 TCGA-19-0963 TCGA-19-1387 
       10.29        13.97        11.77         0.66        14.27         5.95 
TCGA-19-1388 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 
       12.95         3.65        12.66         3.25         0.13         4.87 
TCGA-19-2623 TCGA-19-2625 TCGA-19-5958 TCGA-19-5959 TCGA-26-5132 TCGA-26-5135 
        7.53         4.08        14.07        16.80         9.40         8.88 
TCGA-27-1830 TCGA-27-1834 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-28-1745 
        5.06        40.54        11.51        24.76        10.39        11.34 
TCGA-28-1747 TCGA-28-1750 TCGA-28-1752 TCGA-28-1753 TCGA-28-2506 TCGA-28-5220 
        2.53         8.35         8.48         1.22         6.74        12.76 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-2615 
       15.39        21.07        19.50         1.18         4.67        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-4211 TCGA-32-4213 TCGA-41-3392 TCGA-41-3393 
        7.36         8.84        12.59        19.86         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6192 
       11.84         0.20         3.65         9.17        10.78         3.29 

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    14.73    13.78    10.34 
[1] "0.1 - 91.0 (12.2)"  "0.2 - 115.9 (14.7)" "0.1 - 94.8 (13.8)" 
[4] "0.1 - 127.6 (10.3)"
D2V2, continuous
D2V3, 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"
D2V4, 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
D2V5, 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"
D2V6, binary
          cls
clus         0   1
  subtype1 114  39
  subtype2  78  29
  subtype3  73  30
  subtype4  95  67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  114   39
  subtype2   78   29
  subtype3   73   30
  subtype4   95   67
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       114       78       73       95
  YES       39       29       30       67
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        13   130
  subtype2     4                         6    95
  subtype3     3                         4    93
  subtype4     2                         8   144
D2V7, 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"
D2V8, 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  25 140
  subtype2  35 147
  subtype3  18  72
  subtype4  21 103
subtype1 subtype2 subtype3 subtype4 
     165      182       90      124 
subtype1 subtype2 subtype3 subtype4 
     140      147       72      103 
$subtype1
TCGA-02-0001 TCGA-02-0004 TCGA-02-0006 TCGA-02-0009 TCGA-02-0015 TCGA-02-0027 
       11.77        11.34        18.35        10.59        20.61        12.16 
TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0051 TCGA-02-0054 
        2.83         3.62        10.72        10.52        15.09         6.54 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 
        2.50        19.86         9.57        25.05         5.49        20.84 
TCGA-02-0079 TCGA-02-0086 TCGA-02-0099 TCGA-02-0115 TCGA-02-0289 TCGA-02-0290 
       27.25         8.81         3.48        15.65        14.20        15.95 
TCGA-02-0324 TCGA-02-0326 TCGA-02-0422 TCGA-02-2486 TCGA-06-0122 TCGA-06-0147 
        7.73         7.33        14.50        20.32         6.15        17.79 
TCGA-06-0151 TCGA-06-0159 TCGA-06-0174 TCGA-06-0176 TCGA-06-0184 TCGA-06-0187 
       46.59         9.44         3.22        91.00        69.90        27.22 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0211 TCGA-06-0213 
       10.42        38.96         4.67         5.56        11.84         0.53 
TCGA-06-0214 TCGA-06-0394 TCGA-06-0397 TCGA-06-0412 TCGA-06-0644 TCGA-06-0649 
       15.02        10.82         9.01         9.57        12.62         2.10 
TCGA-06-0745 TCGA-06-0749 TCGA-06-0878 TCGA-06-1800 TCGA-06-2562 TCGA-06-5414 
        7.86         2.70         7.17        26.79        12.56         8.98 
TCGA-06-5418 TCGA-06-5858 TCGA-06-6390 TCGA-06-6697 TCGA-06-6698 TCGA-08-0244 
        2.73         6.15         5.39        12.85         4.77        22.68 
TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0352 TCGA-08-0354 TCGA-08-0360 
        4.18         1.74         8.42         1.28        17.95        15.39 
TCGA-08-0380 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0511 TCGA-08-0512 
       14.93        13.97        12.56         4.27         7.73        42.15 
TCGA-08-0514 TCGA-08-0518 TCGA-08-0521 TCGA-08-0522 TCGA-08-0525 TCGA-08-0529 
       11.08        19.33         4.80        20.88        15.98        18.41 
TCGA-08-0531 TCGA-12-0619 TCGA-12-0657 TCGA-12-0662 TCGA-12-0776 TCGA-12-0822 
        7.56        34.92         0.10        38.17         9.73        23.51 
TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 
       27.78         8.94        20.58        12.23        15.85        14.53 
TCGA-12-1599 TCGA-12-3648 TCGA-12-3649 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       25.68        26.93        15.22        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0789 TCGA-14-0862 TCGA-14-1034 TCGA-14-1037 
       15.12         0.95        11.24         2.89        15.95        19.30 
TCGA-14-1043 TCGA-14-1450 TCGA-14-1452 TCGA-14-1459 TCGA-14-1823 TCGA-14-1829 
        0.79        58.78         7.10        12.43        17.85         7.17 
TCGA-15-0742 TCGA-16-1045 TCGA-16-1055 TCGA-16-1060 TCGA-19-0955 TCGA-19-0962 
       13.78        29.03        10.29         9.14        11.77         0.66 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1790 TCGA-19-2619 
       10.75         9.07        12.95         4.64         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-26-5139 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
       14.07        10.03         1.58        16.60         9.86        40.54 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1745 TCGA-28-1751 
        7.59         2.86        14.40        15.78        11.34         7.63 
TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 
        1.22         0.66         4.77         7.30        14.93        17.88 
TCGA-28-5209 TCGA-32-1979 TCGA-32-1987 TCGA-32-1991 TCGA-32-2616 TCGA-32-2632 
       14.53        19.50        14.86        16.93         7.36         8.84 
TCGA-32-2638 TCGA-32-4209 TCGA-32-4213 TCGA-32-4719 TCGA-41-3915 TCGA-41-4097 
       25.18        20.32        19.86        10.85        11.84         0.20 
TCGA-74-6578 TCGA-76-4927 TCGA-76-4931 TCGA-76-4932 TCGA-76-6193 TCGA-76-6282 
       14.33        17.59         9.17        47.93         2.70        17.06 
TCGA-76-6657 TCGA-76-6662 TCGA-81-5911 
        5.03         9.27        17.72 

$subtype2
TCGA-02-0003 TCGA-02-0007 TCGA-02-0010 TCGA-02-0014 TCGA-02-0016 TCGA-02-0026 
        4.73        23.18        35.41        82.59        87.06        24.59 
TCGA-02-0043 TCGA-02-0048 TCGA-02-0069 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 
       18.31         3.22        28.70        10.19        89.72        22.72 
TCGA-02-0084 TCGA-02-0087 TCGA-02-0102 TCGA-02-0104 TCGA-02-0114 TCGA-02-0116 
       12.62        57.76        27.02        65.00        99.98        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0321 
       16.54        16.93        10.75        14.47         3.98         9.90 
TCGA-02-0430 TCGA-02-0440 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-06-0125 
       10.55        11.34        16.80        15.32        15.45        47.61 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0137 TCGA-06-0138 TCGA-06-0145 TCGA-06-0146 
       22.72        33.67        26.70        24.23         2.33        20.09 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0173 TCGA-06-0178 TCGA-06-0182 TCGA-06-0185 
        3.19        10.82         4.47        88.14         3.65        73.84 
TCGA-06-0208 TCGA-06-0216 TCGA-06-0237 TCGA-06-0402 TCGA-06-0410 TCGA-06-0646 
        8.42        24.16        13.64         0.26         4.70         5.75 
TCGA-06-0648 TCGA-06-0875 TCGA-06-0879 TCGA-06-1087 TCGA-06-2557 TCGA-06-2559 
        9.80        43.46        40.41         4.04         1.08         4.93 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5413 TCGA-06-5416 
       16.64         4.37        31.50        11.74         8.81         6.71 
TCGA-06-5417 TCGA-06-5856 TCGA-06-5859 TCGA-06-6389 TCGA-06-6695 TCGA-06-6699 
        5.10         3.75         4.57         7.79         8.32         1.55 
TCGA-06-6701 TCGA-08-0245 TCGA-08-0344 TCGA-08-0349 TCGA-08-0350 TCGA-08-0355 
        4.96        37.84       115.86         9.80        29.23        24.56 
TCGA-08-0357 TCGA-08-0375 TCGA-08-0385 TCGA-08-0386 TCGA-08-0389 TCGA-08-0516 
       37.58        12.23         2.70        18.02        15.35        19.59 
TCGA-08-0517 TCGA-08-0520 TCGA-12-0618 TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 
       58.68        10.75        12.99        25.97        12.13         3.65 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0820 
       28.41        15.06        53.85        43.23         7.63        18.48 
TCGA-12-0821 TCGA-12-0827 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
       10.62        38.76       127.59         5.82         7.59        33.21 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1600 TCGA-12-3646 TCGA-12-3650 TCGA-12-3653 
        3.98        15.65        14.73        44.02        10.95        14.53 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0790 TCGA-14-0817 TCGA-14-0865 
        6.21        23.05         2.24        13.78         5.39        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-15-1444 TCGA-16-0848 
        7.63        17.49         3.78         3.42        50.53        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 
       26.07        16.37         4.57        14.01        21.24        13.97 
TCGA-16-1460 TCGA-19-0960 TCGA-19-0964 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        6.41         8.61         3.39        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 
       12.66         3.25         0.13         0.16        24.23         7.00 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 
       17.19         8.02         4.73        22.49        16.80        14.96 
TCGA-26-1440 TCGA-26-5133 TCGA-26-5135 TCGA-26-5136 TCGA-27-1833 TCGA-27-1835 
        9.73        14.86         8.88        18.97        24.23        21.30 
TCGA-27-1837 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-28-1746 TCGA-28-1747 
       14.04        10.39        10.39        16.08         0.20         2.53 
TCGA-28-1749 TCGA-28-2514 TCGA-28-5207 TCGA-28-5215 TCGA-28-5220 TCGA-28-6450 
        9.21         5.26        11.28        11.01        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-2634 TCGA-32-4208 TCGA-32-4210 
       15.39        21.07         0.49        22.78        21.14         3.72 
TCGA-32-4211 TCGA-32-5222 TCGA-41-2575 TCGA-41-3393 TCGA-41-5651 TCGA-74-6573 
       12.59        19.23         9.53         4.44        15.12         3.45 
TCGA-74-6577 TCGA-76-4925 TCGA-76-4929 TCGA-76-6191 TCGA-76-6285 TCGA-76-6286 
        4.34         4.80         3.65        16.70         8.35        20.98 
TCGA-76-6656 TCGA-87-5896 
        4.83        26.30 

$subtype3
TCGA-02-0011 TCGA-02-0023 TCGA-02-0024 TCGA-02-0052 TCGA-02-0058 TCGA-02-0060 
       20.71        20.12        53.10        12.59         8.35         6.02 
TCGA-02-0085 TCGA-02-0089 TCGA-02-0325 TCGA-02-0330 TCGA-02-0338 TCGA-02-0339 
       51.32        16.96        10.62        15.91        10.59        12.39 
TCGA-02-0439 TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 TCGA-06-0126 TCGA-06-0142 
        0.66         9.27        16.21        12.92         6.94         2.20 
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-06-2561 TCGA-06-2564 TCGA-06-2566 TCGA-06-5411 
       13.61        12.49        17.65         5.95         5.98         8.35 
TCGA-06-5415 TCGA-06-6388 TCGA-06-6391 TCGA-06-6694 TCGA-06-6700 TCGA-08-0347 
        8.55         5.23         1.48         7.36         4.77        25.71 
TCGA-08-0348 TCGA-08-0351 TCGA-08-0359 TCGA-12-0780 TCGA-12-1099 TCGA-12-1597 
       12.16        65.33         3.39        14.86         4.14        22.19 
TCGA-14-0812 TCGA-14-0866 TCGA-14-0867 TCGA-14-1451 TCGA-14-1458 TCGA-14-1827 
        3.25        26.33         2.04        23.11         6.67         5.88 
TCGA-14-3476 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0861 TCGA-19-0963 
        0.39        19.10        13.28         3.91         4.31        14.27 
TCGA-19-1387 TCGA-19-1788 TCGA-19-2620 TCGA-26-1442 TCGA-26-1799 TCGA-26-5134 
        5.95         3.68         4.87        31.33         9.37         5.49 
TCGA-26-6174 TCGA-27-1836 TCGA-27-2518 TCGA-28-1752 TCGA-28-1756 TCGA-28-2506 
        2.33        30.05        24.76         8.48         2.83         6.74 
TCGA-28-5219 TCGA-32-1980 TCGA-32-2495 TCGA-41-2573 TCGA-41-3392 TCGA-74-6575 
       22.68         1.18        15.02         8.94         0.99        20.91 
TCGA-74-6584 TCGA-76-4926 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 TCGA-76-6663 
        7.50         4.54         2.53        10.78         3.29         7.73 

$subtype4
TCGA-02-0021 TCGA-02-0025 TCGA-02-0028 TCGA-02-0034 TCGA-02-0047 TCGA-02-0064 
       77.65        42.74        90.58        14.14        14.73        19.73 
TCGA-02-0068 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0266 
       26.43        11.67        17.65        23.18        92.65        17.72 
TCGA-02-0285 TCGA-02-0317 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0432 
       13.87        12.23        25.71         4.37        25.12        47.11 
TCGA-02-0456 TCGA-06-0124 TCGA-06-0127 TCGA-06-0130 TCGA-06-0133 TCGA-06-0139 
        3.35        20.38         3.98        12.95        14.30        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 
        0.20        10.29        11.74         8.61        19.46        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0156 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
       13.94        10.45         5.85        56.91         5.85        19.66 
TCGA-06-0169 TCGA-06-0175 TCGA-06-0188 TCGA-06-0189 TCGA-06-0210 TCGA-06-0238 
        3.29         4.04        44.58        15.42         7.40        13.32 
TCGA-06-0409 TCGA-06-0645 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0876 
       72.36         5.75        23.57        26.40        46.88        46.19 
TCGA-06-0877 TCGA-06-0881 TCGA-06-1084 TCGA-06-1086 TCGA-06-1802 TCGA-06-1805 
        5.65        16.57        23.93         6.84        15.32        33.90 
TCGA-06-1806 TCGA-06-2563 TCGA-06-2569 TCGA-06-5410 TCGA-06-5412 TCGA-06-6693 
       15.32        30.64         0.43         3.55         4.54       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-12-1092 TCGA-12-1093 TCGA-12-1096 TCGA-12-1602 TCGA-12-3644 
       14.93        21.73        15.98         9.11         6.77        59.77 
TCGA-12-3651 TCGA-12-3652 TCGA-14-0740 TCGA-14-0813 TCGA-14-0871 TCGA-14-1396 
       12.69        34.92        11.97         1.35        28.93         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1794 TCGA-14-1795 TCGA-14-2555 TCGA-15-1447 
        3.75        32.05         0.99         1.97         7.96        53.19 
TCGA-19-0957 TCGA-19-2625 TCGA-19-4068 TCGA-26-1439 TCGA-26-1443 TCGA-26-5132 
       21.90         4.08         4.50        13.87         7.13         9.40 
TCGA-26-6173 TCGA-27-1830 TCGA-27-1838 TCGA-28-1750 TCGA-28-1755 TCGA-28-1757 
        7.92         5.06        11.51         8.35         1.55         0.13 
TCGA-28-1760 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
        4.70        11.77        31.27        23.44        13.64         5.16 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1982 TCGA-32-1986 TCGA-32-2491 TCGA-32-2494 
        0.10        15.85         4.67        12.69        12.23        20.78 
TCGA-32-2615 TCGA-41-2571 TCGA-41-2572 TCGA-41-6646 TCGA-74-6581 TCGA-76-4928 
       15.95         0.85        13.35        12.46         8.22         3.09 
TCGA-76-6280 TCGA-76-6661 TCGA-76-6664 TCGA-81-5910 
       11.38         0.23         7.79         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 
  11.340   13.315    9.105   12.575 
[1] "0.1 - 91.0 (11.3)"  "0.1 - 127.6 (13.3)" "0.4 - 65.3 (9.1)"  
[4] "0.1 - 120.6 (12.6)"
D3V2, continuous
D3V3, binary
          cls
clus         0   1
  subtype1  63 102
  subtype2  76 106
  subtype3  36  54
  subtype4  43  81
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63  102
  subtype2   76  106
  subtype3   36   54
  subtype4   43   81
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       63       76       36       43
  MALE        102      106       54       81
[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"
D3V4, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             2                   4
  subtype2                             1                   8
  subtype3                             3                   5
  subtype4                             3                   3
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             159
  subtype2                             173
  subtype3                              82
  subtype4                             118
D3V5, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  GLIOBLASTOMA MULTIFORME (GBM)          2        1        3        3
  TREATED PRIMARY GBM                    4        8        5        3
  UNTREATED PRIMARY (DE NOVO) GBM      159      173       82      118
[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"
D3V6, binary
          cls
clus         0   1
  subtype1 118  47
  subtype2 131  51
  subtype3  57  33
  subtype4  83  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  118   47
  subtype2  131   51
  subtype3   57   33
  subtype4   83   41
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       118      131       57       83
  YES       47       51       33       41
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                        13   140
  subtype2     7                         9   157
  subtype3     1                         1    85
  subtype4     2                         7   111
D3V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        7        1        2
  BLACK OR AFRICAN AMERICAN       13        9        1        7
  WHITE                          140      157       85      111
[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"
D3V8, binary
          cls
clus         0   1
  subtype1   5 134
  subtype2   4 153
  subtype3   1  71
  subtype4   2 101
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  134
  subtype2    4  153
  subtype3    1   71
  subtype4    2  101
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        4        1        2
  NOT HISPANIC OR LATINO      134      153       71      101
[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  53 249
  subtype2  23 106
  subtype3  23 107
subtype1 subtype2 subtype3 
     302      129      130 
subtype1 subtype2 subtype3 
     249      106      107 
$subtype1
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
       11.77         4.73        23.18        35.41        20.71        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 
       20.61        87.06        20.12        53.10        24.59        12.16 
TCGA-02-0028 TCGA-02-0038 TCGA-02-0039 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 
       90.58        10.72        10.52        14.73         3.22        12.59 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0069 TCGA-02-0071 TCGA-02-0074 
       19.86         8.35         6.02        28.70         5.49        10.19 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 
       27.25        89.72        12.62        51.32        57.76        16.96 
TCGA-02-0104 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0266 
       65.00        99.98        15.65        48.95        16.54        17.72 
TCGA-02-0281 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        3.98         9.90        10.62         7.33        15.91        25.71 
TCGA-02-0337 TCGA-02-0339 TCGA-02-0432 TCGA-02-0439 TCGA-02-0440 TCGA-02-0446 
       25.12        12.39        47.11         0.66        11.34         9.27 
TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-06-0122 TCGA-06-0126 
       16.21        16.80        12.92        15.32         6.15         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0133 TCGA-06-0138 TCGA-06-0142 
        3.98        22.72        33.67        14.30        24.23         2.20 
TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 TCGA-06-0150 TCGA-06-0156 TCGA-06-0158 
       11.74        20.09        17.79        19.46         5.85        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0166 TCGA-06-0168 TCGA-06-0171 
        9.44        11.80         3.42         5.85        19.66        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        4.47         3.22         4.04         4.18        88.14        20.25 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0195 TCGA-06-0208 TCGA-06-0213 
       69.90        73.84        44.58         7.40         8.42         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0646 
       20.42        48.69         4.70         3.16        35.11         5.75 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        9.80        23.57        14.20        46.88         7.86         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0882 TCGA-06-0939 TCGA-06-1087 TCGA-06-1801 
        0.92        43.46        20.78        26.76         4.04        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       15.32        13.61        33.90        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 TCGA-06-2570 TCGA-06-5410 
       12.56        30.64         5.95         5.98        31.50         3.55 
TCGA-06-5411 TCGA-06-5415 TCGA-06-5416 TCGA-06-5417 TCGA-06-5856 TCGA-06-6388 
        8.35         8.55         6.71         5.10         3.75         5.23 
TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6700 TCGA-06-6701 TCGA-08-0244 
        7.79         1.48       120.56         4.77         4.96        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
       37.84       115.86         1.74        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0357 TCGA-08-0359 TCGA-08-0373 
       29.23        65.33         1.28        37.58         3.39         4.41 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0385 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
       12.23        14.93         2.70        18.02        15.35        13.97 
TCGA-08-0509 TCGA-08-0511 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 
       12.56         7.73        19.59        58.68         4.80         7.27 
TCGA-12-0618 TCGA-12-0656 TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       12.99        94.78        25.97        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0780 TCGA-12-0820 
       28.41        15.06        53.85        43.23        14.86        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-1089 TCGA-12-1092 TCGA-12-1095 
       10.62        23.51        38.76         5.82        21.73        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1597 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         4.14        22.19        15.65        25.68 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-5299 
       59.77        44.02        15.22        10.95        12.69         3.22 
TCGA-12-5301 TCGA-14-0740 TCGA-14-0812 TCGA-14-0813 TCGA-14-0865 TCGA-14-0866 
        2.04        11.97         3.25         1.35        16.50        26.33 
TCGA-14-0867 TCGA-14-1043 TCGA-14-1401 TCGA-14-1451 TCGA-14-1454 TCGA-14-1455 
        2.04         0.79         3.75        23.11        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-3476 TCGA-14-3477 TCGA-14-4157 
        7.63         5.88         7.17         0.39         3.78         3.42 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 
       50.53        19.10        53.19        13.28         3.91        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1055 TCGA-16-1060 TCGA-16-1063 
       16.37         4.31        29.03        10.29         9.14        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1788 
        5.95        12.95         4.64        25.38         3.65         3.68 
TCGA-19-1791 TCGA-19-2620 TCGA-19-2624 TCGA-19-4068 TCGA-19-5950 TCGA-19-5955 
        0.13         4.87         0.16         4.50        17.19         1.78 
TCGA-19-5956 TCGA-19-5960 TCGA-26-1442 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 
       22.49        14.96        31.33         9.37        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 TCGA-27-1836 TCGA-27-1837 
        8.88        18.97         1.58         2.33        30.05        14.04 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 
       24.76        10.39        10.39        16.08         7.59        14.40 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1752 TCGA-28-1756 TCGA-28-2502 TCGA-28-2506 
        0.20         2.53         8.48         2.83         0.66         6.74 
TCGA-28-2514 TCGA-28-5207 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5219 
        5.26        11.28        31.27        23.44        13.64        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1980 
       12.76         5.42        15.39        21.07         0.49         1.18 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2634 
       16.93        12.23        20.78        15.02         7.36        22.78 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       21.14         3.72        10.85         0.85        13.35         8.94 
TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-74-6581 TCGA-74-6584 
        0.99        11.84        15.12        12.46         8.22         7.50 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        4.54        17.59         2.53        10.78        16.70         3.29 
TCGA-76-6662 TCGA-76-6663 
        9.27         7.73 

$subtype2
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-06-0877 TCGA-06-0878 TCGA-06-0881 
        5.75        26.40        46.19         5.65         7.17        16.57 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1806 TCGA-06-2569 TCGA-06-5412 
       23.93         6.84        26.79        15.32         0.43         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5418 TCGA-06-6694 TCGA-08-0246 TCGA-08-0346 
        8.81         8.98         2.73         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-12-1602 TCGA-12-5295 
        8.94        20.58        15.98        12.23         6.77        14.93 
TCGA-14-0781 TCGA-14-0789 TCGA-14-0862 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
        0.95        11.24         2.89        28.93        15.95        19.30 
TCGA-14-1396 TCGA-14-1402 TCGA-14-2555 TCGA-19-0964 TCGA-19-1385 TCGA-19-1790 
        1.12        32.05         7.96         3.39        10.75         5.06 
TCGA-19-2625 TCGA-19-5947 TCGA-19-5952 TCGA-26-1439 TCGA-26-1443 TCGA-26-5132 
        4.08         6.64        18.90        13.87         7.13         9.40 
TCGA-26-6173 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1838 TCGA-27-2528 
        7.92         5.06        16.60         9.86        11.51        15.78 
TCGA-28-1745 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-1760 
       11.34         7.63         1.22         1.55         0.13         4.70 
TCGA-28-2513 TCGA-28-5211 TCGA-28-5218 TCGA-32-1977 TCGA-32-1978 TCGA-32-1982 
        7.30        11.77         5.16         0.10        15.85         4.67 
TCGA-32-1986 TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-76-4928 TCGA-76-6280 
       12.69        15.95         8.84        25.18         3.09        11.38 
TCGA-76-6661 TCGA-76-6664 TCGA-81-5910 
        0.23         7.79         1.61 

$subtype3
TCGA-02-0009 TCGA-02-0043 TCGA-02-0054 TCGA-02-0075 TCGA-02-0083 TCGA-02-0099 
       10.59        18.31         6.54        20.84        22.72         3.48 
TCGA-02-0102 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0289 TCGA-02-0324 
       27.02        16.93        10.75        14.47        14.20         7.73 
TCGA-02-0422 TCGA-02-0430 TCGA-02-2485 TCGA-06-0125 TCGA-06-0137 TCGA-06-0145 
       14.50        10.55        15.45        47.61        26.70         2.33 
TCGA-06-0157 TCGA-06-0182 TCGA-06-0187 TCGA-06-0192 TCGA-06-0211 TCGA-06-0402 
        3.19         3.65        27.22        38.96        11.84         0.26 
TCGA-06-0649 TCGA-06-0749 TCGA-06-0879 TCGA-06-2557 TCGA-06-2565 TCGA-06-2567 
        2.10         2.70        40.41         1.08        16.64         4.37 
TCGA-06-5408 TCGA-06-5858 TCGA-06-5859 TCGA-06-6390 TCGA-06-6695 TCGA-06-6697 
       11.74         6.15         4.57         5.39         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-08-0355 TCGA-08-0360 TCGA-08-0510 TCGA-08-0514 
        4.77         1.55        24.56        15.39         4.27        11.08 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0619 
       19.33        10.75        15.98        18.41         7.56        34.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 TCGA-12-0775 TCGA-12-0826 TCGA-12-1088 
        0.10        38.17        26.66         7.63        27.78       127.59 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1098 TCGA-12-1600 TCGA-12-3648 TCGA-12-3652 
        7.59        33.21         3.98        14.73        26.93        34.92 
TCGA-12-3653 TCGA-14-0736 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0790 
       14.53        15.12         6.21        23.05         2.24        13.78 
TCGA-14-0817 TCGA-14-1395 TCGA-14-1450 TCGA-14-1452 TCGA-14-1453 TCGA-14-1823 
        5.39         1.38        58.78         7.10         1.15        17.85 
TCGA-14-2554 TCGA-15-0742 TCGA-16-0848 TCGA-16-1047 TCGA-16-1056 TCGA-16-1062 
       17.49        13.78        17.59         4.57        14.01        21.24 
TCGA-19-1386 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2621 
        9.07         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-28-5204 
       21.30         2.86         9.21         8.35         4.77        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5215 TCGA-32-1979 TCGA-32-1987 TCGA-32-4209 
       17.88        14.53        11.01        19.50        14.86        20.32 
TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 
       12.59        19.86        19.23         9.53         4.44         0.20 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-76-4925 TCGA-76-4929 
        3.45        20.91         4.34        14.33         4.80         3.65 
TCGA-76-4931 TCGA-76-4932 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        9.17        47.93         2.70        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-81-5911 TCGA-87-5896 
        4.83         5.03        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 
  12.525   10.590   11.970 
[1] "0.1 - 120.6 (12.5)" "0.1 - 92.7 (10.6)"  "0.1 - 127.6 (12.0)"
D4V2, continuous
D4V3, binary
          cls
clus         0   1
  subtype1 110 192
  subtype2  48  81
  subtype3  60  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  110  192
  subtype2   48   81
  subtype3   60   70
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      110       48       60
  MALE        192       81       70
[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"
D4V4, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             6                  13
  subtype2                             3                   2
  subtype3                             0                   5
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             283
  subtype2                             124
  subtype3                             125
D4V5, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)          6        3        0
  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"
D4V6, binary
          cls
clus         0   1
  subtype1 208  94
  subtype2  90  39
  subtype3  91  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  208   94
  subtype2   90   39
  subtype3   91   39
     clus
vv    subtype1 subtype2 subtype3
  NO       208       90       91
  YES       94       39       39
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                        10   272
  subtype2     3                        11   113
  subtype3     3                         9   108
D4V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            7        3        3
  BLACK OR AFRICAN AMERICAN       10       11        9
  WHITE                          272      113      108
[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"
D4V8, binary
          cls
clus         0   1
  subtype1   6 249
  subtype2   2 109
  subtype3   4 101
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  249
  subtype2    2  109
  subtype3    4  101
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        2        4
  NOT HISPANIC OR LATINO      249      109      101
[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  22 138
  subtype2  39 178
  subtype3  43 149
subtype1 subtype2 subtype3 
     160      217      192 
subtype1 subtype2 subtype3 
     138      178      149 
$subtype1
TCGA-02-0001 TCGA-02-0007 TCGA-02-0024 TCGA-02-0039 TCGA-02-0048 TCGA-02-0051 
       11.77        23.18        53.10        10.52         3.22        15.09 
TCGA-02-0074 TCGA-02-0099 TCGA-02-0106 TCGA-02-0113 TCGA-02-0266 TCGA-02-0324 
       10.19         3.48        11.67        92.65        17.72         7.73 
TCGA-02-0325 TCGA-02-0330 TCGA-02-0440 TCGA-02-0446 TCGA-02-2466 TCGA-06-0128 
       10.62        15.91        11.34         9.27        16.80        22.72 
TCGA-06-0138 TCGA-06-0149 TCGA-06-0152 TCGA-06-0162 TCGA-06-0166 TCGA-06-0168 
       24.23         8.61        12.33         3.42         5.85        19.66 
TCGA-06-0173 TCGA-06-0177 TCGA-06-0182 TCGA-06-0184 TCGA-06-0188 TCGA-06-0192 
        4.47         4.18         3.65        69.90        44.58        38.96 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0206 TCGA-06-0209 TCGA-06-0214 TCGA-06-0216 
        7.40         5.56         7.66         7.63        15.02        24.16 
TCGA-06-0219 TCGA-06-0238 TCGA-06-0241 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
        0.72        13.32        48.69         0.26        72.36         4.70 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0875 
       35.11        12.62         9.80         2.10        14.20        43.46 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 
        4.04        26.79        13.61         1.08        12.49        17.65 
TCGA-06-5408 TCGA-06-5856 TCGA-06-5859 TCGA-06-6390 TCGA-06-6694 TCGA-06-A6S1 
       11.74         3.75         4.57         5.39         7.36         2.56 
TCGA-06-A7TK TCGA-08-0245 TCGA-08-0246 TCGA-08-0349 TCGA-08-0359 TCGA-08-0389 
        5.39        37.84         4.18         9.80         3.39        15.35 
TCGA-08-0520 TCGA-12-0615 TCGA-12-0616 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       10.75        15.35        14.73        34.92        10.45         7.59 
TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 TCGA-12-0772 TCGA-12-0821 TCGA-12-0826 
       38.17        12.13         3.65        53.85        10.62        27.78 
TCGA-12-1088 TCGA-12-1091 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
      127.59        33.21         9.11        14.53         3.98         4.14 
TCGA-12-1598 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3653 TCGA-12-5295 
       15.65         6.77        59.77        44.02        14.53        14.93 
TCGA-14-0736 TCGA-14-0783 TCGA-14-0787 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       15.12         6.21         2.24         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1396 TCGA-14-1451 TCGA-14-1453 
       16.50         2.04        28.93         1.12        23.11         1.15 
TCGA-14-1454 TCGA-14-1823 TCGA-14-1825 TCGA-14-3477 TCGA-15-0742 TCGA-15-1449 
       30.18        17.85         7.63         3.78        13.78        13.28 
TCGA-16-0850 TCGA-16-1045 TCGA-19-0957 TCGA-19-1387 TCGA-19-1392 TCGA-19-1791 
       16.37        29.03        21.90         5.95         3.65         0.13 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-5947 TCGA-19-5960 
        1.08         7.53         4.08        24.23         6.64        14.96 
TCGA-19-A60I TCGA-26-1439 TCGA-26-1440 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 
       17.79        13.87         9.73         8.88        18.97         5.06 
TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-2519 TCGA-28-1746 TCGA-28-1750 
        9.86        40.54        21.30        10.39         0.20         8.35 
TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
        6.74         4.77        11.28        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-32-1976 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       22.68        12.76         0.49        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-4210 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 
       22.78         3.72        19.23         0.85         8.94         9.53 
TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9S TCGA-74-6577 TCGA-76-4929 
        0.99        11.84        15.12         4.14         4.34         3.65 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6285 TCGA-76-6286 
        2.53        10.78         8.35        20.98 

$subtype2
TCGA-02-0003 TCGA-02-0009 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0037 
        4.73        10.59        87.06        77.65        20.12         3.62 
TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
       10.72        18.31         6.87        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0089 TCGA-02-0102 TCGA-02-0116 TCGA-02-0260 TCGA-02-0269 
        5.49        16.96        27.02        48.95        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-02-0451 TCGA-02-2485 TCGA-02-2486 TCGA-06-0122 TCGA-06-0124 
       10.55        16.21        15.45        20.32         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0133 TCGA-06-0137 TCGA-06-0145 TCGA-06-0148 
       47.61         6.94        14.30        26.70         2.33        10.09 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        46.59        13.94        10.45         3.19        10.82 
TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0185 TCGA-06-0187 TCGA-06-0208 
       13.12         3.22         4.04        73.84        27.22         8.42 
TCGA-06-0211 TCGA-06-0237 TCGA-06-0412 TCGA-06-0645 TCGA-06-0646 TCGA-06-0743 
       11.84        13.64         9.57         5.75         5.75        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 
       46.88         7.86         2.70         0.92        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-1801 TCGA-06-1802 TCGA-06-2562 TCGA-06-2563 
        7.17        40.41        11.84        15.32        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        5.95        16.64         4.37         8.81         8.98         8.55 
TCGA-06-5418 TCGA-06-6388 TCGA-06-6693 TCGA-06-6695 TCGA-06-6699 TCGA-06-A6S0 
        2.73         5.23       120.56         8.32         1.55         3.12 
TCGA-08-0244 TCGA-08-0348 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       22.68        12.16         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0386 TCGA-08-0510 
       31.10        37.58        22.29        12.23        18.02         4.27 
TCGA-08-0514 TCGA-08-0518 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 
       11.08        19.33        15.98        18.41         7.56        12.99 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 
       94.78         0.10        25.97        26.66        20.38        28.41 
TCGA-12-0769 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0828 
       15.06        14.93        14.86        24.79        18.48         8.94 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 
       12.23        15.85        25.68        14.73        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0786 
       10.95        12.69        34.92         3.22         2.04        23.05 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 TCGA-14-1401 
       11.24        13.78        26.33        15.95         1.38         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1455 TCGA-14-1459 TCGA-14-1795 
       32.05        58.78         7.10         0.92        12.43         1.97 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-15-1446 TCGA-16-0848 
        5.88         7.17        17.49         7.96        19.10        17.59 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1386 TCGA-19-1786 TCGA-19-1789 
        0.66        14.27         3.39         9.07         7.17         3.25 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2624 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 
        9.67         4.87         0.16         7.00        17.19         8.02 
TCGA-19-5952 TCGA-19-5954 TCGA-19-5959 TCGA-19-A6J5 TCGA-26-1443 TCGA-26-1799 
       18.90        12.10        16.80        28.54         7.13         9.37 
TCGA-26-5132 TCGA-26-5139 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1833 TCGA-27-1837 
        9.40         1.58        19.33        16.60        24.23        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 
       11.51        24.76        16.08         7.59         2.86        15.78 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1752 TCGA-28-1753 TCGA-28-1757 TCGA-28-2514 
        2.53         9.21         8.48         1.22         0.13         5.26 
TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5214 TCGA-28-6450 TCGA-32-1970 
       14.93        17.88        14.53        23.44         5.42        15.39 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-2494 TCGA-32-2495 
        0.10        15.85        19.50         4.67        20.78        15.02 
TCGA-32-2638 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-41-3393 
       25.18        12.59        19.86        10.85        13.35         4.44 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       14.76         3.45        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4931 TCGA-76-6191 TCGA-76-6280 TCGA-76-6656 TCGA-76-6657 
        4.54         9.17        16.70        11.38         4.83         5.03 
TCGA-76-6661 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        0.23         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

$subtype3
TCGA-02-0006 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0025 
       18.35        35.41        20.71        82.59        20.61        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0047 
       24.59        12.16        90.58         2.83        14.14        14.73 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       12.59         6.54         2.50        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0069 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        6.02        28.70        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0104 TCGA-02-0107 
       12.62        51.32         8.81        57.76        65.00        17.65 
TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0258 TCGA-02-0271 TCGA-02-0281 
       23.18        99.98        15.65        16.54        14.47         3.98 
TCGA-02-0321 TCGA-02-0326 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        9.90         7.33        25.71        25.12        10.59        12.39 
TCGA-02-0432 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-06-0119 TCGA-06-0127 
       47.11         3.35        12.92        15.32         2.70         3.98 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       33.67        12.95        25.35        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 TCGA-06-0159 TCGA-06-0160 
        2.20        11.74        20.09        17.79         9.44        11.80 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0169 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
       56.91        10.65         3.29        91.00        88.14        20.25 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0201 TCGA-06-0210 TCGA-06-0213 
       15.42        10.42         4.67         0.39         7.40         0.53 
TCGA-06-0221 TCGA-06-0240 TCGA-06-0394 TCGA-06-0397 TCGA-06-0413 TCGA-06-0650 
       19.82        20.42        10.82         9.01         3.16        23.57 
TCGA-06-0749 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
        2.70        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2559 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
       33.90        15.32         4.93         5.98         0.43        31.50 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5416 TCGA-06-5858 TCGA-06-6389 
        3.55         8.35         4.54         6.71         6.15         7.79 
TCGA-06-6391 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
        1.48        12.85         4.77         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A7TL TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        1.87         5.42       115.86         1.74         8.42        25.71 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0380 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       29.23        65.33        14.93        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 TCGA-12-0773 
       42.15        19.59        58.68         4.80         7.27        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0818 TCGA-12-0822 TCGA-12-0827 TCGA-12-0829 
        7.63         9.73        91.76        23.51        38.76        20.58 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1093 TCGA-14-0740 TCGA-14-0781 
        5.82         7.59        21.73        15.98        11.97         0.95 
TCGA-14-0812 TCGA-14-1037 TCGA-14-1043 TCGA-14-1456 TCGA-14-1458 TCGA-14-1794 
        3.25        19.30         0.79        40.96         6.67         0.99 
TCGA-14-1821 TCGA-14-4157 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 
       17.79         3.42        50.53        53.19         3.91        26.07 
TCGA-16-0861 TCGA-16-1460 TCGA-19-0955 TCGA-19-0960 TCGA-19-1385 TCGA-19-1388 
        4.31         6.41        11.77         8.61        10.75        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1787 TCGA-19-4065 TCGA-19-5953 TCGA-19-5955 
        4.64        25.38        12.66         7.04         4.73         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1442 TCGA-26-5133 
       22.49        14.07         3.98        10.03        31.33        14.86 
TCGA-26-5134 TCGA-26-6173 TCGA-26-6174 TCGA-27-1836 TCGA-27-2521 TCGA-27-2527 
        5.49         7.92         2.33        30.05        10.39        14.40 
TCGA-28-1751 TCGA-28-1755 TCGA-28-1756 TCGA-28-2502 TCGA-28-2513 TCGA-28-5211 
        7.63         1.55         2.83         0.66         7.30        11.77 
TCGA-28-5213 TCGA-32-1973 TCGA-32-1980 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       31.27        21.07         1.18        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-4208 TCGA-41-4097 TCGA-41-6646 TCGA-74-6575 TCGA-76-4928 
       12.23        21.14         0.20        12.46        20.91         3.09 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        3.29         2.70        17.06         9.27         7.73         7.79 

subtype1 subtype2 subtype3 
    0.13     0.10     0.20 
subtype1 subtype2 subtype3 
  127.59   120.56   115.86 
subtype1 subtype2 subtype3 
  10.620   12.560   12.195 
[1] "0.1 - 127.6 (10.6)" "0.1 - 120.6 (12.6)" "0.2 - 115.9 (12.2)"
D5V2, continuous
D5V3, binary
          cls
clus         0   1
  subtype1  69  91
  subtype2  80 137
  subtype3  75 118
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69   91
  subtype2   80  137
  subtype3   75  118
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       69       80       75
  MALE         91      137      118
[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, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             4                   4
  subtype2                             9                   5
  subtype3                            14                   9
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             152
  subtype2                             203
  subtype3                             170
D5V5, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)          4        9       14
  TREATED PRIMARY GBM                    4        5        9
  UNTREATED PRIMARY (DE NOVO) GBM      152      203      170
[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"
D5V6, binary
          cls
clus         0   1
  subtype1  98  62
  subtype2 150  67
  subtype3 134  59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   98   62
  subtype2  150   67
  subtype3  134   59
     clus
vv    subtype1 subtype2 subtype3
  NO        98      150      134
  YES       62       67       59
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                        14   139
  subtype2     3                        17   188
  subtype3     9                        18   158
D5V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        3        9
  BLACK OR AFRICAN AMERICAN       14       17       18
  WHITE                          139      188      158
[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"
D5V8, binary
          cls
clus         0   1
  subtype1   2 133
  subtype2   5 176
  subtype3   5 163
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  133
  subtype2    5  176
  subtype3    5  163
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        5        5
  NOT HISPANIC OR LATINO      133      176      163
[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 20 72
  subtype2 16 94
  subtype3 21 60
subtype1 subtype2 subtype3 
      92      110       81 
subtype1 subtype2 subtype3 
      72       94       60 
$subtype1
TCGA-02-0001 TCGA-02-0006 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0054 
       11.77        18.35        12.16         2.83        14.14         6.54 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0060 TCGA-02-0075 TCGA-02-0085 TCGA-02-0086 
        2.50        19.86         6.02        20.84        51.32         8.81 
TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 TCGA-02-2470 TCGA-06-0119 TCGA-06-0124 
       17.65        92.65        15.65        12.92         2.70        20.38 
TCGA-06-0130 TCGA-06-0133 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       12.95        14.30        11.90         0.20        10.29         2.20 
TCGA-06-0147 TCGA-06-0169 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 
       17.79         3.29        46.19         7.17        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-2561 TCGA-06-2562 TCGA-06-2566 
       26.76        23.93         6.84        17.65        12.56         5.98 
TCGA-06-2567 TCGA-12-0822 TCGA-12-0826 TCGA-12-0829 TCGA-12-1089 TCGA-12-1093 
        4.37        23.51        27.78        20.58         5.82        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1098 TCGA-12-1599 TCGA-14-0736 
       12.23        15.85         9.11         3.98        25.68        15.12 
TCGA-14-0789 TCGA-14-1034 TCGA-14-1037 TCGA-14-1827 TCGA-14-2554 TCGA-14-2555 
       11.24        15.95        19.30         5.88        17.49         7.96 
TCGA-15-1446 TCGA-16-1045 TCGA-16-1060 TCGA-19-0955 TCGA-19-0962 TCGA-19-1385 
       19.10        29.03         9.14        11.77         0.66        10.75 
TCGA-19-1389 TCGA-19-1787 TCGA-19-2619 TCGA-19-2623 TCGA-19-2625 TCGA-19-4068 
        4.64        12.66         9.67         7.53         4.08         4.50 
TCGA-26-1438 TCGA-26-1439 TCGA-27-1831 TCGA-27-1832 TCGA-27-2518 TCGA-27-2519 
       10.03        13.87        16.60         9.86        24.76        10.39 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-28-1745 TCGA-28-1751 TCGA-28-1752 
        7.59         2.86        14.40        11.34         7.63         8.48 
TCGA-28-1757 TCGA-28-1760 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-32-1977 
        0.13         4.70         0.66         6.74         7.30         0.10 
TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.69        14.86        12.23        15.95         7.36         8.84 
TCGA-32-4209 TCGA-41-4097 
       20.32         0.20 

$subtype2
TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0021 TCGA-02-0037 TCGA-02-0038 
        4.73        23.18        10.59        77.65         3.62        10.72 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0064 TCGA-02-0071 TCGA-02-0074 TCGA-02-0083 
       18.31         6.87        19.73         5.49        10.19        22.72 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0116 TCGA-02-2485 TCGA-02-2486 
       16.96         3.48        27.02        48.95        15.45        20.32 
TCGA-06-0122 TCGA-06-0125 TCGA-06-0126 TCGA-06-0137 TCGA-06-0145 TCGA-06-0148 
        6.15        47.61         6.94        26.70         2.33        10.09 
TCGA-06-0155 TCGA-06-0877 TCGA-06-0879 TCGA-06-1802 TCGA-06-2557 TCGA-06-2563 
       10.45         5.65        40.41        15.32         1.08        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-12-0670 TCGA-12-0819 TCGA-12-0820 TCGA-12-0828 
        5.95        16.64        25.97        24.79        18.48         8.94 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1597 TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 
        7.59        33.21        22.19        15.65        14.73         6.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-14-0783 
       44.02        26.93        15.22        10.95        34.92         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
       23.05         2.24        13.78         3.25         1.35         5.39 
TCGA-14-0866 TCGA-14-0867 TCGA-14-1396 TCGA-14-1402 TCGA-14-1452 TCGA-14-1453 
       26.33         2.04         1.12        32.05         7.10         1.15 
TCGA-14-1454 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1829 TCGA-16-0846 
       30.18         0.99         1.97        17.85         7.17         3.91 
TCGA-16-0848 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 
       17.59         4.57        10.29        14.01        21.24        13.97 
TCGA-19-0964 TCGA-19-1386 TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        3.39         9.07         5.95        25.38         3.65         7.17 
TCGA-19-1789 TCGA-19-1790 TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 TCGA-19-2631 
        3.25         5.06         0.13         4.87         1.08         7.00 
TCGA-26-1443 TCGA-26-1799 TCGA-27-1833 TCGA-27-1835 TCGA-27-1838 TCGA-27-2523 
        7.13         9.37        24.23        21.30        11.51        16.08 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1753 TCGA-28-2499 
       15.78         2.53         9.21         8.35         1.22         3.12 
TCGA-28-2509 TCGA-28-2514 TCGA-32-1970 TCGA-32-1978 TCGA-32-1982 TCGA-32-1991 
        4.77         5.26        15.39        15.85         4.67        16.93 
TCGA-32-2495 TCGA-32-2634 TCGA-32-2638 TCGA-32-4211 TCGA-32-4719 TCGA-41-2572 
       15.02        22.78        25.18        12.59        10.85        13.35 
TCGA-41-3392 TCGA-41-3393 
        0.99         4.44 

$subtype3
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0024 TCGA-02-0028 TCGA-02-0047 
       35.41        20.71        82.59        53.10        90.58        14.73 
TCGA-02-0052 TCGA-02-0058 TCGA-02-0069 TCGA-02-0080 TCGA-02-0114 TCGA-02-2466 
       12.59         8.35        28.70        89.72        99.98        16.80 
TCGA-02-2483 TCGA-06-0128 TCGA-06-0129 TCGA-06-0143 TCGA-06-0875 TCGA-06-1087 
       15.32        22.72        33.67        11.74        43.46         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2569 
       26.79        11.84        33.90        12.49         4.93         0.43 
TCGA-06-2570 TCGA-12-0818 TCGA-12-0821 TCGA-12-0827 TCGA-12-1088 TCGA-12-1092 
       31.50        91.76        10.62        38.76       127.59        21.73 
TCGA-12-1097 TCGA-12-1099 TCGA-12-3644 TCGA-12-3651 TCGA-12-3653 TCGA-14-0865 
       14.53         4.14        59.77        12.69        14.53        16.50 
TCGA-14-0871 TCGA-14-1401 TCGA-14-1451 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       28.93         3.75        23.11         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1821 TCGA-14-1825 TCGA-14-3476 TCGA-14-3477 TCGA-14-4157 
       12.43        17.79         7.63         0.39         3.78         3.42 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1460 
       53.19        13.28        26.07        16.37         4.31         6.41 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-1388 TCGA-19-1788 TCGA-19-2624 
       21.90         8.61        14.27        12.95         3.68         0.16 
TCGA-19-2629 TCGA-26-1440 TCGA-27-1830 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 
       24.23         9.73         5.06        40.54        30.05        14.04 
TCGA-27-2521 TCGA-28-1746 TCGA-28-1755 TCGA-28-1756 TCGA-28-2512 TCGA-32-1973 
       10.39         0.20         1.55         2.83        11.28        21.07 
TCGA-32-1976 TCGA-32-2494 TCGA-32-4208 TCGA-32-4210 TCGA-32-4213 TCGA-41-2571 
        0.49        20.78        21.14         3.72        19.86         0.85 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3915 
        8.94         9.53        11.84 

subtype1 subtype2 subtype3 
    0.10     0.13     0.16 
subtype1 subtype2 subtype3 
   92.65    77.65   127.59 
subtype1 subtype2 subtype3 
   11.77    10.52    14.27 
[1] "0.1 - 92.7 (11.8)"  "0.1 - 77.7 (10.5)"  "0.2 - 127.6 (14.3)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 41 51
  subtype2 44 66
  subtype3 30 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41   51
  subtype2   44   66
  subtype3   30   51
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       41       44       30
  MALE         51       66       51
[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"
D6V4, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             3                   6
  subtype2                             0                   7
  subtype3                             0                   6
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                              83
  subtype2                             103
  subtype3                              75
D6V5, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)          3        0        0
  TREATED PRIMARY GBM                    6        7        6
  UNTREATED PRIMARY (DE NOVO) GBM       83      103       75
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 73 19
  subtype2 75 35
  subtype3 62 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73   19
  subtype2   75   35
  subtype3   62   19
     clus
vv    subtype1 subtype2 subtype3
  NO        73       75       62
  YES       19       35       19
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         6    82
  subtype2     4                         6    98
  subtype3     3                         4    74
D6V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        4        3
  BLACK OR AFRICAN AMERICAN        6        6        4
  WHITE                           82       98       74
[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"
D6V8, binary
          cls
clus        0  1
  subtype1  3 80
  subtype2  2 88
  subtype3  2 64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   80
  subtype2    2   88
  subtype3    2   64
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        2        2
  NOT HISPANIC OR LATINO       80       88       64
[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(7) Variable = RPPA_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 10 47
  subtype2 17 44
  subtype3 13 31
  subtype4 12 37
subtype1 subtype2 subtype3 subtype4 
      57       61       44       49 
subtype1 subtype2 subtype3 subtype4 
      47       44       31       37 
$subtype1
TCGA-02-0003 TCGA-02-0004 TCGA-02-0068 TCGA-02-0069 TCGA-02-0116 TCGA-02-2470 
        4.73        11.34        26.43        28.70        48.95        12.92 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0154 TCGA-06-0155 TCGA-06-0171 TCGA-06-0189 
       22.72        12.95        13.94        10.45        13.12        15.42 
TCGA-06-0238 TCGA-06-0650 TCGA-06-0882 TCGA-06-1084 TCGA-06-1802 TCGA-06-2557 
       13.32        23.57        20.78        23.93        15.32         1.08 
TCGA-06-2567 TCGA-06-5410 TCGA-06-5412 TCGA-06-5416 TCGA-06-6697 TCGA-08-0245 
        4.37         3.55         4.54         6.71        12.85        37.84 
TCGA-08-0348 TCGA-08-0352 TCGA-08-0353 TCGA-08-0373 TCGA-14-0871 TCGA-15-1447 
       12.16         1.28         8.42         4.41        28.93        53.19 
TCGA-19-1389 TCGA-19-1790 TCGA-19-2625 TCGA-19-2631 TCGA-19-5947 TCGA-19-5952 
        4.64         5.06         4.08         7.00         6.64        18.90 
TCGA-19-5953 TCGA-26-5133 TCGA-26-5134 TCGA-27-1832 TCGA-27-2528 TCGA-28-1750 
        4.73        14.86         5.49         9.86        15.78         8.35 
TCGA-28-1753 TCGA-28-1757 TCGA-28-5214 TCGA-32-1982 TCGA-32-1986 TCGA-32-4211 
        1.22         0.13        23.44         4.67        12.69        12.59 
TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-74-6573 TCGA-76-4926 TCGA-76-4927 
        4.44        11.84        12.46         3.45         4.54        17.59 
TCGA-76-4928 TCGA-76-6282 TCGA-76-6662 
        3.09        17.06         9.27 

$subtype2
TCGA-02-0011 TCGA-02-0014 TCGA-06-0129 TCGA-06-0875 TCGA-06-1804 TCGA-06-1805 
       20.71        82.59        33.67        43.46        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2564 TCGA-06-2566 TCGA-06-2570 TCGA-06-5411 
       15.32        12.49         5.95         5.98        31.50         8.35 
TCGA-06-5417 TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 TCGA-06-6695 TCGA-06-6700 
        5.10         5.23         7.79         1.48         8.32         4.77 
TCGA-06-6701 TCGA-08-0344 TCGA-08-0347 TCGA-08-0350 TCGA-08-0351 TCGA-08-0359 
        4.96       115.86        25.71        29.23        65.33         3.39 
TCGA-08-0380 TCGA-08-0385 TCGA-08-0389 TCGA-12-0691 TCGA-12-1597 TCGA-12-3649 
       14.93         2.70        15.35        12.13        22.19        15.22 
TCGA-12-3651 TCGA-14-0813 TCGA-15-1449 TCGA-16-0846 TCGA-16-1460 TCGA-19-0957 
       12.69         1.35        13.28         3.91         6.41        21.90 
TCGA-19-0962 TCGA-19-1390 TCGA-19-1786 TCGA-19-1788 TCGA-19-2620 TCGA-19-5956 
        0.66        25.38         7.17         3.68         4.87        22.49 
TCGA-19-5958 TCGA-19-5960 TCGA-26-1442 TCGA-26-6174 TCGA-27-1834 TCGA-27-1836 
       14.07        14.96        31.33         2.33        40.54        30.05 
TCGA-27-2518 TCGA-28-1746 TCGA-32-1976 TCGA-32-4210 TCGA-32-5222 TCGA-41-2573 
       24.76         0.20         0.49         3.72        19.23         8.94 
TCGA-41-2575 TCGA-41-5651 TCGA-74-6581 TCGA-76-6193 TCGA-76-6285 TCGA-76-6657 
        9.53        15.12         8.22         2.70         8.35         5.03 
TCGA-76-6663 
        7.73 

$subtype3
TCGA-02-2485 TCGA-06-0126 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-2563 
       15.45         6.94        46.19         5.65         7.17        30.64 
TCGA-06-2565 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5856 TCGA-06-6693 
       16.64         8.81         8.98         8.55         3.75       120.56 
TCGA-06-6699 TCGA-08-0349 TCGA-08-0354 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 
        1.55         9.80        17.95        37.58        22.29        12.23 
TCGA-08-0386 TCGA-12-3646 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       18.02        44.02        10.95        34.92        14.53        14.93 
TCGA-14-1823 TCGA-15-1446 TCGA-19-1386 TCGA-19-1789 TCGA-19-1791 TCGA-19-5950 
       17.85        19.10         9.07         3.25         0.13        17.19 
TCGA-19-5951 TCGA-19-5959 TCGA-26-1440 TCGA-26-5132 TCGA-27-1831 TCGA-27-1833 
        8.02        16.80         9.73         9.40        16.60        24.23 
TCGA-28-1747 TCGA-28-1752 TCGA-32-1970 TCGA-32-1978 TCGA-32-1991 TCGA-41-3392 
        2.53         8.48        15.39        15.85        16.93         0.99 
TCGA-76-4931 TCGA-76-6656 
        9.17         4.83 

$subtype4
TCGA-06-0125 TCGA-06-0156 TCGA-06-0644 TCGA-06-0879 TCGA-06-0939 TCGA-06-1086 
       47.61         5.85        12.62        40.41        26.76         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-2559 TCGA-06-2562 TCGA-06-5408 TCGA-06-5418 
        4.04        26.79         4.93        12.56        11.74         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6390 TCGA-06-6694 TCGA-06-6698 TCGA-08-0345 
        6.15         4.57         5.39         7.36         4.77         1.74 
TCGA-08-0346 TCGA-08-0355 TCGA-08-0356 TCGA-08-0360 TCGA-08-0390 TCGA-08-0392 
        8.42        24.56        31.10        15.39        13.97         0.72 
TCGA-12-0692 TCGA-12-1598 TCGA-12-1599 TCGA-12-5301 TCGA-14-0862 TCGA-19-1392 
        3.65        15.65        25.68         2.04         2.89         3.65 
TCGA-19-2619 TCGA-19-4068 TCGA-19-5954 TCGA-19-5955 TCGA-26-6173 TCGA-27-1830 
        9.67         4.50        12.10         1.78         7.92         5.06 
TCGA-28-1760 TCGA-28-5208 TCGA-32-1987 TCGA-41-4097 TCGA-74-6575 TCGA-74-6577 
        4.70        17.88        14.86         0.20        20.91         4.34 
TCGA-74-6578 TCGA-74-6584 TCGA-76-4929 TCGA-76-4932 TCGA-76-6192 TCGA-76-6664 
       14.33         7.50         3.65        47.93         3.29         7.79 
TCGA-81-5910 
        1.61 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.20     0.13     0.20 
subtype1 subtype2 subtype3 subtype4 
   53.19   115.86   120.56    47.93 
subtype1 subtype2 subtype3 subtype4 
   11.84    12.13    13.38     7.36 
[1] "0.1 - 53.2 (11.8)"  "0.2 - 115.9 (12.1)" "0.1 - 120.6 (13.4)"
[4] "0.2 - 47.9 (7.4)"  
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 17 40
  subtype2 26 35
  subtype3 18 26
  subtype4 24 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   40
  subtype2   26   35
  subtype3   18   26
  subtype4   24   25
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17       26       18       24
  MALE         40       35       26       25
[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, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             0                   2
  subtype2                             1                   0
  subtype3                             0                   0
  subtype4                             0                   1
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                              55
  subtype2                              60
  subtype3                              44
  subtype4                              48
D7V5, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  GLIOBLASTOMA MULTIFORME (GBM)          0        1        0        0
  TREATED PRIMARY GBM                    2        0        0        1
  UNTREATED PRIMARY (DE NOVO) GBM       55       60       44       48
[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"
D7V6, binary
          cls
clus        0  1
  subtype1 42 15
  subtype2 44 17
  subtype3 37  7
  subtype4 33 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   15
  subtype2   44   17
  subtype3   37    7
  subtype4   33   16
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        42       44       37       33
  YES       15       17        7       16
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         4    50
  subtype2     2                         1    52
  subtype3     1                         3    38
  subtype4     0                         3    40
D7V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        2        1        0
  BLACK OR AFRICAN AMERICAN        4        1        3        3
  WHITE                           50       52       38       40
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1  1 48
  subtype2  1 52
  subtype3  0 39
  subtype4  0 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   48
  subtype2    1   52
  subtype3    0   39
  subtype4    0   38
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        0        0
  NOT HISPANIC OR LATINO       48       52       39       38
[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 14 58
  subtype2 25 57
  subtype3 13 44
subtype1 subtype2 subtype3 
      72       82       57 
subtype1 subtype2 subtype3 
      58       57       44 
$subtype1
TCGA-02-0003 TCGA-02-0004 TCGA-02-0069 TCGA-02-2470 TCGA-06-0130 TCGA-06-0189 
        4.73        11.34        28.70        12.92        12.95        15.42 
TCGA-06-0238 TCGA-06-0644 TCGA-06-0879 TCGA-06-0882 TCGA-06-1084 TCGA-06-1086 
       13.32        12.62        40.41        20.78        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1802 TCGA-06-2559 TCGA-06-2562 TCGA-06-5410 
        4.04        26.79        15.32         4.93        12.56         3.55 
TCGA-06-5412 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-6694 TCGA-06-6695 
        4.54         6.71         2.73         6.15         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       12.85         4.77         1.74         8.42        25.71        12.16 
TCGA-08-0350 TCGA-08-0356 TCGA-08-0373 TCGA-08-0385 TCGA-08-0390 TCGA-08-0392 
       29.23        31.10         4.41         2.70        13.97         0.72 
TCGA-12-1598 TCGA-12-1599 TCGA-12-3649 TCGA-12-5301 TCGA-14-0813 TCGA-14-0862 
       15.65        25.68        15.22         2.04         1.35         2.89 
TCGA-14-0871 TCGA-15-1447 TCGA-19-0962 TCGA-19-1392 TCGA-19-1790 TCGA-19-2625 
       28.93        53.19         0.66         3.65         5.06         4.08 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-27-1832 
        7.00         6.64         4.73        12.10         1.78         9.86 
TCGA-28-1750 TCGA-28-1753 TCGA-28-1760 TCGA-28-5208 TCGA-32-1986 TCGA-32-1987 
        8.35         1.22         4.70        17.88        12.69        14.86 
TCGA-32-4211 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-74-6575 TCGA-74-6577 
       12.59        11.84         0.20        12.46        20.91         4.34 
TCGA-74-6578 TCGA-76-4926 TCGA-76-4928 TCGA-76-6192 TCGA-76-6662 TCGA-81-5910 
       14.33         4.54         3.09         3.29         9.27         1.61 

$subtype2
TCGA-02-0011 TCGA-02-0014 TCGA-02-0068 TCGA-02-0116 TCGA-06-0125 TCGA-06-0128 
       20.71        82.59        26.43        48.95        47.61        22.72 
TCGA-06-0129 TCGA-06-0156 TCGA-06-0171 TCGA-06-0650 TCGA-06-0875 TCGA-06-0939 
       33.67         5.85        13.12        23.57        43.46        26.76 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2564 TCGA-06-2566 
       13.61        33.90        15.32        12.49         5.95         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5411 TCGA-06-5417 TCGA-06-5859 
        4.37        31.50        11.74         8.35         5.10         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6700 TCGA-06-6701 
        5.23         7.79         5.39         1.48         4.77         4.96 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0351 TCGA-08-0359 TCGA-08-0360 TCGA-08-0380 
       37.84       115.86        65.33         3.39        15.39        14.93 
TCGA-08-0389 TCGA-12-0691 TCGA-12-0692 TCGA-12-1597 TCGA-12-3651 TCGA-15-1446 
       15.35        12.13         3.65        22.19        12.69        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-1460 TCGA-19-0957 TCGA-19-1389 TCGA-19-1390 
       13.28         3.91         6.41        21.90         4.64        25.38 
TCGA-19-1788 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-4068 
        3.68         3.25         0.13         9.67         4.87         4.50 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5960 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
       22.49        14.07        14.96        31.33        14.86         5.49 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1834 TCGA-27-1836 TCGA-27-2518 
        7.92         2.33         5.06        40.54        30.05        24.76 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1752 TCGA-32-1976 TCGA-32-4210 TCGA-41-2573 
        0.20         2.53         8.48         0.49         3.72         8.94 
TCGA-41-2575 TCGA-41-5651 TCGA-74-6581 TCGA-74-6584 TCGA-76-4927 TCGA-76-4929 
        9.53        15.12         8.22         7.50        17.59         3.65 
TCGA-76-6193 TCGA-76-6285 TCGA-76-6657 TCGA-76-6663 
        2.70         8.35         5.03         7.73 

$subtype3
TCGA-02-2485 TCGA-06-0126 TCGA-06-0154 TCGA-06-0155 TCGA-06-0876 TCGA-06-0877 
       15.45         6.94        13.94        10.45        46.19         5.65 
TCGA-06-0878 TCGA-06-2557 TCGA-06-2563 TCGA-06-2565 TCGA-06-5413 TCGA-06-5414 
        7.17         1.08        30.64        16.64         8.81         8.98 
TCGA-06-5415 TCGA-06-5856 TCGA-06-6693 TCGA-06-6699 TCGA-08-0349 TCGA-08-0352 
        8.55         3.75       120.56         1.55         9.80         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 
        8.42        17.95        24.56        37.58        22.29        12.23 
TCGA-08-0386 TCGA-12-3646 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       18.02        44.02        10.95        34.92        14.53        14.93 
TCGA-14-1823 TCGA-19-1386 TCGA-19-1786 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       17.85         9.07         7.17        17.19         8.02        18.90 
TCGA-19-5959 TCGA-26-1440 TCGA-26-5132 TCGA-27-1831 TCGA-27-1833 TCGA-27-2528 
       16.80         9.73         9.40        16.60        24.23        15.78 
TCGA-28-1757 TCGA-28-5214 TCGA-32-1970 TCGA-32-1978 TCGA-32-1982 TCGA-32-1991 
        0.13        23.44        15.39        15.85         4.67        16.93 
TCGA-32-5222 TCGA-41-3392 TCGA-41-3393 TCGA-74-6573 TCGA-76-4931 TCGA-76-4932 
       19.23         0.99         4.44         3.45         9.17        47.93 
TCGA-76-6282 TCGA-76-6656 TCGA-76-6664 
       17.06         4.83         7.79 

subtype1 subtype2 subtype3 
    0.20     0.13     0.13 
subtype1 subtype2 subtype3 
   53.19   115.86   120.56 
subtype1 subtype2 subtype3 
   8.385    9.600   13.940 
[1] "0.2 - 53.2 (8.4)"   "0.1 - 115.9 (9.6)"  "0.1 - 120.6 (13.9)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 27 45
  subtype2 37 45
  subtype3 21 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   45
  subtype2   37   45
  subtype3   21   36
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27       37       21
  MALE         45       45       36
[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, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             0                   1
  subtype2                             1                   1
  subtype3                             0                   1
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                              71
  subtype2                              80
  subtype3                              56
D8V5, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)          0        1        0
  TREATED PRIMARY GBM                    1        1        1
  UNTREATED PRIMARY (DE NOVO) GBM       71       80       56
[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"
D8V6, binary
          cls
clus        0  1
  subtype1 48 24
  subtype2 63 19
  subtype3 45 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48   24
  subtype2   63   19
  subtype3   45   12
     clus
vv    subtype1 subtype2 subtype3
  NO        48       63       45
  YES       24       19       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         4    59
  subtype2     1                         3    73
  subtype3     2                         4    48
D8V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        2
  BLACK OR AFRICAN AMERICAN        4        3        4
  WHITE                           59       73       48
[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"
D8V8, binary
          cls
clus        0  1
  subtype1  1 56
  subtype2  1 72
  subtype3  0 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   56
  subtype2    1   72
  subtype3    0   49
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        1        0
  NOT HISPANIC OR LATINO       56       72       49
[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 14 33
  subtype2 14 56
  subtype3  6 29
subtype1 subtype2 subtype3 
      47       70       35 
subtype1 subtype2 subtype3 
      33       56       29 
$subtype1
TCGA-02-0047 TCGA-02-2483 TCGA-06-0129 TCGA-06-0138 TCGA-06-0156 TCGA-06-0157 
       14.73        15.32        33.67        24.23         5.85         3.19 
TCGA-06-0174 TCGA-06-0178 TCGA-06-0238 TCGA-06-0646 TCGA-06-0686 TCGA-06-0745 
        3.22        88.14        13.32         5.75        14.20         7.86 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        1.08        12.49         4.93         0.43        31.50        11.74 
TCGA-06-5413 TCGA-06-5416 TCGA-06-5417 TCGA-06-5856 TCGA-06-5859 TCGA-12-0616 
        8.81         6.71         5.10         3.75         4.57        14.73 
TCGA-12-0618 TCGA-12-0821 TCGA-12-1597 TCGA-12-3650 TCGA-14-1825 TCGA-15-1444 
       12.99        10.62        22.19        10.95         7.63        50.53 
TCGA-19-1390 TCGA-19-2624 TCGA-19-2629 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
       25.38         0.16        24.23        14.86         5.49         8.88 
TCGA-27-1830 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-28-1753 TCGA-28-5215 
        5.06        10.39        10.39        16.08         1.22        11.01 
TCGA-28-5216 TCGA-32-2634 TCGA-41-2571 TCGA-41-5651 TCGA-76-4929 
       13.64        22.78         0.85        15.12         3.65 

$subtype2
TCGA-02-0055 TCGA-02-2486 TCGA-06-0125 TCGA-06-0130 TCGA-06-0141 TCGA-06-0184 
        2.50        20.32        47.61        12.95        10.29        69.90 
TCGA-06-0187 TCGA-06-0190 TCGA-06-0210 TCGA-06-0644 TCGA-06-0645 TCGA-06-0649 
       27.22        10.42         7.40        12.62         5.75         2.10 
TCGA-06-0743 TCGA-06-0750 TCGA-06-0878 TCGA-06-2565 TCGA-06-2567 TCGA-06-5410 
       26.40         0.92         7.17        16.64         4.37         3.55 
TCGA-06-5412 TCGA-06-5414 TCGA-06-5418 TCGA-06-5858 TCGA-12-0619 TCGA-12-3652 
        4.54         8.98         2.73         6.15        34.92        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0781 TCGA-14-0789 TCGA-14-0790 
       14.53        14.93         3.22         0.95        11.24        13.78 
TCGA-14-1034 TCGA-14-1823 TCGA-14-1829 TCGA-14-2554 TCGA-16-1045 TCGA-19-1787 
       15.95        17.85         7.17        17.49        29.03        12.66 
TCGA-19-2619 TCGA-19-2625 TCGA-19-4065 TCGA-26-5132 TCGA-26-5136 TCGA-26-5139 
        9.67         4.08         7.04         9.40        18.97         1.58 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-2524 TCGA-27-2526 
       16.60         9.86        40.54        21.30         7.59         2.86 
TCGA-27-2528 TCGA-28-2499 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 
       15.78         3.12         4.77         7.30        14.93        17.88 
TCGA-28-5209 TCGA-28-5213 TCGA-28-5218 TCGA-28-5220 TCGA-32-2615 TCGA-32-2616 
       14.53        31.27         5.16        12.76        15.95         7.36 
TCGA-32-2632 TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2572 TCGA-41-3915 
        8.84        25.18        19.86        19.23        13.35        11.84 
TCGA-76-4925 TCGA-76-4927 TCGA-76-4928 TCGA-76-4932 
        4.80        17.59         3.09        47.93 

$subtype3
TCGA-02-2485 TCGA-06-0132 TCGA-06-0158 TCGA-06-0168 TCGA-06-0211 TCGA-06-0219 
       15.45        25.35        10.82        19.66        11.84         0.72 
TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0882 TCGA-06-1804 TCGA-06-2561 
       46.88         2.70         2.70        20.78        13.61        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-5411 TCGA-06-5415 TCGA-08-0386 
       12.56        30.64         5.95         8.35         8.55        18.02 
TCGA-14-0787 TCGA-14-0817 TCGA-15-0742 TCGA-16-0846 TCGA-19-2620 TCGA-19-5960 
        2.24         5.39        13.78         3.91         4.87        14.96 
TCGA-26-1442 TCGA-27-1837 TCGA-28-1747 TCGA-28-2514 TCGA-28-5207 TCGA-32-1970 
       31.33        14.04         2.53         5.26        11.28        15.39 
TCGA-32-1980 TCGA-32-1982 TCGA-41-4097 TCGA-76-4926 TCGA-76-4931 
        1.18         4.67         0.20         4.54         9.17 

subtype1 subtype2 subtype3 
    0.16     0.92     0.20 
subtype1 subtype2 subtype3 
   88.14    69.90    46.88 
subtype1 subtype2 subtype3 
   10.62    12.23    10.82 
[1] "0.2 - 88.1 (10.6)" "0.9 - 69.9 (12.2)" "0.2 - 46.9 (10.8)"
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1 14 33
  subtype2 31 39
  subtype3  8 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   33
  subtype2   31   39
  subtype3    8   27
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       31        8
  MALE         33       39       27
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             1                   0
  subtype2                             0                   1
  subtype3                             0                   0
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                              46
  subtype2                              69
  subtype3                              35
D9V5, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)          1        0        0
  TREATED PRIMARY GBM                    0        1        0
  UNTREATED PRIMARY (DE NOVO) GBM       46       69       35
[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"
D9V6, binary
          cls
clus        0  1
  subtype1 32 15
  subtype2 48 22
  subtype3 22 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   15
  subtype2   48   22
  subtype3   22   13
     clus
vv    subtype1 subtype2 subtype3
  NO        32       48       22
  YES       15       22       13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         3    42
  subtype2     1                         5    63
  subtype3     2                         2    31
D9V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        2
  BLACK OR AFRICAN AMERICAN        3        5        2
  WHITE                           42       63       31
[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"
D9V8, binary
          cls
clus        0  1
  subtype1  1 44
  subtype2  2 51
  subtype3  0 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   44
  subtype2    2   51
  subtype3    0   30
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        0
  NOT HISPANIC OR LATINO       44       51       30
[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 10 22
  subtype2 20 76
  subtype3  4 20
subtype1 subtype2 subtype3 
      32       96       24 
subtype1 subtype2 subtype3 
      22       76       20 
$subtype1
TCGA-02-0047 TCGA-02-2483 TCGA-06-0129 TCGA-06-0174 TCGA-06-0178 TCGA-06-0238 
       14.73        15.32        33.67         3.22        88.14        13.32 
TCGA-06-0686 TCGA-06-2558 TCGA-06-2559 TCGA-06-2570 TCGA-06-5416 TCGA-06-5417 
       14.20        12.49         4.93        31.50         6.71         5.10 
TCGA-12-0618 TCGA-12-1597 TCGA-12-3650 TCGA-14-1825 TCGA-15-1444 TCGA-19-1390 
       12.99        22.19        10.95         7.63        50.53        25.38 
TCGA-19-2624 TCGA-19-2629 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        0.16        24.23        31.33        14.86         5.49         8.88 
TCGA-27-1837 TCGA-27-2521 TCGA-27-2523 TCGA-28-5215 TCGA-28-5216 TCGA-32-2634 
       14.04        10.39        16.08        11.01        13.64        22.78 
TCGA-41-2571 TCGA-41-5651 
        0.85        15.12 

$subtype2
TCGA-02-0055 TCGA-02-2485 TCGA-02-2486 TCGA-06-0125 TCGA-06-0130 TCGA-06-0138 
        2.50        15.45        20.32        47.61        12.95        24.23 
TCGA-06-0141 TCGA-06-0156 TCGA-06-0157 TCGA-06-0184 TCGA-06-0187 TCGA-06-0190 
       10.29         5.85         3.19        69.90        27.22        10.42 
TCGA-06-0210 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0649 TCGA-06-0743 
        7.40        12.62         5.75         5.75         2.10        26.40 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0878 TCGA-06-1804 TCGA-06-2557 
        7.86         2.70         0.92         7.17        13.61         1.08 
TCGA-06-2562 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 
       12.56        16.64         4.37         0.43        11.74         3.55 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        4.54         8.81         8.98         2.73         3.75         6.15 
TCGA-06-5859 TCGA-08-0386 TCGA-12-0616 TCGA-12-0619 TCGA-12-0821 TCGA-12-3652 
        4.57        18.02        14.73        34.92        10.62        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0781 TCGA-14-0787 TCGA-14-0789 
       14.53        14.93         3.22         0.95         2.24        11.24 
TCGA-14-0790 TCGA-14-0817 TCGA-14-1034 TCGA-14-1823 TCGA-14-1829 TCGA-14-2554 
       13.78         5.39        15.95        17.85         7.17        17.49 
TCGA-15-0742 TCGA-16-1045 TCGA-19-1787 TCGA-19-2619 TCGA-19-2625 TCGA-19-4065 
       13.78        29.03        12.66         9.67         4.08         7.04 
TCGA-26-5132 TCGA-26-5136 TCGA-26-5139 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        9.40        18.97         1.58         5.06        16.60         9.86 
TCGA-27-1834 TCGA-27-1835 TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 
       40.54        21.30        10.39         7.59         2.86        15.78 
TCGA-28-1753 TCGA-28-2499 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 
        1.22         3.12         4.77         7.30        14.93        17.88 
TCGA-28-5209 TCGA-28-5213 TCGA-28-5218 TCGA-28-5220 TCGA-32-1982 TCGA-32-2615 
       14.53        31.27         5.16        12.76         4.67        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2572 
        7.36         8.84        25.18        19.86        19.23        13.35 
TCGA-41-3915 TCGA-76-4925 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4932 
       11.84         4.80        17.59         3.09         3.65        47.93 

$subtype3
TCGA-06-0132 TCGA-06-0158 TCGA-06-0168 TCGA-06-0211 TCGA-06-0219 TCGA-06-0744 
       25.35        10.82        19.66        11.84         0.72        46.88 
TCGA-06-0749 TCGA-06-0882 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 TCGA-06-5411 
        2.70        20.78        17.65        30.64         5.95         8.35 
TCGA-06-5415 TCGA-16-0846 TCGA-19-2620 TCGA-19-5960 TCGA-28-1747 TCGA-28-2514 
        8.55         3.91         4.87        14.96         2.53         5.26 
TCGA-28-5207 TCGA-32-1970 TCGA-32-1980 TCGA-41-4097 TCGA-76-4926 TCGA-76-4931 
       11.28        15.39         1.18         0.20         4.54         9.17 

subtype1 subtype2 subtype3 
    0.16     0.43     0.20 
subtype1 subtype2 subtype3 
   88.14    69.90    46.88 
subtype1 subtype2 subtype3 
   13.84    10.34     8.86 
[1] "0.2 - 88.1 (13.8)" "0.4 - 69.9 (10.3)" "0.2 - 46.9 (8.9)" 
D10V2, continuous
D10V3, binary
          cls
clus        0  1
  subtype1  9 23
  subtype2 39 57
  subtype3  5 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   23
  subtype2   39   57
  subtype3    5   19
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9       39        5
  MALE         23       57       19
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             1                   0
  subtype2                             0                   1
  subtype3                             0                   0
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                              31
  subtype2                              95
  subtype3                              24
D10V5, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)          1        0        0
  TREATED PRIMARY GBM                    0        1        0
  UNTREATED PRIMARY (DE NOVO) GBM       31       95       24
[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"
D10V6, binary
          cls
clus        0  1
  subtype1 24  8
  subtype2 62 34
  subtype3 16  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    8
  subtype2   62   34
  subtype3   16    8
     clus
vv    subtype1 subtype2 subtype3
  NO        24       62       16
  YES        8       34        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    29
  subtype2     2                         8    85
  subtype3     1                         1    22
D10V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        2        1
  BLACK OR AFRICAN AMERICAN        1        8        1
  WHITE                           29       85       22
[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"
D10V8, binary
          cls
clus        0  1
  subtype1  0 30
  subtype2  3 75
  subtype3  0 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   30
  subtype2    3   75
  subtype3    0   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        3        0
  NOT HISPANIC OR LATINO       30       75       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
