[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/22506586/GBM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBM-TP/22555065/GBM-TP.mergedcluster.txt"

nPatients in clinical file=595, in cluster file=599, common to both=595
[1]  10 595
[1] "MRNA_CNMF"
[1] 3
  1   2   3   4 
167  97 139 122 
  1   2   3   4 
167  97 139 122 
[1] "MRNA_CHIERARCHICAL"
[1] 3
  1   2   3   4 
153 107 103 162 
  1   2   3   4 
153 107 103 162 
[1] "MIR_CNMF"
[1] 3
  1   2   3   4 
151 189  93 130 
  1   2   3   4 
151 189  93 130 
[1] "MIR_CHIERARCHICAL"
[1] 3
  1   2   3 
303 129 131 
  1   2   3 
303 129 131 
[1] "CN_CNMF"
[1] 3
  1   2   3 
252 196 125 
  1   2   3 
252 196 125 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
71 44 83 85 
 1  2  3  4 
71 44 83 85 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
46 61 46 31 48 
 1  2  3  4  5 
46 61 46 31 48 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
94 77 61 
 1  2  3 
94 77 61 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
48 71 33 
 1  2  3 
48 71 33 
[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] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "RADIATION_THERAPY"                   
 [9] "KARNOFSKY_PERFORMANCE_SCORE"         
[10] "HISTOLOGICAL_TYPE"                   
[11] "RACE"                                
[12] "ETHNICITY"                           

Input Data has 12 rows and 595 columns.

[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=384,	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=94,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 595 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"              "GENDER"                     
[3] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
[5] "HISTOLOGICAL_TYPE"           "RACE"                       
[7] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=72, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, 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  18 149
  subtype2  14  83
  subtype3  24 114
  subtype4  19 102
subtype1 subtype2 subtype3 subtype4 
     167       97      138      121 
subtype1 subtype2 subtype3 subtype4 
     149       83      114      102 
$subtype1
TCGA-06-5410 TCGA-06-5412 TCGA-06-5418 TCGA-12-1092 TCGA-12-5295 TCGA-14-0736 
        3.55         4.54         2.73        21.73        14.93        15.12 
TCGA-14-0781 TCGA-14-0783 TCGA-14-1034 TCGA-14-1396 TCGA-14-1452 TCGA-14-1823 
        0.95         6.21        15.95         1.12         7.10        17.85 
TCGA-14-1829 TCGA-14-2554 TCGA-16-1045 TCGA-16-1055 TCGA-16-1060 TCGA-19-1787 
        7.17        17.49        29.03        10.29         9.14        12.66 
TCGA-19-1790 TCGA-19-2623 TCGA-19-5947 TCGA-19-5955 TCGA-26-1438 TCGA-27-1830 
        5.06         7.53         6.64         1.78        10.03         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1838 TCGA-27-2524 TCGA-27-2527 TCGA-28-1745 
       16.60         9.86        11.51         7.59        14.40        11.34 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1760 TCGA-28-2502 TCGA-28-2509 
        8.35         7.63         8.48         4.70         0.66         4.77 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 
        0.10        19.50         4.67        12.69        14.86        12.23 
TCGA-32-2494 TCGA-32-2615 TCGA-32-2632 TCGA-32-4208 TCGA-32-4209 TCGA-32-4213 
       20.78        15.95         8.84        21.14        20.32        19.86 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-76-4926 TCGA-76-4927 TCGA-76-6193 
        4.44        11.84         0.20         4.54        17.59         2.70 
TCGA-76-6282 TCGA-02-0001 TCGA-02-0003 TCGA-02-0004 TCGA-02-0009 TCGA-02-0025 
       17.06        11.77         4.73        11.34        10.59        42.74 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0043 
       12.16        90.58         2.83        14.14        10.52        18.31 
TCGA-02-0046 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
        6.87        15.09        12.59         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0075 TCGA-02-0079 TCGA-02-0086 
        9.57         6.02        19.73        20.84        27.25         8.81 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0337 
       16.96         3.48        11.67        17.65        23.18        25.12 
TCGA-02-0456 TCGA-02-2470 TCGA-02-2486 TCGA-06-0122 TCGA-06-0124 TCGA-06-0130 
        3.35        12.92        20.32         6.15        20.38        12.95 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0147 TCGA-06-0149 
       11.90         0.20        10.29        11.74        17.79         8.61 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0156 TCGA-06-0164 TCGA-06-0168 
       12.33        13.94        10.45         5.85        56.91        19.66 
TCGA-06-0169 TCGA-06-0175 TCGA-06-0176 TCGA-06-0184 TCGA-06-0189 TCGA-06-0190 
        3.29         4.04        91.00        69.90        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0210 
       38.96         4.67         5.56         0.39         7.66         7.40 
TCGA-06-0213 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 TCGA-06-0645 
        0.53         9.01        72.36         9.57        12.62         5.75 
TCGA-06-0646 TCGA-06-0649 TCGA-06-0650 TCGA-06-0750 TCGA-06-0878 TCGA-06-0881 
        5.75         2.10        23.57         0.92         7.17        16.57 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1802 TCGA-08-0346 TCGA-08-0352 
       26.76        23.93        26.79        15.32         8.42         1.28 
TCGA-08-0360 TCGA-08-0373 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       15.39         4.41        13.97         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0522 TCGA-08-0525 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       42.15        20.88        15.98        34.92        10.45         7.59 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0822 
       53.85        43.23         7.63         9.73        14.93        23.51 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1093 TCGA-12-1095 TCGA-12-1096 TCGA-14-0789 
       20.58       127.59        15.98        15.85         9.11        11.24 
TCGA-14-0817 TCGA-14-1037 TCGA-19-1385 TCGA-19-1389 TCGA-26-5139 TCGA-28-2513 
        5.39        19.30        10.75         4.64         1.58         7.30 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5214 TCGA-28-5215 
       11.28        17.88        14.53        23.44        11.01 

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

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

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

subtype1 subtype2 subtype3 subtype4 
    0.10     0.16     0.10     0.20 
subtype1 subtype2 subtype3 subtype4 
  127.59   115.86    94.78    91.76 
subtype1 subtype2 subtype3 subtype4 
  11.340   13.640   13.825   12.690 
[1] "0.1 - 127.6 (11.3)" "0.2 - 115.9 (13.6)" "0.1 - 94.8 (13.8)" 
[4] "0.2 - 91.8 (12.7)" 
D1V2, continuous
D1V3, binary
          cls
clus         0   1
  subtype1  63 104
  subtype2  44  53
  subtype3  60  79
  subtype4  38  84
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63  104
  subtype2   44   53
  subtype3   60   79
  subtype4   38   84
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       63       44       60       38
  MALE        104       53       79       84
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
          cls
clus         0   1
  subtype1  21 138
  subtype2  16  77
  subtype3  14 121
  subtype4  19  99
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21  138
  subtype2   16   77
  subtype3   14  121
  subtype4   19   99
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        21       16       14       19
  YES      138       77      121       99
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             1                   8
  subtype2                             0                   8
  subtype3                             0                   3
  subtype4                             5                   1
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             158
  subtype2                              89
  subtype3                             136
  subtype4                             116
D1V6, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  GLIOBLASTOMA MULTIFORME (GBM)          1        0        0        5
  TREATED PRIMARY GBM                    8        8        3        1
  UNTREATED PRIMARY (DE NOVO) GBM      158       89      136      116
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        12   146
  subtype2     2                         7    84
  subtype3     4                         7   125
  subtype4     3                         5   107
D1V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        2        4        3
  BLACK OR AFRICAN AMERICAN       12        7        7        5
  WHITE                          146       84      125      107
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus         0   1
  subtype1   3 139
  subtype2   5  72
  subtype3   3 121
  subtype4   1 106
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  139
  subtype2    5   72
  subtype3    3  121
  subtype4    1  106
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        5        3        1
  NOT HISPANIC OR LATINO      139       72      121      106
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2        0   1
  subtype1  15 138
  subtype2  26  81
  subtype3  16  86
  subtype4  18 143
subtype1 subtype2 subtype3 subtype4 
     153      107      102      161 
subtype1 subtype2 subtype3 subtype4 
     138       81       86      143 
$subtype1
TCGA-06-5410 TCGA-06-5412 TCGA-06-5418 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 
        3.55         4.54         2.73        15.12         0.95         6.21 
TCGA-14-1034 TCGA-14-1396 TCGA-14-1452 TCGA-16-1045 TCGA-16-1060 TCGA-19-1790 
       15.95         1.12         7.10        29.03         9.14         5.06 
TCGA-19-5947 TCGA-19-5952 TCGA-19-5955 TCGA-26-1438 TCGA-26-1439 TCGA-26-5136 
        6.64        18.90         1.78        10.03        13.87        18.97 
TCGA-27-1832 TCGA-27-2524 TCGA-27-2527 TCGA-28-1751 TCGA-28-1760 TCGA-28-2502 
        9.86         7.59        14.40         7.63         4.70         0.66 
TCGA-28-2509 TCGA-32-1977 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 
        4.77         0.10        12.69        14.86        12.23        20.78 
TCGA-32-2638 TCGA-32-4209 TCGA-76-4926 TCGA-76-6193 TCGA-76-6282 TCGA-02-0001 
       25.18        20.32         4.54         2.70        17.06        11.77 
TCGA-02-0003 TCGA-02-0004 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        11.34        23.18        10.59        35.41        20.71 
TCGA-02-0015 TCGA-02-0021 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 
       20.61        77.65        53.10        42.74        12.16        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
        2.83        14.14        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
       14.73        15.09        12.59         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        9.57         6.02        19.73        26.43        25.05         5.49 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0086 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 
       20.84        27.25         8.81        27.02        11.67        17.65 
TCGA-02-0111 TCGA-02-0116 TCGA-02-0266 TCGA-02-0271 TCGA-02-0337 TCGA-02-0456 
       23.18        48.95        17.72        14.47        25.12         3.35 
TCGA-02-2486 TCGA-06-0122 TCGA-06-0124 TCGA-06-0130 TCGA-06-0139 TCGA-06-0141 
       20.32         6.15        20.38        12.95        11.90        10.29 
TCGA-06-0143 TCGA-06-0147 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0164 
       11.74        17.79        12.33        13.94        10.45        56.91 
TCGA-06-0169 TCGA-06-0175 TCGA-06-0176 TCGA-06-0184 TCGA-06-0189 TCGA-06-0190 
        3.29         4.04        91.00        69.90        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0206 TCGA-06-0210 TCGA-06-0394 
       38.96         4.67         5.56         7.66         7.40        10.82 
TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 TCGA-06-0645 TCGA-06-0650 
        9.01        72.36         9.57        12.62         5.75        23.57 
TCGA-06-0750 TCGA-06-0878 TCGA-06-0881 TCGA-06-1084 TCGA-06-1086 TCGA-06-2562 
        0.92         7.17        16.57        23.93         6.84        12.56 
TCGA-06-2569 TCGA-08-0346 TCGA-08-0352 TCGA-08-0356 TCGA-08-0360 TCGA-08-0390 
        0.43         8.42         1.28        31.10        15.39        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0522 TCGA-08-0525 
        0.72        12.56         4.27        42.15        20.88        15.98 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 
       34.92        10.45         7.59        53.85         7.63         9.73 
TCGA-12-0778 TCGA-12-0822 TCGA-12-0829 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 
       14.93        23.51        20.58        15.98        12.23         9.11 
TCGA-14-0789 TCGA-14-0867 TCGA-14-0871 TCGA-19-1385 TCGA-19-1389 TCGA-26-5139 
       11.24         2.04        28.93        10.75         4.64         1.58 
TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 
        7.30        11.28        17.88        14.53        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.01        13.64         5.16 

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

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

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

subtype1 subtype2 subtype3 subtype4 
    0.10     0.16     0.10     0.13 
subtype1 subtype2 subtype3 subtype4 
   91.00   115.86    94.78   127.59 
subtype1 subtype2 subtype3 subtype4 
   12.23    14.86    13.78    10.62 
[1] "0.1 - 91.0 (12.2)"  "0.2 - 115.9 (14.9)" "0.1 - 94.8 (13.8)" 
[4] "0.1 - 127.6 (10.6)"
D2V2, continuous
D2V3, binary
          cls
clus         0   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, binary
          cls
clus         0   1
  subtype1  17 131
  subtype2  13  91
  subtype3  11  88
  subtype4  29 125
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17  131
  subtype2   13   91
  subtype3   11   88
  subtype4   29  125
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        17       13       11       29
  YES      131       91       88      125
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, 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
D2V6, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  GLIOBLASTOMA MULTIFORME (GBM)          0        1        0        5
  TREATED PRIMARY GBM                   11        3        3        3
  UNTREATED PRIMARY (DE NOVO) GBM      142      103      100      154
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        13   130
  subtype2     4                         6    95
  subtype3     3                         4    93
  subtype4     2                         8   144
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  21 130
  subtype2  34 155
  subtype3  14  78
  subtype4  23 106
subtype1 subtype2 subtype3 subtype4 
     151      189       92      129 
subtype1 subtype2 subtype3 subtype4 
     130      155       78      106 
$subtype1
TCGA-06-5414 TCGA-06-5418 TCGA-06-5858 TCGA-06-6697 TCGA-06-6698 TCGA-12-1599 
        8.98         2.73         6.15        12.85         4.77        25.68 
TCGA-12-3649 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       15.22        14.93         3.22         2.04        15.12         0.95 
TCGA-14-0862 TCGA-14-1034 TCGA-14-1450 TCGA-14-1452 TCGA-14-1459 TCGA-14-1823 
        2.89        15.95        58.78         7.10        12.43        17.85 
TCGA-14-1829 TCGA-16-1045 TCGA-16-1055 TCGA-16-1060 TCGA-19-1790 TCGA-19-2619 
        7.17        29.03        10.29         9.14         5.06         9.67 
TCGA-19-2621 TCGA-19-2623 TCGA-19-5947 TCGA-19-5952 TCGA-19-5954 TCGA-19-5955 
        1.08         7.53         6.64        18.90        12.10         1.78 
TCGA-19-5958 TCGA-26-1438 TCGA-26-1439 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
       14.07        10.03        13.87        16.60         9.86        40.54 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1745 TCGA-28-1751 TCGA-28-2502 
        2.86        14.40        15.78        11.34         7.63         0.66 
TCGA-28-2509 TCGA-32-1979 TCGA-32-1987 TCGA-32-1991 TCGA-32-2632 TCGA-32-2638 
        4.77        19.50        14.86        16.93         8.84        25.18 
TCGA-32-4213 TCGA-41-3915 TCGA-74-6575 TCGA-74-6578 TCGA-76-4927 TCGA-76-4932 
       19.86        11.84        20.91        14.33        17.59        47.93 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6657 TCGA-76-6662 TCGA-02-0001 TCGA-02-0004 
        2.70        17.06         5.03        34.45        11.77        11.34 
TCGA-02-0006 TCGA-02-0009 TCGA-02-0015 TCGA-02-0027 TCGA-02-0033 TCGA-02-0037 
       18.35        10.59        20.61        12.16         2.83         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0051 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
       10.72        10.52        15.09         6.54         2.50        19.86 
TCGA-02-0059 TCGA-02-0075 TCGA-02-0079 TCGA-02-0086 TCGA-02-0115 TCGA-02-0289 
        9.57        20.84        27.25         8.81        15.65        14.20 
TCGA-02-0290 TCGA-02-0326 TCGA-02-0422 TCGA-02-2486 TCGA-06-0122 TCGA-06-0147 
       15.95         7.33        14.50        20.32         6.15        17.79 
TCGA-06-0151 TCGA-06-0159 TCGA-06-0176 TCGA-06-0184 TCGA-06-0187 TCGA-06-0190 
       46.59         9.44        91.00        69.90        27.22        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
       38.96         4.67         5.56        11.84         0.53        15.02 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0412 TCGA-06-0644 TCGA-06-0649 TCGA-06-0745 
       10.82         9.01         9.57        12.62         2.10         7.86 
TCGA-06-0749 TCGA-06-1800 TCGA-06-2561 TCGA-06-2562 TCGA-06-6390 TCGA-08-0244 
        2.70        26.79        17.65        12.56         5.39        22.68 
TCGA-08-0246 TCGA-08-0346 TCGA-08-0352 TCGA-08-0354 TCGA-08-0360 TCGA-08-0380 
        4.18         8.42         1.28        17.95        15.39        14.93 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0511 TCGA-08-0512 TCGA-08-0514 
       13.97        12.56         4.27         7.73        42.15        11.08 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0522 TCGA-08-0525 TCGA-08-0529 TCGA-12-0657 
       19.33         4.80        20.88        15.98        18.41         0.10 
TCGA-12-0662 TCGA-12-0776 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 
       38.17         9.73        23.51        27.78         8.94        20.58 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-14-0789 TCGA-14-1037 TCGA-14-1043 
       12.23        15.85        14.53        11.24        19.30         0.79 
TCGA-15-0742 TCGA-19-0955 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 
       13.78        11.77         0.66        10.75         9.07        12.95 
TCGA-19-1389 TCGA-26-5139 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-32-2616 
        4.64         1.58         7.30        14.93        17.88         7.36 
TCGA-81-5911 
       17.72 

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

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

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

subtype1 subtype2 subtype3 subtype4 
    0.10     0.13     0.39     0.10 
subtype1 subtype2 subtype3 subtype4 
   91.00   127.59    65.33   120.56 
subtype1 subtype2 subtype3 subtype4 
  12.100   12.990    9.635   12.460 
[1] "0.1 - 91.0 (12.1)"  "0.1 - 127.6 (13.0)" "0.4 - 65.3 (9.6)"  
[4] "0.1 - 120.6 (12.5)"
D3V2, continuous
D3V3, binary
          cls
clus         0   1
  subtype1  59  92
  subtype2  80 109
  subtype3  36  57
  subtype4  44  86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   92
  subtype2   80  109
  subtype3   36   57
  subtype4   44   86
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       59       80       36       44
  MALE         92      109       57       86
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
          cls
clus         0   1
  subtype1  17 129
  subtype2  22 157
  subtype3  18  72
  subtype4  16 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17  129
  subtype2   22  157
  subtype3   18   72
  subtype4   16  108
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        17       22       18       16
  YES      129      157       72      108
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             2                   3
  subtype2                             3                   9
  subtype3                             3                   5
  subtype4                             3                   3
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             146
  subtype2                             177
  subtype3                              85
  subtype4                             124
D3V6, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  GLIOBLASTOMA MULTIFORME (GBM)          2        3        3        3
  TREATED PRIMARY GBM                    3        9        5        3
  UNTREATED PRIMARY (DE NOVO) GBM      146      177       85      124
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                        13   127
  subtype2     7                         9   162
  subtype3     1                         1    89
  subtype4     2                         7   117
D3V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        7        1        2
  BLACK OR AFRICAN AMERICAN       13        9        1        7
  WHITE                          127      162       89      117
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus         0   1
  subtype1   3 124
  subtype2   4 158
  subtype3   2  74
  subtype4   3 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  124
  subtype2    4  158
  subtype3    2   74
  subtype4    3  105
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        4        2        3
  NOT HISPANIC OR LATINO      124      158       74      105
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MIR_CHIERARCHICAL
D4V1, survival
          sevent
clus2        0   1
  subtype1  47 255
  subtype2  22 106
  subtype3  23 108
subtype1 subtype2 subtype3 
     302      128      131 
subtype1 subtype2 subtype3 
     255      106      108 
$subtype1
TCGA-06-6391 TCGA-06-5410 TCGA-06-5411 TCGA-06-5415 TCGA-06-5416 TCGA-06-5417 
        1.48         3.55         8.35         8.55         6.71         5.10 
TCGA-06-5856 TCGA-06-6388 TCGA-06-6700 TCGA-06-6701 TCGA-12-1092 TCGA-12-1597 
        3.75         5.23         4.77         4.96        21.73        22.19 
TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3646 TCGA-12-3649 TCGA-12-3650 
       15.65        25.68        59.77        44.02        15.22        10.95 
TCGA-12-3651 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0812 TCGA-14-0865 
       12.69         3.22         2.04        11.97         3.25        16.50 
TCGA-14-0866 TCGA-14-1401 TCGA-14-1451 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       26.33         3.75        23.11        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-3476 TCGA-14-3477 TCGA-14-4157 TCGA-16-1045 
        5.88         7.17         0.39         3.78         3.42        29.03 
TCGA-16-1055 TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 
       10.29         9.14        13.97         6.41         8.61        14.27 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1788 TCGA-19-1791 TCGA-19-2620 TCGA-19-2624 
       25.38         3.65         3.68         0.13         4.87         0.16 
TCGA-19-4068 TCGA-19-5950 TCGA-19-5955 TCGA-19-5956 TCGA-19-5960 TCGA-26-1799 
        4.50        17.19         1.78        22.49        14.96         9.37 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 
        8.88        18.97        30.05        14.04        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 
       16.77        16.08         7.59        14.40         0.20         2.53 
TCGA-28-1752 TCGA-28-1756 TCGA-28-2502 TCGA-28-2506 TCGA-32-1970 TCGA-32-1973 
        8.48         2.83         0.66         6.74        15.39        21.07 
TCGA-32-1976 TCGA-32-1980 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        0.49         1.18        16.93        12.23        20.78        15.02 
TCGA-32-2634 TCGA-32-4208 TCGA-32-4210 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 
       22.78        21.14         3.72        10.85         0.85        13.35 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-74-6581 
        8.94         0.99        11.84        15.12        12.46         8.22 
TCGA-74-6584 TCGA-76-4926 TCGA-76-4927 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        7.50         4.54        17.59         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6662 TCGA-76-6663 TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 
        3.29        34.45        18.64        11.77         4.73        23.18 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0023 
       35.41        20.71        82.59        20.61        87.06        20.12 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0038 TCGA-02-0039 
       53.10        24.59        12.16        90.58        10.72        10.52 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 
       14.73         3.22        12.59        19.86         8.35         6.02 
TCGA-02-0069 TCGA-02-0071 TCGA-02-0074 TCGA-02-0079 TCGA-02-0080 TCGA-02-0084 
       28.70         5.49        10.19        27.25        89.72        12.62 
TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0104 TCGA-02-0114 TCGA-02-0115 
       51.32        57.76        16.96        65.00        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0266 TCGA-02-0281 TCGA-02-0321 TCGA-02-0325 
       48.95        16.54        17.72         3.98         9.90        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0339 TCGA-02-0432 
        7.33        15.91        25.71        25.12        12.39        47.11 
TCGA-02-0439 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 
        0.66        11.34         9.27        16.21        16.80        12.92 
TCGA-02-2483 TCGA-06-0122 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       15.32         6.15         6.94         3.98        22.72        33.67 
TCGA-06-0133 TCGA-06-0138 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 
       14.30        24.23         2.20        11.74        20.09        17.79 
TCGA-06-0150 TCGA-06-0156 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       19.46         5.85        10.82         9.44        11.80         3.42 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
        5.85        19.66        13.12         4.47         3.22         4.04 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 
        4.18        88.14        20.25        69.90        73.84        44.58 
TCGA-06-0195 TCGA-06-0208 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40         8.42         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0410 
       19.82        13.64        13.32        20.42        48.69         4.70 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
        3.16        35.11         5.75         9.80        23.57        14.20 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 TCGA-06-0882 
       46.88         7.86         2.70         0.92        43.46        20.78 
TCGA-06-0939 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
       26.76         4.04        11.84        15.32        13.61        33.90 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2566 TCGA-06-2570 TCGA-06-6389 TCGA-06-6693 TCGA-08-0244 TCGA-08-0245 
        5.98        31.50         7.79       120.56        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
      115.86         1.74        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0357 TCGA-08-0359 TCGA-08-0373 TCGA-08-0375 
       65.33         1.28        37.58         3.39         4.41        12.23 
TCGA-08-0380 TCGA-08-0385 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 
       14.93         2.70        18.02        15.35        13.97        12.56 
TCGA-08-0511 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 TCGA-12-0618 
        7.73        19.59        58.68         4.80         7.27        12.99 
TCGA-12-0656 TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       94.78        25.97        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0780 TCGA-12-0820 TCGA-12-0821 
       15.06        53.85        43.23        14.86        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-1089 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       23.51        38.76         5.82        15.85         9.11        14.53 
TCGA-12-1099 TCGA-14-0813 TCGA-14-0867 TCGA-14-1043 TCGA-15-1444 TCGA-15-1446 
        4.14         1.35         2.04         0.79        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 
       53.19        13.28         3.91        26.07        16.37        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 
       21.90         0.66         5.95        12.95         4.64        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 TCGA-28-2514 TCGA-28-5207 
       14.86         5.49         1.58         2.33         5.26        11.28 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       31.27        23.44        13.64        22.68        12.76         5.42 
TCGA-32-2616 TCGA-76-6283 
        7.36         5.42 

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

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

subtype1 subtype2 subtype3 
    0.13     0.10     0.10 
subtype1 subtype2 subtype3 
  120.56    92.65   127.59 
subtype1 subtype2 subtype3 
  12.725   11.030   11.840 
[1] "0.1 - 120.6 (12.7)" "0.1 - 92.7 (11.0)"  "0.1 - 127.6 (11.8)"
D4V2, continuous
D4V3, binary
          cls
clus         0   1
  subtype1 111 192
  subtype2  48  81
  subtype3  60  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  111  192
  subtype2   48   81
  subtype3   60   71
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      111       48       60
  MALE        192       81       71
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
          cls
clus         0   1
  subtype1  44 246
  subtype2  13 109
  subtype3  16 111
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44  246
  subtype2   13  109
  subtype3   16  111
     clus
vv    subtype1 subtype2 subtype3
  NO        44       13       16
  YES      246      109      111
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             7                  13
  subtype2                             3                   2
  subtype3                             1                   5
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             283
  subtype2                             124
  subtype3                             125
D4V6, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)          7        3        1
  TREATED PRIMARY GBM                   13        2        5
  UNTREATED PRIMARY (DE NOVO) GBM      283      124      125
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                        10   273
  subtype2     3                        11   113
  subtype3     3                         9   109
D4V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            7        3        3
  BLACK OR AFRICAN AMERICAN       10       11        9
  WHITE                          273      113      109
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus         0   1
  subtype1   6 250
  subtype2   2 109
  subtype3   4 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  250
  subtype2    2  109
  subtype3    4  102
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        2        4
  NOT HISPANIC OR LATINO      250      109      102
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = CN_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  48 202
  subtype2  26 170
  subtype3  23 101
subtype1 subtype2 subtype3 
     250      196      124 
subtype1 subtype2 subtype3 
     202      170      101 
$subtype1
TCGA-06-6391 TCGA-19-A6J4 TCGA-06-1806 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48         3.98        15.32         3.55         8.35         4.54 
TCGA-06-5416 TCGA-06-5858 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 
        6.71         6.15        12.85         4.77         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-12-1092 
       26.79         1.87         2.56        14.60        17.72        21.73 
TCGA-12-1602 TCGA-14-0740 TCGA-14-0781 TCGA-14-0812 TCGA-14-0862 TCGA-14-1396 
        6.77        11.97         0.95         3.25         2.89         1.12 
TCGA-14-1401 TCGA-14-1450 TCGA-14-1456 TCGA-14-1458 TCGA-14-1794 TCGA-14-1821 
        3.75        58.78        40.96         6.67         0.99        17.79 
TCGA-14-3477 TCGA-14-4157 TCGA-16-1045 TCGA-16-1060 TCGA-16-1460 TCGA-19-0960 
        3.78         3.42        29.03         9.14         6.41         8.61 
TCGA-19-1390 TCGA-19-1787 TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 
       25.38        12.66        24.23         7.04         6.64        18.90 
TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-26-1438 TCGA-27-1830 TCGA-27-1832 
        4.73         1.78        22.49        10.03         5.06         9.86 
TCGA-27-2521 TCGA-27-2527 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
       16.77        14.40         8.35         7.63         8.48         1.22 
TCGA-28-1756 TCGA-28-2502 TCGA-28-2506 TCGA-32-1973 TCGA-32-1980 TCGA-32-1982 
        2.83         0.66         6.74        21.07         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-4208 TCGA-41-2573 
       12.69        14.86        12.23        20.78        21.14         8.94 
TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-74-6575 TCGA-74-6577 TCGA-76-4928 
       11.84         0.20        12.46        20.91         4.34         3.09 
TCGA-76-4934 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6662 TCGA-76-6663 
        2.53         3.29         2.70        17.06        34.45        18.64 
TCGA-RR-A6KA TCGA-06-0209 TCGA-02-0001 TCGA-02-0006 TCGA-02-0010 TCGA-02-0011 
        6.28         7.63        11.77        18.35        35.41        20.71 
TCGA-02-0014 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
       82.59        53.10        42.74        24.59        12.16        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0047 TCGA-02-0052 TCGA-02-0054 
        2.83        14.14        10.52        14.73        12.59         6.54 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        2.50        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0074 TCGA-02-0079 TCGA-02-0080 
       26.43        28.70        25.05        10.19        27.25        89.72 
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-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0258 TCGA-02-0271 
       23.18        92.65        99.98        15.65        16.54        14.47 
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-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-0446 TCGA-02-0456 
       25.12        10.59        12.39        47.11         9.27         3.35 
TCGA-02-2470 TCGA-02-2483 TCGA-06-0119 TCGA-06-0124 TCGA-06-0128 TCGA-06-0129 
       12.92        15.32         2.70        20.38        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       12.95        25.35        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 
       11.74        20.09        17.79         9.44        11.80        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
       10.65         5.85         3.29        91.00        88.14        20.25 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0201 TCGA-06-0210 
       15.42        10.42        38.96         4.67         0.39         7.40 
TCGA-06-0213 TCGA-06-0219 TCGA-06-0221 TCGA-06-0240 TCGA-06-0394 TCGA-06-0397 
        0.53         0.72        19.82        20.42        10.82         9.01 
TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0649 TCGA-06-0650 
        4.70         3.16        35.11        12.62         2.10        23.57 
TCGA-06-0749 TCGA-06-0876 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        2.70        46.19        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1805 TCGA-06-2561 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
        6.84        33.90        17.65         5.98         0.43        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6694 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        7.79         5.39         7.36        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 
        1.74         8.42        25.71        29.23        65.33         8.42 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0380 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       31.10        37.58        14.93        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 TCGA-12-0656 
       42.15        19.59        58.68         4.80         7.27        94.78 
TCGA-12-0662 TCGA-12-0691 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       38.17        12.13        43.23         7.63         9.73        14.93 
TCGA-12-0818 TCGA-12-0822 TCGA-12-0827 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       91.76        23.51        38.76       127.59         5.82         7.59 
TCGA-12-1093 TCGA-12-1095 TCGA-12-1096 TCGA-12-1099 TCGA-14-0867 TCGA-14-1037 
       15.98        15.85         9.11         4.14         2.04        19.30 
TCGA-14-1043 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 
        0.79        50.53        53.19        13.28         3.91        26.07 
TCGA-16-0850 TCGA-19-1385 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 TCGA-26-5133 
       16.37        10.75        12.95         4.64        31.33        14.86 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 
        7.92         2.33         7.30        11.77        31.27        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-32-2616 TCGA-76-6660 
       13.64         5.16         7.36         3.75 

$subtype2
TCGA-06-5408 TCGA-06-5413 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-12-0615 
       11.74         8.81         2.73         3.75         4.57        15.35 
TCGA-12-1598 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3651 TCGA-12-3653 
       15.65        14.73        59.77        44.02        12.69        14.53 
TCGA-12-5295 TCGA-12-5301 TCGA-14-0736 TCGA-14-0783 TCGA-14-0865 TCGA-14-1395 
       14.93         2.04        15.12         6.21        16.50         1.38 
TCGA-14-1451 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1459 TCGA-14-1795 
       23.11         1.15        30.18         0.92        12.43         1.97 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-16-0848 TCGA-16-1047 
       17.85         7.63         5.88         7.17        17.59         4.57 
TCGA-16-1056 TCGA-16-1063 TCGA-19-0963 TCGA-19-1392 TCGA-19-1791 TCGA-19-2621 
       14.01        13.97        14.27         3.65         0.13         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        7.53         0.16         4.08        16.80        14.96        17.79 
TCGA-26-1439 TCGA-26-1440 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX 
       13.87         9.73         9.40         8.88        18.97        19.33 
TCGA-27-1831 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 
       16.60        40.54        21.30        14.04        11.51        18.08 
TCGA-27-2523 TCGA-28-1746 TCGA-28-1755 TCGA-28-1757 TCGA-28-2509 TCGA-32-1970 
       16.08         0.20         1.55         0.13         4.77        15.39 
TCGA-32-1976 TCGA-32-1978 TCGA-32-1991 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
        0.49        15.85        16.93        15.95         8.84        22.78 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 TCGA-41-2571 TCGA-41-2575 TCGA-41-3392 
        3.72        12.59        10.85         0.85         9.53         0.99 
TCGA-41-5651 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-74-6573 TCGA-74-6581 TCGA-74-6584 
       15.12         4.08         1.45         3.45         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4935 TCGA-76-6191 TCGA-76-6285 
        4.80         4.54         3.65        36.85        16.70         8.35 
TCGA-76-6286 TCGA-76-6657 TCGA-76-6661 TCGA-OX-A56R TCGA-02-0003 TCGA-02-0009 
       20.98         5.03        23.90         5.92         4.73        10.59 
TCGA-02-0016 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 TCGA-02-0075 TCGA-02-0099 
       87.06         6.87         3.22        15.09        20.84         3.48 
TCGA-02-0102 TCGA-02-0106 TCGA-02-0266 TCGA-02-0269 TCGA-02-0285 TCGA-02-0317 
       27.02        11.67        17.72        10.75        13.87        12.23 
TCGA-02-0324 TCGA-02-0440 TCGA-02-0451 TCGA-02-2466 TCGA-02-2486 TCGA-06-0133 
        7.73        11.34        16.21        16.80        20.32        14.30 
TCGA-06-0138 TCGA-06-0145 TCGA-06-0149 TCGA-06-0152 TCGA-06-0157 TCGA-06-0158 
       24.23         2.33         8.61        12.33         3.19        10.82 
TCGA-06-0162 TCGA-06-0168 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 
        3.42        19.66        13.12         4.47         3.22         4.18 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0195 TCGA-06-0197 
        3.65        69.90        27.22        44.58         7.40         5.56 
TCGA-06-0206 TCGA-06-0214 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 
        7.66        15.02        24.16        13.64        13.32        48.69 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.26        72.36         9.57         5.75         5.75         9.80 
TCGA-06-0686 TCGA-06-0745 TCGA-06-0875 TCGA-06-0878 TCGA-06-1087 TCGA-06-1800 
       14.20         7.86        43.46         7.17         4.04        26.79 
TCGA-06-1801 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 
       11.84        13.61         1.08        12.49         4.93        12.56 
TCGA-06-2564 TCGA-06-2567 TCGA-08-0244 TCGA-08-0348 TCGA-08-0349 TCGA-08-0354 
        5.95         4.37        22.68        12.16         9.80        17.95 
TCGA-08-0359 TCGA-08-0386 TCGA-08-0389 TCGA-08-0520 TCGA-12-0616 TCGA-12-0618 
        3.39        18.02        15.35        10.75        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0657 TCGA-12-0670 TCGA-12-0692 
       34.92        10.45         7.59         0.10        25.97         3.65 
TCGA-12-0707 TCGA-12-0772 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0828 
       28.41        53.85        18.48        10.62        27.78         8.94 
TCGA-12-1091 TCGA-12-1097 TCGA-12-1098 TCGA-14-0787 TCGA-14-0813 TCGA-14-0817 
       33.21        14.53         3.98         2.24         1.35         5.39 
TCGA-14-0871 TCGA-15-0742 TCGA-19-0957 TCGA-19-0962 TCGA-19-1387 TCGA-26-5134 
       28.93        13.78        21.90         0.66         5.95         5.49 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5214 TCGA-28-5219 TCGA-28-5220 
        5.26        14.93        11.28        23.44        22.68        12.76 
TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         1.61        17.72        26.30 

$subtype3
TCGA-06-5414 TCGA-06-5415 TCGA-06-6388 TCGA-06-6695 TCGA-06-6699 TCGA-06-A6S0 
        8.98         8.55         5.23         8.32         1.55         3.12 
TCGA-12-1599 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5299 
       25.68        26.93        15.22        10.95        34.92         3.22 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0866 TCGA-14-1034 TCGA-14-1402 TCGA-14-1452 
       23.05        13.78        26.33        15.95        32.05         7.10 
TCGA-14-2554 TCGA-14-2555 TCGA-16-1055 TCGA-16-1062 TCGA-19-0964 TCGA-19-1786 
       17.49         7.96        10.29        21.24         3.39         7.17 
TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 
        3.25         9.67         4.87         7.00        17.19         8.02 
TCGA-19-5954 TCGA-19-5958 TCGA-19-A6J5 TCGA-26-1443 TCGA-26-1799 TCGA-27-1833 
       12.10        14.07        28.54         7.13         9.37        24.23 
TCGA-27-1836 TCGA-27-2518 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1747 
       30.05        24.76         7.59         2.86        15.78         2.53 
TCGA-28-1749 TCGA-32-1977 TCGA-32-1979 TCGA-32-2495 TCGA-32-2638 TCGA-32-4213 
        9.21         0.10        19.50        15.02        25.18        19.86 
TCGA-32-5222 TCGA-41-2572 TCGA-41-3393 TCGA-4W-AA9T TCGA-74-6578 TCGA-76-4931 
       19.23        13.35         4.44        25.58        14.33         9.17 
TCGA-76-6656 TCGA-76-6664 TCGA-RR-A6KC TCGA-02-0007 TCGA-02-0015 TCGA-02-0021 
        4.83        36.20        20.55        23.18        20.61        77.65 
TCGA-02-0023 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0071 TCGA-02-0083 
       20.12         3.62        10.72        18.31         5.49        22.72 
TCGA-02-0089 TCGA-02-0116 TCGA-02-0260 TCGA-02-0289 TCGA-02-0290 TCGA-02-0333 
       16.96        48.95        16.93        14.20        15.95         4.37 
TCGA-02-0422 TCGA-02-0430 TCGA-02-2485 TCGA-06-0122 TCGA-06-0125 TCGA-06-0126 
       14.50        10.55        15.45         6.15        47.61         6.94 
TCGA-06-0127 TCGA-06-0137 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 
        3.98        26.70        10.09        19.46        46.59        13.94 
TCGA-06-0155 TCGA-06-0175 TCGA-06-0185 TCGA-06-0208 TCGA-06-0211 TCGA-06-0743 
       10.45         4.04        73.84         8.42        11.84        26.40 
TCGA-06-0744 TCGA-06-0747 TCGA-06-0750 TCGA-06-0879 TCGA-06-1802 TCGA-06-2563 
       46.88         2.70         0.92        40.41        15.32        30.64 
TCGA-06-2565 TCGA-06-6693 TCGA-08-0352 TCGA-08-0355 TCGA-08-0358 TCGA-08-0375 
       16.64       120.56         1.28        24.56        22.29        12.23 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
        4.27        11.08        19.33        15.98        18.41         7.56 
TCGA-12-0688 TCGA-12-0703 TCGA-12-0769 TCGA-12-0780 TCGA-12-0819 TCGA-12-0829 
       26.66        20.38        15.06        14.86        24.79        20.58 
TCGA-12-1094 TCGA-14-0789 TCGA-15-1446 TCGA-19-0955 TCGA-19-1386 TCGA-26-5139 
       12.23        11.24        19.10        11.77         9.07         1.58 
TCGA-28-5208 TCGA-28-5209 TCGA-28-6450 TCGA-76-6280 
       17.88        14.53         5.42        11.38 

subtype1 subtype2 subtype3 
     0.2      0.1      0.1 
subtype1 subtype2 subtype3 
  127.59    87.06   120.56 
subtype1 subtype2 subtype3 
  12.145   11.590   14.415 
[1] "0.2 - 127.6 (12.1)" "0.1 - 87.1 (11.6)"  "0.1 - 120.6 (14.4)"
D5V2, continuous
D5V3, binary
          cls
clus         0   1
  subtype1 105 147
  subtype2  64 132
  subtype3  56  69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  105  147
  subtype2   64  132
  subtype3   56   69
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      105       64       56
  MALE        147      132       69
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
          cls
clus         0   1
  subtype1  29 213
  subtype2  36 150
  subtype3   9 112
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29  213
  subtype2   36  150
  subtype3    9  112
     clus
vv    subtype1 subtype2 subtype3
  NO        29       36        9
  YES      213      150      112
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                            18                  10
  subtype2                             6                   2
  subtype3                             6                   6
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             224
  subtype2                             188
  subtype3                             113
D5V6, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)         18        6        6
  TREATED PRIMARY GBM                   10        2        6
  UNTREATED PRIMARY (DE NOVO) GBM      224      188      113
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     8                        29   206
  subtype2     2                        11   174
  subtype3     3                        10   107
D5V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            8        2        3
  BLACK OR AFRICAN AMERICAN       29       11       10
  WHITE                          206      174      107
[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   7 210
  subtype2   1 161
  subtype3   4 104
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  210
  subtype2    1  161
  subtype3    4  104
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        1        4
  NOT HISPANIC OR LATINO      210      161      104
[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 14 57
  subtype2  6 37
  subtype3 14 68
  subtype4 19 65
subtype1 subtype2 subtype3 subtype4 
      71       43       82       84 
subtype1 subtype2 subtype3 subtype4 
      57       37       68       65 
$subtype1
TCGA-12-1599 TCGA-14-0736 TCGA-14-1034 TCGA-16-1045 TCGA-16-1060 TCGA-19-1787 
       25.68        15.12        15.95        29.03         9.14        12.66 
TCGA-19-2623 TCGA-19-2625 TCGA-26-1438 TCGA-27-1832 TCGA-27-2518 TCGA-27-2519 
        7.53         4.08        10.03         9.86        24.76        18.08 
TCGA-27-2527 TCGA-28-1745 TCGA-28-1751 TCGA-28-1752 TCGA-28-1760 TCGA-28-2502 
       14.40        11.34         7.63         8.48         4.70         0.66 
TCGA-28-2506 TCGA-32-1977 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2632 
        6.74         0.10        12.69        14.86        12.23         8.84 
TCGA-32-4209 TCGA-41-4097 TCGA-02-0001 TCGA-02-0006 TCGA-02-0033 TCGA-02-0034 
       20.32         0.20        11.77        18.35         2.83        14.14 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0060 TCGA-02-0075 TCGA-02-0085 
        6.54         2.50        19.86         6.02        20.84        51.32 
TCGA-02-0086 TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 TCGA-02-2470 TCGA-06-0119 
        8.81        17.65        92.65        15.65        12.92         2.70 
TCGA-06-0124 TCGA-06-0130 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       20.38        12.95        11.90         0.20        10.29         2.20 
TCGA-06-0147 TCGA-06-0169 TCGA-06-0876 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       17.79         3.29        46.19        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-2561 TCGA-12-0822 TCGA-12-0826 TCGA-12-0829 
       23.93         6.84        17.65        23.51        27.78        20.58 
TCGA-12-1093 TCGA-12-1095 TCGA-12-1096 TCGA-14-0789 TCGA-14-1037 TCGA-15-1446 
       15.98        15.85         9.11        11.24        19.30        19.10 
TCGA-19-0955 TCGA-19-1385 TCGA-19-1389 TCGA-28-2513 TCGA-32-2616 
       11.77        10.75         4.64         7.30         7.36 

$subtype2
TCGA-12-3648 TCGA-12-3653 TCGA-14-0786 TCGA-14-1402 TCGA-14-1827 TCGA-14-2554 
       26.93        14.53        23.05        32.05         5.88        17.49 
TCGA-14-2555 TCGA-16-1047 TCGA-16-1063 TCGA-19-1789 TCGA-19-2619 TCGA-19-2631 
        7.96         4.57        13.97         3.25         9.67         7.00 
TCGA-19-4068 TCGA-26-1439 TCGA-26-1443 TCGA-26-1799 TCGA-27-1831 TCGA-27-1833 
        4.50        13.87         7.13         9.37        16.60        24.23 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1757 
        7.59         2.86        15.78         2.53         9.21         0.13 
TCGA-32-2615 TCGA-41-3392 TCGA-02-0003 TCGA-02-0009 TCGA-02-0021 TCGA-02-0027 
       15.95         0.99         4.73        10.59        77.65        12.16 
TCGA-02-0089 TCGA-02-0102 TCGA-06-2562 TCGA-06-2566 TCGA-06-2567 TCGA-12-0819 
       16.96        27.02        12.56         5.98         4.37        24.79 
TCGA-12-0820 TCGA-12-0828 TCGA-12-1089 TCGA-12-1094 TCGA-12-1098 TCGA-19-0962 
       18.48         8.94         5.82        12.23         3.98         0.66 
TCGA-19-1386 
        9.07 

$subtype3
TCGA-12-1597 TCGA-12-1598 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-12-3649 
       22.19        15.65        14.73         6.77        44.02        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-14-0783 TCGA-14-0790 TCGA-14-0812 TCGA-14-0866 
       10.95        34.92         6.21        13.78         3.25        26.33 
TCGA-14-1396 TCGA-14-1452 TCGA-14-1453 TCGA-14-1795 TCGA-14-1823 TCGA-14-1829 
        1.12         7.10         1.15         1.97        17.85         7.17 
TCGA-16-0848 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-19-0964 TCGA-19-1390 
       17.59        10.29        14.01        21.24         3.39        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1790 TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 
        3.65         7.17         5.06         0.13         4.87         1.08 
TCGA-27-1835 TCGA-27-2523 TCGA-28-1750 TCGA-28-1753 TCGA-28-2509 TCGA-32-1970 
       21.30        16.08         8.35         1.22         4.77        15.39 
TCGA-32-1978 TCGA-32-1982 TCGA-32-1991 TCGA-32-2495 TCGA-32-2634 TCGA-32-2638 
       15.85         4.67        16.93        15.02        22.78        25.18 
TCGA-32-4211 TCGA-32-4719 TCGA-41-2572 TCGA-41-3393 TCGA-02-0007 TCGA-02-0037 
       12.59        10.85        13.35         4.44        23.18         3.62 
TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0064 TCGA-02-0071 TCGA-02-0074 
       10.72        18.31         6.87        19.73         5.49        10.19 
TCGA-02-0083 TCGA-02-0099 TCGA-02-0116 TCGA-02-2485 TCGA-02-2486 TCGA-06-0122 
       22.72         3.48        48.95        15.45        20.32         6.15 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0137 TCGA-06-0145 TCGA-06-0148 TCGA-06-0155 
       47.61         6.94        26.70         2.33        10.09        10.45 
TCGA-06-0878 TCGA-06-0879 TCGA-06-1802 TCGA-06-2557 TCGA-06-2563 TCGA-06-2564 
        7.17        40.41        15.32         1.08        30.64         5.95 
TCGA-06-2565 TCGA-12-0670 TCGA-12-1090 TCGA-12-1091 TCGA-14-0787 TCGA-14-0813 
       16.64        25.97         7.59        33.21         2.24         1.35 
TCGA-14-0817 TCGA-14-0867 TCGA-19-1387 TCGA-28-2514 
        5.39         2.04         5.95         5.26 

$subtype4
TCGA-12-1092 TCGA-12-3644 TCGA-12-3651 TCGA-14-0865 TCGA-14-1401 TCGA-14-1451 
       21.73        59.77        12.69        16.50         3.75        23.11 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1821 TCGA-14-1825 TCGA-14-3476 TCGA-14-3477 TCGA-14-4157 TCGA-16-1460 
       17.79         7.63         0.39         3.78         3.42         6.41 
TCGA-19-0960 TCGA-19-0963 TCGA-19-1788 TCGA-19-2624 TCGA-19-2629 TCGA-26-1440 
        8.61        14.27         3.68         0.16        24.23         9.73 
TCGA-27-1830 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2521 
        5.06        40.54        30.05        14.04        11.51        16.77 
TCGA-28-1746 TCGA-28-1755 TCGA-28-1756 TCGA-32-1973 TCGA-32-1976 TCGA-32-2494 
        0.20         1.55         2.83        21.07         0.49        20.78 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4213 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 
       21.14         3.72        19.86         0.85         8.94         9.53 
TCGA-41-3915 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0024 TCGA-02-0028 
       11.84        35.41        20.71        82.59        53.10        90.58 
TCGA-02-0047 TCGA-02-0052 TCGA-02-0058 TCGA-02-0069 TCGA-02-0080 TCGA-02-0114 
       14.73        12.59         8.35        28.70        89.72        99.98 
TCGA-02-2466 TCGA-02-2483 TCGA-06-0128 TCGA-06-0129 TCGA-06-0133 TCGA-06-0143 
       16.80        15.32        22.72        33.67        14.30        11.74 
TCGA-06-0875 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1805 TCGA-06-2558 
       43.46         4.04        26.79        11.84        33.90        12.49 
TCGA-06-2559 TCGA-06-2569 TCGA-06-2570 TCGA-12-0818 TCGA-12-0821 TCGA-12-0827 
        4.93         0.43        31.50        91.76        10.62        38.76 
TCGA-12-1088 TCGA-12-1097 TCGA-12-1099 TCGA-14-0871 TCGA-15-1447 TCGA-15-1449 
      127.59        14.53         4.14        28.93        53.19        13.28 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0957 TCGA-19-1388 TCGA-28-2512 
        3.91        26.07        16.37        21.90        12.95        11.28 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.13     0.13     0.16 
subtype1 subtype2 subtype3 subtype4 
   92.65    77.65    48.95   127.59 
subtype1 subtype2 subtype3 subtype4 
  12.660    9.370   10.585   14.285 
[1] "0.1 - 92.7 (12.7)"  "0.1 - 77.7 (9.4)"   "0.1 - 49.0 (10.6)" 
[4] "0.2 - 127.6 (14.3)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 32 39
  subtype2 21 23
  subtype3 31 52
  subtype4 31 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   39
  subtype2   21   23
  subtype3   31   52
  subtype4   31   54
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       32       21       31       31
  MALE         39       23       52       54
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
          cls
clus        0  1
  subtype1  7 62
  subtype2  5 37
  subtype3 17 62
  subtype4 10 73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   62
  subtype2    5   37
  subtype3   17   62
  subtype4   10   73
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         7        5       17       10
  YES       62       37       62       73
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             3                   6
  subtype2                             0                   2
  subtype3                             0                   5
  subtype4                             0                   6
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                              62
  subtype2                              42
  subtype3                              78
  subtype4                              79
D6V6, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  GLIOBLASTOMA MULTIFORME (GBM)          3        0        0        0
  TREATED PRIMARY GBM                    6        2        5        6
  UNTREATED PRIMARY (DE NOVO) GBM       62       42       78       79
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         5    62
  subtype2     0                         2    41
  subtype3     4                         5    74
  subtype4     3                         4    77
D6V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        0        4        3
  BLACK OR AFRICAN AMERICAN        5        2        5        4
  WHITE                           62       41       74       77
[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"
D6V8, binary
          cls
clus        0  1
  subtype1  3 62
  subtype2  0 38
  subtype3  2 66
  subtype4  2 66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   62
  subtype2    0   38
  subtype3    2   66
  subtype4    2   66
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        2        2
  NOT HISPANIC OR LATINO       62       38       66       66
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = RPPA_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 11 35
  subtype2 12 49
  subtype3 13 32
  subtype4  9 22
  subtype5 14 33
subtype1 subtype2 subtype3 subtype4 subtype5 
      46       61       45       31       47 
subtype1 subtype2 subtype3 subtype4 subtype5 
      35       49       32       22       33 
$subtype1
TCGA-06-5410 TCGA-06-5412 TCGA-06-5858 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        3.55         4.54         6.15         8.32        12.85         4.77 
TCGA-06-A5U1 TCGA-14-0862 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 TCGA-19-5955 
        1.87         2.89         7.04         6.64        18.90         1.78 
TCGA-19-A60I TCGA-27-1830 TCGA-27-1832 TCGA-28-1760 TCGA-32-1986 TCGA-41-3915 
       17.79         5.06         9.86         4.70        12.69        11.84 
TCGA-41-4097 TCGA-4W-AA9S TCGA-74-6575 TCGA-74-6577 TCGA-76-6192 TCGA-76-6282 
        0.20         1.45        20.91         4.34         3.29        17.06 
TCGA-76-6662 TCGA-02-0003 TCGA-06-0125 TCGA-06-0130 TCGA-06-0154 TCGA-06-0155 
       34.45         4.73        47.61        12.95        13.94        10.45 
TCGA-06-0644 TCGA-06-0879 TCGA-06-0882 TCGA-06-1086 TCGA-06-1800 TCGA-06-2562 
       12.62        40.41        20.78         6.84        26.79        12.56 
TCGA-06-6694 TCGA-08-0346 TCGA-08-0355 TCGA-08-0356 TCGA-08-0360 TCGA-08-0390 
        7.36         8.42        24.56        31.10        15.39        13.97 
TCGA-08-0392 TCGA-19-1389 TCGA-26-6173 TCGA-28-5208 
        0.72         4.64         7.92        17.88 

$subtype2
TCGA-19-A6J4 TCGA-06-5414 TCGA-06-6701 TCGA-12-3646 TCGA-12-3650 TCGA-19-1390 
        3.98         8.98         4.96        44.02        10.95        25.38 
TCGA-19-1790 TCGA-19-2625 TCGA-19-2631 TCGA-19-5953 TCGA-26-5132 TCGA-27-1833 
        5.06         4.08         7.00         4.73         9.40        24.23 
TCGA-27-2528 TCGA-28-1750 TCGA-28-1753 TCGA-28-1757 TCGA-32-1978 TCGA-32-1982 
       15.78         8.35         1.22         0.13        15.85         4.67 
TCGA-32-4211 TCGA-41-3393 TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6573 TCGA-76-4926 
       12.59         4.44        12.46        25.58         3.45         4.54 
TCGA-76-4927 TCGA-76-4928 TCGA-76-6656 TCGA-76-6661 TCGA-RR-A6KA TCGA-02-0004 
       17.59         3.09         4.83        23.90         6.28        11.34 
TCGA-02-0011 TCGA-02-0068 TCGA-02-0069 TCGA-02-0116 TCGA-02-2470 TCGA-02-2485 
       20.71        26.43        28.70        48.95        12.92        15.45 
TCGA-06-0128 TCGA-06-0171 TCGA-06-0189 TCGA-06-0190 TCGA-06-0238 TCGA-06-0650 
       22.72        13.12        15.42        10.42        13.32        23.57 
TCGA-06-1084 TCGA-06-1802 TCGA-06-2557 TCGA-06-2567 TCGA-08-0245 TCGA-08-0347 
       23.93        15.32         1.08         4.37        37.84        25.71 
TCGA-08-0348 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0358 TCGA-08-0373 
       12.16         1.28         8.42        17.95        22.29         4.41 
TCGA-08-0375 TCGA-08-0386 TCGA-15-1447 TCGA-26-5133 TCGA-26-5134 TCGA-28-5214 
       12.23        18.02        53.19        14.86         5.49        23.44 
TCGA-76-6660 
        3.75 

$subtype3
TCGA-06-6391 TCGA-06-5411 TCGA-06-6388 TCGA-06-6700 TCGA-06-A7TL TCGA-12-1597 
        1.48         8.35         5.23         4.77        17.72        22.19 
TCGA-12-3649 TCGA-12-3651 TCGA-16-1460 TCGA-19-1786 TCGA-19-1788 TCGA-19-2620 
       15.22        12.69         6.41         7.17         3.68         4.87 
TCGA-27-1836 TCGA-27-2518 TCGA-32-1976 TCGA-32-5222 TCGA-41-2573 TCGA-4W-AA9R 
       30.05        24.76         0.49        19.23         8.94         4.08 
TCGA-74-6581 TCGA-76-6193 TCGA-76-6657 TCGA-76-6663 TCGA-RR-A6KC TCGA-02-0014 
        8.22         2.70         5.03        18.64        20.55        82.59 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2564 TCGA-06-2566 TCGA-06-2570 
       13.61        33.90        12.49         5.95         5.98        31.50 
TCGA-06-6389 TCGA-08-0344 TCGA-08-0345 TCGA-08-0349 TCGA-08-0351 TCGA-08-0357 
        7.79       115.86         1.74         9.80        65.33        37.58 
TCGA-08-0359 TCGA-08-0385 TCGA-14-0813 TCGA-15-1449 TCGA-16-0846 TCGA-19-0957 
        3.39         2.70         1.35        13.28         3.91        21.90 
TCGA-19-0962 TCGA-26-1442 TCGA-26-6174 
        0.66        31.33         2.33 

$subtype4
TCGA-06-5408 TCGA-06-5416 TCGA-06-5856 TCGA-06-6699 TCGA-12-1598 TCGA-12-5301 
       11.74         6.71         3.75         1.55        15.65         2.04 
TCGA-19-1392 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J5 TCGA-28-1746 TCGA-32-1987 
        3.65        22.49        14.96        28.54         0.20        14.86 
TCGA-32-4210 TCGA-41-2575 TCGA-41-5651 TCGA-74-6578 TCGA-74-6584 TCGA-76-6664 
        3.72         9.53        15.12        14.33         7.50        36.20 
TCGA-OX-A56R TCGA-06-0126 TCGA-06-0129 TCGA-06-0156 TCGA-06-0875 TCGA-06-1087 
        5.92         6.94        33.67         5.85        43.46         4.04 
TCGA-06-2559 TCGA-06-2563 TCGA-08-0350 TCGA-08-0389 TCGA-14-0871 TCGA-76-6283 
        4.93        30.64        29.23        15.35        28.93         5.42 
TCGA-81-5910 
        1.61 

$subtype5
TCGA-06-1806 TCGA-06-5413 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5859 
       15.32         8.81         8.55         5.10         2.73         4.57 
TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-12-1599 TCGA-12-3652 TCGA-12-3653 
       26.79         3.12         2.56        25.68        34.92        14.53 
TCGA-12-5295 TCGA-14-1823 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-4068 
       14.93        17.85         3.25         0.13         9.67         4.50 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5954 TCGA-19-5958 TCGA-19-5959 TCGA-26-1440 
       17.19         8.02        12.10        14.07        16.80         9.73 
TCGA-26-A7UX TCGA-27-1831 TCGA-27-1834 TCGA-28-1747 TCGA-28-1752 TCGA-32-1970 
       19.33        16.60        40.54         2.53         8.48        15.39 
TCGA-32-1991 TCGA-41-3392 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-6285 
       16.93         0.99         3.65         9.17        47.93         8.35 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0939 TCGA-06-2565 TCGA-06-6390 TCGA-06-6693 
       46.19         7.17        26.76        16.64         5.39       120.56 
TCGA-08-0380 TCGA-12-0691 TCGA-12-0692 TCGA-15-1446 TCGA-19-1386 
       14.93        12.13         3.65        19.10         9.07 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     0.13     0.49     0.20     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
   47.61    53.19   115.86    43.46   120.56 
subtype1 subtype2 subtype3 subtype4 subtype5 
    9.14    12.46     8.35     9.53    12.10 
[1] "0.2 - 47.6 (9.1)"   "0.1 - 53.2 (12.5)"  "0.5 - 115.9 (8.3)" 
[4] "0.2 - 43.5 (9.5)"   "0.1 - 120.6 (12.1)"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 13 33
  subtype2 19 42
  subtype3 19 27
  subtype4 15 16
  subtype5 26 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   33
  subtype2   19   42
  subtype3   19   27
  subtype4   15   16
  subtype5   26   22
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       13       19       19       15       26
  MALE         33       42       27       16       22
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
          cls
clus        0  1
  subtype1  6 39
  subtype2  5 48
  subtype3  8 36
  subtype4  4 23
  subtype5  6 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   39
  subtype2    5   48
  subtype3    8   36
  subtype4    4   23
  subtype5    6   41
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         6        5        8        4        6
  YES       39       48       36       23       41
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             3                   0
  subtype2                             4                   2
  subtype3                             4                   0
  subtype4                             3                   0
  subtype5                             5                   1
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                              43
  subtype2                              55
  subtype3                              42
  subtype4                              28
  subtype5                              42
D7V6, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4 subtype5
  GLIOBLASTOMA MULTIFORME (GBM)          3        4        4        3        5
  TREATED PRIMARY GBM                    0        2        0        0        1
  UNTREATED PRIMARY (DE NOVO) GBM       43       55       42       28       42
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         6    37
  subtype2     1                         8    48
  subtype3     1                         4    36
  subtype4     1                         3    24
  subtype5     1                         6    40
D7V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        1        1        1        1
  BLACK OR AFRICAN AMERICAN        6        8        4        3        6
  WHITE                           37       48       36       24       40
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1  1 40
  subtype2  2 49
  subtype3  0 40
  subtype4  0 26
  subtype5  0 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   40
  subtype2    2   49
  subtype3    0   40
  subtype4    0   26
  subtype5    0   41
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        2        0        0        0
  NOT HISPANIC OR LATINO       40       49       40       26       41
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = RPPA_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 19 75
  subtype2 25 51
  subtype3 15 45
subtype1 subtype2 subtype3 
      94       76       60 
subtype1 subtype2 subtype3 
      75       51       45 
$subtype1
TCGA-19-A6J4 TCGA-06-5410 TCGA-06-5412 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        3.98         3.55         4.54         6.71         2.73         6.15 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-A5U1 TCGA-12-1598 TCGA-12-1599 
        8.32        12.85         4.77         1.87        15.65        25.68 
TCGA-14-0862 TCGA-19-1392 TCGA-19-1790 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 
        2.89         3.65         5.06         4.08         7.00         7.04 
TCGA-19-5947 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-A60I TCGA-27-1830 
        6.64         4.73        12.10         1.78        17.79         5.06 
TCGA-27-1832 TCGA-27-2518 TCGA-28-1750 TCGA-28-1753 TCGA-28-1760 TCGA-32-1986 
        9.86        24.76         8.35         1.22         4.70        12.69 
TCGA-32-1987 TCGA-32-4211 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R 
       14.86        12.59        11.84         0.20        12.46         4.08 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        1.45        25.58         3.45        20.91         4.34        14.33 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-6192 TCGA-76-6657 
        4.54        17.59         3.09         3.65         3.29         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-OX-A56R TCGA-RR-A6KA TCGA-02-0003 TCGA-02-0004 
       23.90        34.45         5.92         6.28         4.73        11.34 
TCGA-02-0068 TCGA-02-0116 TCGA-02-2470 TCGA-06-0128 TCGA-06-0130 TCGA-06-0171 
       26.43        48.95        12.92        22.72        12.95        13.12 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0238 TCGA-06-0644 TCGA-06-0650 TCGA-06-0879 
       15.42        10.42        13.32        12.62        23.57        40.41 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 
       20.78        26.76        23.93         6.84        26.79        15.32 
TCGA-06-2559 TCGA-06-2562 TCGA-06-6694 TCGA-08-0245 TCGA-08-0345 TCGA-08-0346 
        4.93        12.56         7.36        37.84         1.74         8.42 
TCGA-08-0348 TCGA-08-0356 TCGA-08-0360 TCGA-08-0380 TCGA-08-0390 TCGA-08-0392 
       12.16        31.10        15.39        14.93        13.97         0.72 
TCGA-12-0692 TCGA-14-0813 TCGA-15-1447 TCGA-19-0962 TCGA-19-1389 TCGA-26-5133 
        3.65         1.35        53.19         0.66         4.64        14.86 
TCGA-26-5134 TCGA-28-5208 TCGA-76-6660 TCGA-81-5910 
        5.49        17.88         3.75         1.61 

$subtype2
TCGA-06-6391 TCGA-06-1806 TCGA-06-5411 TCGA-06-5417 TCGA-06-5859 TCGA-06-6388 
        1.48        15.32         8.35         5.10         4.57         5.23 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S1 TCGA-06-A7TL TCGA-12-1597 
        4.77         4.96        26.79         2.56        17.72        22.19 
TCGA-12-3649 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-12-5301 TCGA-16-1460 
       15.22        12.69        14.53        14.93         2.04         6.41 
TCGA-19-1390 TCGA-19-1788 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-4068 
       25.38         3.68         0.13         9.67         4.87         4.50 
TCGA-19-5951 TCGA-19-5956 TCGA-19-5958 TCGA-19-5960 TCGA-19-A6J5 TCGA-27-1834 
        8.02        22.49        14.07        14.96        28.54        40.54 
TCGA-27-1836 TCGA-28-1746 TCGA-28-1747 TCGA-28-1752 TCGA-32-1976 TCGA-32-4210 
       30.05         0.20         2.53         8.48         0.49         3.72 
TCGA-41-2573 TCGA-41-2575 TCGA-41-5651 TCGA-74-6581 TCGA-74-6584 TCGA-76-6193 
        8.94         9.53        15.12         8.22         7.50         2.70 
TCGA-76-6285 TCGA-76-6663 TCGA-02-0011 TCGA-02-0014 TCGA-02-0069 TCGA-06-0129 
        8.35        18.64        20.71        82.59        28.70        33.67 
TCGA-06-0156 TCGA-06-0875 TCGA-06-1087 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
        5.85        43.46         4.04        13.61        33.90        12.49 
TCGA-06-2564 TCGA-06-2566 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-08-0344 
        5.95         5.98        31.50         7.79         5.39       115.86 
TCGA-08-0347 TCGA-08-0350 TCGA-08-0351 TCGA-08-0359 TCGA-08-0373 TCGA-08-0385 
       25.71        29.23        65.33         3.39         4.41         2.70 
TCGA-08-0389 TCGA-12-0691 TCGA-14-0871 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 
       15.35        12.13        28.93        19.10        13.28         3.91 
TCGA-19-0957 TCGA-26-1442 TCGA-26-6174 TCGA-76-6283 
       21.90        31.33         2.33         5.42 

$subtype3
TCGA-06-5408 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5856 TCGA-06-6699 
       11.74         8.81         8.98         8.55         3.75         1.55 
TCGA-06-A6S0 TCGA-12-3646 TCGA-12-3650 TCGA-12-3652 TCGA-14-1823 TCGA-19-1786 
        3.12        44.02        10.95        34.92        17.85         7.17 
TCGA-19-1789 TCGA-19-5950 TCGA-19-5952 TCGA-19-5959 TCGA-26-1440 TCGA-26-5132 
        3.25        17.19        18.90        16.80         9.73         9.40 
TCGA-26-A7UX TCGA-27-1831 TCGA-27-1833 TCGA-27-2528 TCGA-28-1757 TCGA-32-1970 
       19.33        16.60        24.23        15.78         0.13        15.39 
TCGA-32-1978 TCGA-32-1982 TCGA-32-1991 TCGA-32-5222 TCGA-41-3392 TCGA-41-3393 
       15.85         4.67        16.93        19.23         0.99         4.44 
TCGA-76-4931 TCGA-76-4932 TCGA-76-6282 TCGA-76-6656 TCGA-76-6664 TCGA-RR-A6KC 
        9.17        47.93        17.06         4.83        36.20        20.55 
TCGA-02-2485 TCGA-06-0125 TCGA-06-0126 TCGA-06-0154 TCGA-06-0155 TCGA-06-0876 
       15.45        47.61         6.94        13.94        10.45        46.19 
TCGA-06-0878 TCGA-06-2557 TCGA-06-2563 TCGA-06-2565 TCGA-06-2567 TCGA-06-6693 
        7.17         1.08        30.64        16.64         4.37       120.56 
TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0357 
        9.80         1.28         8.42        17.95        24.56        37.58 
TCGA-08-0358 TCGA-08-0375 TCGA-08-0386 TCGA-19-1386 TCGA-26-6173 TCGA-28-5214 
       22.29        12.23        18.02         9.07         7.92        23.44 

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   14.665 
[1] "0.2 - 53.2 (8.4)"   "0.1 - 115.9 (9.6)"  "0.1 - 120.6 (14.7)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 34 60
  subtype2 37 40
  subtype3 21 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   60
  subtype2   37   40
  subtype3   21   40
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       34       37       21
  MALE         60       40       40
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
          cls
clus        0  1
  subtype1 14 73
  subtype2  9 63
  subtype3  6 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   73
  subtype2    9   63
  subtype3    6   51
     clus
vv    subtype1 subtype2 subtype3
  NO        14        9        6
  YES       73       63       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"
D8V5, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             9                   2
  subtype2                             7                   0
  subtype3                             3                   1
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                              83
  subtype2                              70
  subtype3                              57
D8V6, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)          9        7        3
  TREATED PRIMARY GBM                    2        0        1
  UNTREATED PRIMARY (DE NOVO) GBM       83       70       57
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        13    74
  subtype2     2                         7    61
  subtype3     2                         7    50
D8V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        2        2
  BLACK OR AFRICAN AMERICAN       13        7        7
  WHITE                           74       61       50
[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  2 76
  subtype2  1 66
  subtype3  0 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   76
  subtype2    1   66
  subtype3    0   54
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        0
  NOT HISPANIC OR LATINO       76       66       54
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MRNASEQ_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 12 36
  subtype2 13 57
  subtype3  6 27
subtype1 subtype2 subtype3 
      48       70       33 
subtype1 subtype2 subtype3 
      36       57       27 
$subtype1
TCGA-06-5408 TCGA-06-5413 TCGA-06-5416 TCGA-06-5417 TCGA-06-5856 TCGA-06-5859 
       11.74         8.81         6.71         5.10         3.75         4.57 
TCGA-12-1597 TCGA-12-3650 TCGA-14-1825 TCGA-19-1390 TCGA-19-2624 TCGA-19-2629 
       22.19        10.95         7.63        25.38         0.16        24.23 
TCGA-26-5135 TCGA-27-1830 TCGA-27-1837 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
        8.88         5.06        14.04        18.08        16.77        16.08 
TCGA-28-1753 TCGA-32-2634 TCGA-41-2571 TCGA-41-5651 TCGA-76-4929 TCGA-02-0047 
        1.22        22.78         0.85        15.12         3.65        14.73 
TCGA-02-2483 TCGA-06-0129 TCGA-06-0138 TCGA-06-0156 TCGA-06-0157 TCGA-06-0174 
       15.32        33.67        24.23         5.85         3.19         3.22 
TCGA-06-0178 TCGA-06-0238 TCGA-06-0646 TCGA-06-0686 TCGA-06-0745 TCGA-06-2557 
       88.14        13.32         5.75        14.20         7.86         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2569 TCGA-06-2570 TCGA-12-0616 TCGA-12-0618 
       12.49         4.93         0.43        31.50        14.73        12.99 
TCGA-12-0821 TCGA-15-1444 TCGA-26-5133 TCGA-26-5134 TCGA-28-5215 TCGA-28-5216 
       10.62        50.53        14.86         5.49        11.01        13.64 

$subtype2
TCGA-06-5410 TCGA-06-5412 TCGA-06-5414 TCGA-06-5418 TCGA-06-5858 TCGA-12-3652 
        3.55         4.54         8.98         2.73         6.15        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0781 TCGA-14-0790 TCGA-14-1034 
       14.53        14.93         3.22         0.95        13.78        15.95 
TCGA-14-1823 TCGA-14-1829 TCGA-14-2554 TCGA-16-1045 TCGA-19-1787 TCGA-19-2619 
       17.85         7.17        17.49        29.03        12.66         9.67 
TCGA-19-2625 TCGA-19-4065 TCGA-26-5132 TCGA-26-5136 TCGA-27-1831 TCGA-27-1832 
        4.08         7.04         9.40        18.97        16.60         9.86 
TCGA-27-1834 TCGA-27-1835 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-2509 
       40.54        21.30         7.59         2.86        15.78         4.77 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2572 
       15.95         8.84        25.18        19.86        19.23        13.35 
TCGA-41-3915 TCGA-76-4925 TCGA-76-4927 TCGA-76-4928 TCGA-76-4932 TCGA-02-0055 
       11.84         4.80        17.59         3.09        47.93         2.50 
TCGA-02-2486 TCGA-06-0125 TCGA-06-0130 TCGA-06-0141 TCGA-06-0184 TCGA-06-0187 
       20.32        47.61        12.95        10.29        69.90        27.22 
TCGA-06-0190 TCGA-06-0210 TCGA-06-0644 TCGA-06-0645 TCGA-06-0649 TCGA-06-0743 
       10.42         7.40        12.62         5.75         2.10        26.40 
TCGA-06-0750 TCGA-06-0878 TCGA-06-2565 TCGA-06-2567 TCGA-12-0619 TCGA-14-0789 
        0.92         7.17        16.64         4.37        34.92        11.24 
TCGA-14-0817 TCGA-26-5139 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        5.39         1.58         7.30        14.93        17.88        14.53 
TCGA-28-5213 TCGA-28-5218 TCGA-28-5220 TCGA-32-2616 
       31.27         5.16        12.76         7.36 

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

subtype1 subtype2 subtype3 
    0.16     0.92     0.20 
subtype1 subtype2 subtype3 
   88.14    69.90    46.88 
subtype1 subtype2 subtype3 
  11.375   12.230   10.820 
[1] "0.2 - 88.1 (11.4)" "0.9 - 69.9 (12.2)" "0.2 - 46.9 (10.8)"
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1 14 34
  subtype2 32 39
  subtype3  7 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   34
  subtype2   32   39
  subtype3    7   26
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       32        7
  MALE         34       39       26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
          cls
clus        0  1
  subtype1  6 39
  subtype2 11 56
  subtype3  6 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   39
  subtype2   11   56
  subtype3    6   26
     clus
vv    subtype1 subtype2 subtype3
  NO         6       11        6
  YES       39       56       26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, 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                              47
  subtype2                              70
  subtype3                              33
D9V6, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)          1        0        0
  TREATED PRIMARY GBM                    0        1        0
  UNTREATED PRIMARY (DE NOVO) GBM       47       70       33
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         3    43
  subtype2     1                         5    64
  subtype3     2                         2    29
D9V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        2
  BLACK OR AFRICAN AMERICAN        3        5        2
  WHITE                           43       64       29
[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 45
  subtype2  2 51
  subtype3  0 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   45
  subtype2    2   51
  subtype3    0   29
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        0
  NOT HISPANIC OR LATINO       45       51       29
[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  9 23
  subtype2 18 77
  subtype3  4 20
subtype1 subtype2 subtype3 
      32       95       24 
subtype1 subtype2 subtype3 
      23       77       20 
$subtype1
TCGA-06-5416 TCGA-06-5417 TCGA-12-1597 TCGA-12-3650 TCGA-14-1825 TCGA-19-1390 
        6.71         5.10        22.19        10.95         7.63        25.38 
TCGA-19-2624 TCGA-19-2629 TCGA-26-5135 TCGA-27-1837 TCGA-27-2521 TCGA-27-2523 
        0.16        24.23         8.88        14.04        16.77        16.08 
TCGA-32-2634 TCGA-41-2571 TCGA-41-5651 TCGA-02-0047 TCGA-02-2483 TCGA-06-0129 
       22.78         0.85        15.12        14.73        15.32        33.67 
TCGA-06-0174 TCGA-06-0178 TCGA-06-0238 TCGA-06-0686 TCGA-06-2558 TCGA-06-2559 
        3.22        88.14        13.32        14.20        12.49         4.93 
TCGA-06-2570 TCGA-12-0618 TCGA-15-1444 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
       31.50        12.99        50.53        31.33        14.86         5.49 
TCGA-28-5215 TCGA-28-5216 
       11.01        13.64 

$subtype2
TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5418 
       11.74         3.55         4.54         8.81         8.98         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
        3.75         6.15         4.57        34.92        14.53        14.93 
TCGA-12-5299 TCGA-14-0781 TCGA-14-0790 TCGA-14-1034 TCGA-14-1823 TCGA-14-1829 
        3.22         0.95        13.78        15.95        17.85         7.17 
TCGA-14-2554 TCGA-16-1045 TCGA-19-1787 TCGA-19-2619 TCGA-19-2625 TCGA-19-4065 
       17.49        29.03        12.66         9.67         4.08         7.04 
TCGA-26-5132 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
        9.40        18.97         5.06        16.60         9.86        40.54 
TCGA-27-1835 TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1753 
       21.30        18.08         7.59         2.86        15.78         1.22 
TCGA-28-2509 TCGA-32-1982 TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-32-4213 
        4.77         4.67        15.95         8.84        25.18        19.86 
TCGA-32-5222 TCGA-41-2572 TCGA-41-3915 TCGA-76-4925 TCGA-76-4927 TCGA-76-4928 
       19.23        13.35        11.84         4.80        17.59         3.09 
TCGA-76-4929 TCGA-76-4932 TCGA-02-0055 TCGA-02-2485 TCGA-02-2486 TCGA-06-0125 
        3.65        47.93         2.50        15.45        20.32        47.61 
TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0156 TCGA-06-0157 TCGA-06-0184 
       12.95        24.23        10.29         5.85         3.19        69.90 
TCGA-06-0187 TCGA-06-0190 TCGA-06-0210 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       27.22        10.42         7.40        12.62         5.75         5.75 
TCGA-06-0649 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0878 
        2.10        26.40         7.86         2.70         0.92         7.17 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2562 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 
       13.61         1.08        12.56        16.64         4.37         0.43 
TCGA-08-0386 TCGA-12-0616 TCGA-12-0619 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 
       18.02        14.73        34.92        10.62         2.24        11.24 
TCGA-14-0817 TCGA-15-0742 TCGA-26-5139 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 
        5.39        13.78         1.58         7.30        14.93        17.88 
TCGA-28-5209 TCGA-28-5213 TCGA-28-5218 TCGA-28-5220 TCGA-32-2616 
       14.53        31.27         5.16        12.76         7.36 

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

subtype1 subtype2 subtype3 
    0.16     0.43     0.20 
subtype1 subtype2 subtype3 
   88.14    69.90    46.88 
subtype1 subtype2 subtype3 
   14.12    10.42     8.86 
[1] "0.2 - 88.1 (14.1)" "0.4 - 69.9 (10.4)" "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, binary
          cls
clus        0  1
  subtype1  4 27
  subtype2 15 74
  subtype3  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   27
  subtype2   15   74
  subtype3    4   20
     clus
vv    subtype1 subtype2 subtype3
  NO         4       15        4
  YES       27       74       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"
D10V5, 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
D10V6, 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"
          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"
