[1] "ofn"       "-oTLGG-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/LGG-TP/22506744/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LGG-TP/22553887/LGG-TP.mergedcluster.txt"

nPatients in clinical file=515, in cluster file=516, common to both=515
[1]  12 515
[1] "MRNA_CNMF"
[1] 3
 1  2  3 
 9 10  8 
 1  2  3 
 9 10  8 
[1] "MRNA_CHIERARCHICAL"
[1] 3
1 2 3 4 
7 7 7 6 
1 2 3 4 
7 7 7 6 
[1] "CN_CNMF"
[1] 3
  1   2   3 
226 111 175 
  1   2   3 
226 111 175 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
208 136 158  13 
  1   2   3   4 
208 136 158  13 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4 
 90  95 126 117 
  1   2   3   4 
 90  95 126 117 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
 83 160 185 
  1   2   3 
 83 160 185 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4   5 
129 115 106 135  30 
  1   2   3   4   5 
129 115 106 135  30 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
134  71  36  68  91  41  74 
  1   2   3   4   5   6   7 
134  71  36  68  91  41  74 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
140 106  83 182 
  1   2   3   4 
140 106  83 182 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
222 186 103 
  1   2   3 
222 186 103 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
126 119 106 156 
  1   2   3   4 
126 119 106 156 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
 98  77 120  57  63  92 
  1   2   3   4   5   6 
 98  77 120  57  63  92 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "DAYS_TO_LAST_KNOWN_ALIVE"            
 [9] "RADIATION_THERAPY"                   
[10] "KARNOFSKY_PERFORMANCE_SCORE"         
[11] "HISTOLOGICAL_TYPE"                   
[12] "RACE"                                
[13] "ETHNICITY"                           

Input Data has 13 rows and 515 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=120,	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=333,	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=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 515 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=60, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 4 5
  subtype2 6 3
  subtype3 5 3
subtype1 subtype2 subtype3 
       9        9        8 
subtype1 subtype2 subtype3 
       5        3        3 
$subtype1
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-DB-5273 TCGA-DB-5280 TCGA-DH-5142 
       43.89        36.36        60.10        81.96        36.56        63.88 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5322 
       50.14        67.46       130.78 

$subtype2
TCGA-DH-5141 TCGA-CS-5394 TCGA-CS-5396 TCGA-DB-5274 TCGA-DB-5275 TCGA-DH-5140 
       31.82         0.26        53.62        75.25        47.93        19.96 
TCGA-DH-5144 TCGA-E1-5304 TCGA-E1-5318 
       24.59        41.13        78.21 

$subtype3
TCGA-CS-5395 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5281 
       21.01       122.73        72.92        50.86        91.13        78.28 
TCGA-DH-5143 TCGA-E1-5311 
       46.06       134.27 

subtype1 subtype2 subtype3 
   36.36     0.26    21.01 
subtype1 subtype2 subtype3 
  130.78    78.21   134.27 
subtype1 subtype2 subtype3 
   60.10    41.13    75.60 
[1] "36.4 - 130.8 (60.1)" "0.3 - 78.2 (41.1)"   "21.0 - 134.3 (75.6)"
D1V2, continuous
D1V3, binary
          cls
clus       0 1
  subtype1 2 7
  subtype2 6 4
  subtype3 1 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    6    4
  subtype3    1    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        6        1
  MALE          7        4        7
[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"
D1V4, binary
          cls
clus       0 1
  subtype1 2 6
  subtype2 1 9
  subtype3 2 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    6
  subtype2    1    9
  subtype3    2    6
     clus
vv    subtype1 subtype2 subtype3
  NO         2        1        2
  YES        6        9        6
[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"
D1V5, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1           7                2                 0
  subtype2           2                3                 5
  subtype3           1                4                 3
D1V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA              7        2        1
  OLIGOASTROCYTOMA         2        3        4
  OLIGODENDROGLIOMA        0        5        3
[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       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         1     8
  subtype2                         0    10
  subtype3                         1     7
D1V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        1        0        1
  WHITE                            8       10        7
[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"
D1V8, binary
          cls
clus       0 1
  subtype1 0 6
  subtype2 1 7
  subtype3 0 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    6
  subtype2    1    7
  subtype3    0    7
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        1        0
  NOT HISPANIC OR LATINO        6        7        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2      0 1
  subtype1 3 4
  subtype2 2 5
  subtype3 5 1
  subtype4 5 1
subtype1 subtype2 subtype3 subtype4 
       7        7        6        6 
subtype1 subtype2 subtype3 subtype4 
       4        5        1        1 
$subtype1
TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5395 TCGA-DB-5273 TCGA-DB-5280 TCGA-E1-5302 
       43.89        60.10        21.01        81.96        36.56        50.14 
TCGA-E1-5303 
       67.46 

$subtype2
TCGA-CS-4943 TCGA-DB-5275 TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-5142 TCGA-E1-5304 
       36.36        47.93        50.86        19.96        63.88        41.13 
TCGA-E1-5322 
      130.78 

$subtype3
TCGA-DH-5141 TCGA-CS-5394 TCGA-CS-5396 TCGA-DB-5274 TCGA-DH-5144 TCGA-E1-5318 
       31.82         0.26        53.62        75.25        24.59        78.21 

$subtype4
TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5281 TCGA-DH-5143 TCGA-E1-5311 
      122.73        72.92        91.13        78.28        46.06       134.27 

subtype1 subtype2 subtype3 subtype4 
   21.01    19.96     0.26    46.06 
subtype1 subtype2 subtype3 subtype4 
   81.96   130.78    78.21   134.27 
subtype1 subtype2 subtype3 subtype4 
  50.140   47.930   42.720   84.705 
[1] "21.0 - 82.0 (50.1)"  "20.0 - 130.8 (47.9)" "0.3 - 78.2 (42.7)"  
[4] "46.1 - 134.3 (84.7)"
D2V2, continuous
D2V3, binary
          cls
clus       0 1
  subtype1 1 6
  subtype2 2 5
  subtype3 5 2
  subtype4 1 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2    2    5
  subtype3    5    2
  subtype4    1    5
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        2        5        1
  MALE          6        5        2        5
[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 1 6
  subtype2 1 5
  subtype3 1 6
  subtype4 2 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    6
  subtype2    1    5
  subtype3    1    6
  subtype4    2    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        1        1        2
  YES        6        5        6        4
[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
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       5        5        5        2 
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
 [7] "subtype3" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[13] "subtype2" "subtype3" "subtype2"
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1           5                1                 1
  subtype2           4                3                 0
  subtype3           1                1                 5
  subtype4           0                4                 2
D2V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA              5        4        1        0
  OLIGOASTROCYTOMA         1        3        1        4
  OLIGODENDROGLIOMA        1        0        5        2
[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       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         2     5
  subtype2                         0     7
  subtype3                         0     7
  subtype4                         0     6
D2V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  BLACK OR AFRICAN AMERICAN        2        0        0        0
  WHITE                            5        7        7        6
[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"
D2V8, binary
          cls
clus       0 1
  subtype1 0 4
  subtype2 0 6
  subtype3 1 4
  subtype4 0 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    4
  subtype2    0    6
  subtype3    1    4
  subtype4    0    6
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        0        1        0
  NOT HISPANIC OR LATINO        4        6        4        6
[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 = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 182  44
  subtype2  50  60
  subtype3 151  21
subtype1 subtype2 subtype3 
     226      110      172 
subtype1 subtype2 subtype3 
      44       60       21 
$subtype1
TCGA-CS-6665 TCGA-DB-A4XC TCGA-DH-A66B TCGA-DU-A76O TCGA-E1-A7YN TCGA-FG-A87N 
       51.55        46.72        42.05        17.16        23.90        18.64 
TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-6188 TCGA-CS-6290 
       45.60       117.50        60.10        40.18        26.76        37.38 
TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-5277 
       48.30        49.12       122.73        81.96        72.92        50.86 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE 
       36.56        78.28        46.42        30.21        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75P 
       33.57        27.45        18.51        11.24        17.88        16.18 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       63.88        46.06        17.19        17.46        13.71        18.61 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5871 TCGA-DU-6396 TCGA-DU-6401 
       17.46        13.38         8.45        18.94        75.16        87.45 
TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7011 TCGA-DU-7014 
       16.83       114.08         2.40        62.96       105.21       117.40 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 
       90.77        26.30        44.02        25.91        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP 
        2.76        14.60        20.68        16.96        15.48        33.27 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A6S7 TCGA-DU-A7TC TCGA-DU-A7TI 
       29.85        31.69        26.17        20.98        37.38        38.89 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YH TCGA-E1-A7YI 
       50.14        67.46        79.99        57.93        93.21         3.65 
TCGA-E1-A7YK TCGA-E1-A7YU TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z6 
       12.43         0.76        32.45        36.82       146.14        32.35 
TCGA-F6-A8O4 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7643 
        0.20        18.77        14.93        42.54        41.33        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       28.34        13.68        14.24        14.96        22.52        32.61 
TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A711 
       10.72        18.71        23.70        21.53        28.54        48.69 
TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 
       27.52        40.11        16.54         3.75         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        6.38        40.34       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 
       29.85        23.18       122.47        17.29        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 
       57.60         0.16         0.76         6.05        42.74         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7860 
        0.10        17.52        39.48        19.23         0.23         0.49 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8013 
       23.61         3.68         5.33        11.28        31.43        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A5R5 TCGA-HT-A5R7 
        2.50         0.23        34.19        28.27         0.13        20.22 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74H 
        0.10         2.70         1.81        16.83        17.52         2.43 
TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
        0.10        41.49        69.27        39.75        40.01        42.54 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5F1 
       28.87        20.71        14.40         6.71         2.37         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A733 
        7.96         1.28         0.23        10.42        13.25        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A780 TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CW 
        9.60         7.56         2.37         2.53        19.33        13.61 
TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-RY-A843 TCGA-RY-A845 
       12.23        10.29        16.50        16.70         2.07        19.59 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       62.17        87.12        18.77        36.82        24.39        25.81 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WI 
       35.15        98.24        95.93         5.85        85.55        84.99 
TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 
       18.61        14.07         7.92        18.54        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7CA 
       98.63        31.59        18.71        20.48        48.33        34.78 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84T 
       16.18        59.05        30.44        24.16        40.83        23.80 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RP TCGA-TQ-A7RR TCGA-TQ-A7RV 
       40.41        44.09        36.69        30.05        25.87        61.41 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CH TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 
       45.93        43.20        23.47        16.01        13.32        43.96 
TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       39.88        43.40        45.80        46.88 

$subtype2
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
        7.69        43.89        36.36        21.01        53.62         6.38 
TCGA-CS-6186 TCGA-CS-6666 TCGA-DB-A64O TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-A669 
       17.69        46.95        25.48        30.74        19.96        30.21 
TCGA-DH-A66D TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6392 
       27.81        18.02         6.74         6.81        17.49       211.17 
TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       49.02        65.75         1.22         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7012 
       19.89        94.52        11.47       156.23        14.99         6.54 
TCGA-DU-7013 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 
        8.84         7.96        18.94         5.10        23.74        19.13 
TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T8 
       24.43        24.99        33.96        11.41        26.76       139.04 
TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YD 
       84.33         7.50         0.56        41.13       130.78        14.30 
TCGA-E1-A7YE TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7Z2 
       29.13        19.46        16.18        21.30        51.88        13.08 
TCGA-E1-A7Z3 TCGA-E1-A7Z4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6692 
       73.48       145.05        47.77        25.48        36.82        18.44 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7641 TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z 
       15.35        17.88        20.61        18.38        22.26        10.78 
TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7475 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7858 
        5.72        11.54        17.42        31.69        14.96        50.63 
TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA 
        3.72        16.24        13.78        15.72         0.23        27.35 
TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74J TCGA-HW-A5KK TCGA-IK-7675 
        5.33        16.14        17.65        10.52        12.76        19.00 
TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-QH-A6CV TCGA-QH-A6X9 TCGA-QH-A870 
        0.23         2.30         7.59        14.53         1.91        12.99 
TCGA-RY-A83Z TCGA-S9-A6TY TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 
        9.90        35.38        19.86        26.93        19.99        20.02 
TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84Q 
       10.39        54.77        65.39        24.92        28.08        25.38 
TCGA-TQ-A7RF TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8CD TCGA-VM-A8CF 
       21.37        15.98        26.99        31.36         7.89        20.02 
TCGA-VW-A8FI TCGA-WY-A85E 
        8.05        20.81 

$subtype3
TCGA-CS-6670 TCGA-DH-5141 TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 
       46.88        31.82        62.01        20.09        17.82        20.45 
TCGA-HT-A619 TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-5394 TCGA-CS-6668 TCGA-DB-5274 
       21.40        42.77        59.38         0.26        49.94        75.25 
TCGA-DB-5275 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH 
       47.93        91.13        44.52        18.84        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V 
       24.20        30.12         5.98        31.40        27.81        29.23 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DH-5144 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US 
       14.40        12.10        24.59        17.19        54.25        23.21 
TCGA-DU-5849 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 
       14.56       182.33        15.16        52.11        22.42        46.06 
TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7294 TCGA-DU-7302 
        7.96       154.36        30.67        10.36        94.32        60.30 
TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 
       21.40        14.17        25.55        21.57        95.11        22.29 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TG TCGA-E1-5311 TCGA-E1-5318 
       21.30        17.98        51.52        44.42       134.27        78.21 
TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YS TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5964 
       95.57        75.02        15.32        39.48         0.23        52.21 
TCGA-FG-7638 TCGA-FG-8186 TCGA-FG-A4MT TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 
       22.55        16.01        38.27        14.76        15.02        16.44 
TCGA-FG-A710 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7480 
       36.66         0.10         6.67         0.13         0.03        75.19 
TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 
       95.93         4.57         3.16        22.06         0.23        14.27 
TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
       16.24        44.68         0.10         2.96         6.90        14.53 
TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 
       39.09        37.15         0.33         0.13        35.47         1.64 
TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-A4DV TCGA-HT-A5R9 
        9.40         6.25         5.56        29.59        26.04         0.07 
TCGA-HT-A615 TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 
       16.93        15.35        11.05        56.58        45.44        68.32 
TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 
       35.44        24.92        31.63        14.40         7.99         9.44 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X 
       11.64        10.95         9.01        12.23        19.20         3.45 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
        4.41        15.16        12.62        15.85        14.04        14.83 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X 
       13.41         9.17        14.53        16.34        16.73        11.08 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       88.83        94.03        32.65        30.87         5.46        28.08 
TCGA-RY-A847 TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB 
       30.67        41.10        40.93        29.85        32.61       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP 
       75.25       135.22        38.56        31.10        26.47        18.64 
TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       36.13        23.51         8.19         2.04        20.68        15.06 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M 
       28.37        27.16       169.84        49.32        40.64        24.79 
TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RN 
       33.24        18.61        14.93        19.69         2.04        33.73 
TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       31.20        26.14        33.93        13.51         0.10        39.16 
TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 TCGA-WY-A85D 
       37.05        23.21        51.06        37.71 

subtype1 subtype2 subtype3 
    0.10     0.23     0.03 
subtype1 subtype2 subtype3 
  172.77   211.17   182.33 
subtype1 subtype2 subtype3 
  24.325   19.295   23.210 
[1] "0.1 - 172.8 (24.3)" "0.2 - 211.2 (19.3)" "0.0 - 182.3 (23.2)"
D3V2, continuous
D3V3, binary
          cls
clus         0   1
  subtype1  97 129
  subtype2  51  60
  subtype3  80  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   97  129
  subtype2   51   60
  subtype3   80   95
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       97       51       80
  MALE        129       60       95
[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"
D3V4, binary
          cls
clus         0   1
  subtype1  69 142
  subtype2  21  82
  subtype3  94  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69  142
  subtype2   21   82
  subtype3   94   71
     clus
vv    subtype1 subtype2 subtype3
  NO        69       21       94
  YES      142       82       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"
D3V5, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1         129               68                29
  subtype2          57               21                33
  subtype3           8               40               127
D3V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA            129       57        8
  OLIGOASTROCYTOMA        68       21       40
  OLIGODENDROGLIOMA       29       33      127
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         4
  subtype2                                1     1                        11
  subtype3                                0     5                         6
          vv
clus       WHITE
  subtype1   216
  subtype2    98
  subtype3   158
D3V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   2        1        5
  BLACK OR AFRICAN AMERICAN               4       11        6
  WHITE                                 216       98      158
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus         0   1
  subtype1  13 198
  subtype2   6  97
  subtype3  13 151
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  198
  subtype2    6   97
  subtype3   13  151
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        6       13
  NOT HISPANIC OR LATINO      198       97      151
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1 167  41
  subtype2  78  58
  subtype3 135  20
  subtype4   6   6
subtype1 subtype2 subtype3 subtype4 
     208      136      155       12 
subtype1 subtype2 subtype3 subtype4 
      41       58       20        6 
$subtype1
TCGA-DB-A4XC TCGA-DH-A66B TCGA-DU-A76O TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-4942 
       46.72        42.05        17.16        45.60       117.50        43.89 
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 
       36.36        40.18        37.38        46.95        48.30        81.96 
TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       47.93        50.86        36.56        78.28        46.42        30.21 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75L 
       39.78        37.45        33.57        27.45        18.51        11.24 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66D TCGA-DH-A66G 
       17.88        30.74        63.88        46.06        27.81        17.19 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 
       17.46        13.71        18.61        13.38         6.81        18.94 
TCGA-DU-5872 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 
       17.49        49.02        75.16        65.75        87.45        94.52 
TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7011 TCGA-DU-7014 
      114.08         2.40        62.96       156.23       105.21       117.40 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 
       90.77        26.30        44.02        25.91        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
        2.76        20.68        16.96        15.48        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A7T8 TCGA-DU-A7TA 
       31.69        26.17        24.99        20.98       139.04        84.33 
TCGA-DU-A7TC TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       37.38        38.89        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5322 TCGA-E1-A7YH TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7Z4 
       57.93       130.78        93.21         0.76        36.82       145.05 
TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       32.35         0.20        36.82        14.93        42.54        41.33 
TCGA-FG-7636 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       17.88        13.68        14.24        14.96        32.61        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A711 
       18.71        23.70        14.76        21.53        28.54        48.69 
TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
       27.52         0.03        16.54        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7604 
        6.38       106.95       172.77         4.01         5.03       122.47 
TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7684 
       17.29        45.99        56.09        57.60         0.16         6.05 
TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7855 
       42.74        31.69        14.96         0.10        17.52        19.23 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-8013 TCGA-HT-8108 
       50.63        23.61         3.68        11.28        63.55         2.50 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A61B 
        0.23        34.19         0.10         2.70         1.81        17.52 
TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       10.52         0.10        69.27        39.75        40.01        42.54 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5F1 
       28.87        20.71        19.00         0.23         6.71         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A731 TCGA-P5-A733 
        7.96         7.59        10.42        13.25         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A780 TCGA-QH-A65S TCGA-QH-A6CW TCGA-QH-A6X3 
        9.60         7.56         2.37         2.53        13.61        10.29 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A870 TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 
        1.91        16.50        12.99         9.90         2.07        19.59 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U6 
       62.17        87.12        18.77        36.82        25.81        35.15 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IZ TCGA-S9-A7J0 
       98.24        95.93        18.61        14.07        19.99        20.02 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C4 
       15.06        18.54        99.06        30.05        31.59        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84Q 
       34.78        65.39        30.44        28.08        40.83        25.38 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       23.80        21.37        15.98        40.41        44.09        36.69 
TCGA-TQ-A7RR TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CF 
       25.87        61.41        26.99        31.36        45.93        20.02 
TCGA-VM-A8CH TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.47        16.01        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       45.80        46.88        37.71        20.81 

$subtype2
TCGA-E1-A7YN TCGA-FG-A713 TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5395 TCGA-CS-5397 
       23.90        20.45         7.69        60.10        21.01         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-A64O 
       17.69        26.76        49.12       122.73        72.92        25.48 
TCGA-DB-A64V TCGA-DB-A75P TCGA-DH-5140 TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
       29.23        16.18        19.96        18.02        17.46         6.74 
TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        8.45       211.17         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7292 
       16.83        11.47         6.54         8.84        10.36         7.96 
TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT 
       18.94         5.10        23.74        14.60        19.13        24.43 
TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TG 
       33.96        11.41        26.76        51.52         7.50        44.42 
TCGA-DU-A7TJ TCGA-E1-A7YD TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YM 
        0.56        14.30        19.46        12.43        16.18        21.30 
TCGA-E1-A7YQ TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-FG-5963 TCGA-FG-6688 
       51.88       146.14        13.08        73.48        25.48        18.77 
TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A4MU TCGA-FG-A4MW 
       18.44        20.09        28.34        22.52        10.72        18.38 
TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7474 TCGA-HT-7479 
       10.78         5.72         0.10        11.54         3.75        40.34 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7607 TCGA-HT-7620 TCGA-HT-7680 TCGA-HT-7691 
       29.85        23.18         3.16        14.27         0.76         0.10 
TCGA-HT-7694 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7874 
        6.90        39.48        39.09         0.23         0.49        37.15 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        5.33        35.47         3.72        31.43         1.64        16.24 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         0.10         0.46 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
       13.78        29.59        13.74        28.27        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 
       26.04         0.13        20.22        27.35         5.33        16.14 
TCGA-HT-A61A TCGA-HT-A61C TCGA-HT-A74H TCGA-HW-7489 TCGA-HW-A5KK TCGA-KT-A7W1 
        6.38        17.65         2.43        41.49        12.76        14.40 
TCGA-P5-A5EY TCGA-P5-A5F6 TCGA-P5-A72U TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX 
        2.37         1.28         0.23        19.33        14.53        12.23 
TCGA-QH-A6XC TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WM 
       16.70        24.39         5.85        85.55        84.99        19.86 
TCGA-S9-A6WN TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-S9-A7R7 TCGA-S9-A89V 
       26.47        36.13        26.93        10.39        98.63        18.71 
TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84J TCGA-TM-A84R 
       54.77        24.92        16.18        59.05        24.16        18.61 
TCGA-TQ-A7RP TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VW-A8FI 
       30.05        43.20         7.89         8.05 

$subtype3
TCGA-CS-6670 TCGA-DH-5141 TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A60K TCGA-HT-A619 
       46.88        31.82        62.01        20.09        17.82        21.40 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5274 
       42.77        59.38         0.26        53.62        49.94        75.25 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       91.13        44.52        18.84        72.95        31.63        24.20 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A75K 
       30.12         5.98        31.40        27.81        14.40        12.10 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 
       24.59        30.21        17.19        54.25        23.21        14.56 
TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 
      182.33        15.16        52.11        22.42        46.06         1.22 
TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7302 TCGA-DU-8164 
        7.96       154.36        30.67        94.32        60.30        21.40 
TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R 
       14.17        25.55        21.57        95.11        22.29        21.30 
TCGA-DU-A7T6 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YS 
       17.98       134.27        78.21        95.57        75.02        15.32 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7637 
       39.48         0.23        47.77        52.21        15.35        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8186 TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 
       22.55        20.61        16.01        15.02        16.44        36.66 
TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7608 
        6.67         0.13        75.19        95.93         4.57        22.06 
TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7695 
        0.23        16.24        44.68         0.10         2.96        14.53 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-A5R9 
        0.33         0.13         9.40         6.25         5.56         0.07 
TCGA-HT-A615 TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 
       16.93        15.35        11.05        56.58        45.44        68.32 
TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 
       35.44        24.92        31.63        14.40         7.99         9.44 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 
       11.64        10.95        12.23        19.20         3.45         4.41 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY 
       15.16        12.62        15.85        14.04        14.83        13.41 
TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK 
        9.17        14.53        16.34        16.73        11.08        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 
       94.03        32.65        30.87         5.46        28.08        30.67 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB 
       41.10        40.93        35.38        29.85        32.61       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IY 
       75.25       135.22        38.56        31.10        18.64        23.51 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.19         2.04        20.68        28.37        27.16       169.84 
TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S TCGA-TQ-A7RG 
       49.32        40.64        24.79        33.24        14.93        19.69 
TCGA-TQ-A7RI TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-VM-A8CA 
        2.04        33.73        31.20        26.14        33.93        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 
        0.10        39.16        37.05        23.21        51.06 

$subtype4
TCGA-CS-6665 TCGA-FG-A87N TCGA-DU-7010 TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YV 
       51.55        18.64        14.99        29.13         3.65        32.45 
TCGA-FG-A6J3 TCGA-HT-7470 TCGA-HT-A618 TCGA-P5-A5EZ TCGA-S9-A7IS TCGA-S9-A89Z 
       22.26        40.11        16.83         2.30         7.92        20.48 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.10     0.07     2.30 
subtype1 subtype2 subtype3 subtype4 
  172.77   211.17   182.33    51.55 
subtype1 subtype2 subtype3 subtype4 
  27.665   17.855   23.210   19.560 
[1] "0.0 - 172.8 (27.7)" "0.1 - 211.2 (17.9)" "0.1 - 182.3 (23.2)"
[4] "2.3 - 51.5 (19.6)" 
D4V2, continuous
D4V3, binary
          cls
clus         0   1
  subtype1  89 119
  subtype2  63  73
  subtype3  69  89
  subtype4   9   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   89  119
  subtype2   63   73
  subtype3   69   89
  subtype4    9    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       89       63       69        9
  MALE        119       73       89        4
[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"
D4V4, binary
          cls
clus         0   1
  subtype1  62 135
  subtype2  33  91
  subtype3  88  61
  subtype4   3   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   62  135
  subtype2   33   91
  subtype3   88   61
  subtype4    3    9
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        62       33       88        3
  YES      135       91       61        9
[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"
D4V5, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1         109               67                32
  subtype2          70               27                39
  subtype3           4               35               119
  subtype4          11                1                 1
D4V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA            109       70        4       11
  OLIGOASTROCYTOMA        67       27       35        1
  OLIGODENDROGLIOMA       32       39      119        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         6
  subtype2                                1     2                        11
  subtype3                                0     4                         4
  subtype4                                0     1                         0
          vv
clus       WHITE
  subtype1   199
  subtype2   120
  subtype3   144
  subtype4    12
D4V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   1        2        4        1
  BLACK OR AFRICAN AMERICAN               6       11        4        0
  WHITE                                 199      120      144       12
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus         0   1
  subtype1  14 178
  subtype2   6 122
  subtype3  12 136
  subtype4   0  13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  178
  subtype2    6  122
  subtype3   12  136
  subtype4    0   13
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           14        6       12        0
  NOT HISPANIC OR LATINO      178      122      136       13
[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(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  71  17
  subtype2  57  37
  subtype3 104  22
  subtype4  94  22
subtype1 subtype2 subtype3 subtype4 
      88       94      126      116 
subtype1 subtype2 subtype3 subtype4 
      17       37       22       22 
$subtype1
TCGA-CS-6665 TCGA-E1-A7YN TCGA-FG-8187 TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-6186 
       51.55        23.90        20.09       117.50        43.89        17.69 
TCGA-CS-6188 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-A4XF TCGA-DB-A64U TCGA-DB-A64V 
       26.76        81.96        72.92        33.57        27.81        29.23 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5143 TCGA-DH-A66D TCGA-DU-5854 TCGA-DU-5874 
       17.88        30.74        46.06        27.81         8.45        15.16 
TCGA-DU-6395 TCGA-DU-7012 TCGA-DU-7015 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-8161 
       49.02         6.54        90.77        25.91        23.31        23.74 
TCGA-DU-8163 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-E1-5302 TCGA-E1-5319 TCGA-E1-A7YW 
       20.68        29.85        31.69        50.14        95.57        36.82 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-FG-6688 TCGA-FG-7634 TCGA-FG-8182 TCGA-FG-8186 
       13.08        73.48        18.77        15.35        13.68        16.01 
TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MW TCGA-FG-A60J TCGA-FG-A60L TCGA-HT-7468 
       14.96        32.61        18.38        14.76        21.53         6.67 
TCGA-HT-7472 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7602 
        0.03        40.34        95.93       106.95         4.01        29.85 
TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
       57.60        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7854 TCGA-HT-7873 TCGA-HT-7879 
       42.74         0.10         2.96        39.48        23.61         3.68 
TCGA-HT-8013 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-A5R5 TCGA-HT-A618 TCGA-HT-A74H 
       63.55         0.23        34.19         0.13        16.83         2.43 
TCGA-HT-A74J TCGA-HW-8319 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 
       10.52        39.75         6.71         2.37         2.30         5.88 
TCGA-QH-A65S TCGA-QH-A65Z TCGA-QH-A6CU TCGA-S9-A6TX TCGA-S9-A6U5 TCGA-S9-A6WN 
        2.53        14.04        14.83        40.93        32.61        26.47 
TCGA-S9-A7IY TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RK TCGA-TQ-A7RV TCGA-VM-A8C9 
       23.51        19.69        15.98        44.09        61.41        43.20 
TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH TCGA-WY-A85B 
       13.51        39.16        23.47        45.80 

$subtype2
TCGA-DU-A76O TCGA-FG-A87N TCGA-HT-A619 TCGA-CS-4943 TCGA-CS-6666 TCGA-DB-5274 
       17.16        18.64        21.40        36.36        46.95        75.25 
TCGA-DB-5277 TCGA-DB-A4XG TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64X TCGA-DH-5140 
       50.86        72.95         5.98        31.40        18.51        19.96 
TCGA-DH-5142 TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5855 TCGA-DU-6393 
       63.88        17.19        18.02         6.74         6.81        52.11 
TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 
       22.42        75.16         1.22         7.04       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83       114.08         7.96         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-8158 TCGA-DU-8165 
      156.23        14.99         8.84        10.36         5.10        19.13 
TCGA-DU-8168 TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S8 TCGA-DU-A76L 
       14.17        24.43        26.17        33.96        22.29        26.76 
TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5318 
       17.98        84.33         7.50         0.56        41.13        78.21 
TCGA-E1-5322 TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YS TCGA-EZ-7264 TCGA-FG-6691 
      130.78         3.65        19.46        15.32        39.48        41.33 
TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MT TCGA-FG-A6J3 TCGA-HT-7469 TCGA-HT-7477 
       17.88        14.24        38.27        22.26        11.54        24.26 
TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7690 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 
      122.47        17.29         0.10         0.23         0.49         3.72 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8104 TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A61B 
       16.24         9.40        12.23         0.07        16.93        17.52 
TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A735 
       68.32        24.92        12.76        20.71        19.00         9.60 
TCGA-QH-A6CV TCGA-RY-A83Z TCGA-RY-A845 TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U6 
       14.53         9.90        19.59        24.39        25.81        35.15 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-TQ-A7RQ TCGA-TQ-A7RW 
       85.55        38.56         7.92        20.02        26.14        26.99 
TCGA-TQ-A8XE TCGA-VM-A8CB TCGA-VV-A829 TCGA-VW-A7QS 
       31.36         0.10        37.05        23.21 

$subtype3
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-HW-7490 TCGA-IK-8125 
       46.88        46.72        31.82        42.05        45.60        42.77 
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6668 
       60.10        40.18         0.26        53.62         6.38        49.94 
TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XD 
       47.93        44.52        36.56        78.28        18.84        39.78 
TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64S TCGA-DB-A75K TCGA-DB-A75L TCGA-DH-5144 
       31.63        30.12        27.45        12.10        11.24        24.59 
TCGA-DH-A66F TCGA-DH-A7US TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       17.19        23.21        13.38       182.33        18.94        17.49 
TCGA-DU-6392 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6407 
      211.17        46.06        65.75        87.45        11.64        94.52 
TCGA-DU-7011 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7306 TCGA-DU-8167 
      105.21       117.40        30.67        26.30        41.98        15.48 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A76K TCGA-E1-5303 TCGA-E1-A7YL 
       24.99        25.55        21.57        11.41        67.46        16.18 
TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-E1-A7Z6 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5964 
       51.88        32.45        32.35         0.23         0.20        52.21 
TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY 
       40.08        22.55        20.61        10.72        18.71        23.70 
TCGA-FG-A70Y TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7483 TCGA-HT-7601 
       28.54        16.54         6.54         6.38       172.77         5.03 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7693 
       22.06        45.99         0.23         6.05        14.96        17.52 
TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7875 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8110 
       19.23        50.63         0.33         6.25         0.10        13.78 
TCGA-HT-A74O TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ 
        0.10        45.44        41.49        40.01        42.54        31.63 
TCGA-P5-A5EV TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X 
        0.23         7.96         1.28         0.23        10.42        13.25 
TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A780 
       10.95         9.01         7.56        12.23        19.20         2.37 
TCGA-QH-A65X TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
       15.85        13.61        12.23        11.08        12.99        88.83 
TCGA-R8-A6ML TCGA-RY-A83X TCGA-RY-A83Y TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        30.87         5.46        62.17        87.12        18.77 
TCGA-S9-A6U9 TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A7IZ TCGA-S9-A7J2 TCGA-S9-A7QX 
       95.93        75.25       135.22        19.99         2.04        18.54 
TCGA-S9-A7R1 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A84S TCGA-TQ-A7RF 
      169.84        30.05        31.59        49.32        14.93        21.37 
TCGA-TQ-A7RN TCGA-VM-A8C8 TCGA-VV-A86M TCGA-W9-A837 TCGA-WY-A85C TCGA-WY-A85D 
       33.73        45.93        16.01        51.06        46.88        37.71 

$subtype4
TCGA-DU-7300 TCGA-FG-A713 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5278 TCGA-DB-A4X9 
       62.01        20.45        49.12       122.73        91.13        46.42 
TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64W TCGA-DB-A75P 
       30.21        37.45        24.20        25.48        14.40        16.18 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-7009 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       14.56        17.46       154.36         7.96        94.32        18.94 
TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TP 
       60.30         2.76        14.60        21.40        16.96        33.27 
TCGA-DU-A76R TCGA-DU-A7TB TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5305 TCGA-E1-5307 
       21.30        51.52        44.42        38.89        79.99        57.93 
TCGA-E1-5311 TCGA-E1-A7YH TCGA-E1-A7YM TCGA-E1-A7YY TCGA-FG-5962 TCGA-FG-5963 
      134.27        93.21        21.30       146.14        47.77        25.48 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 
       36.82        14.93        42.54        20.09        28.34        22.52 
TCGA-FG-A6IZ TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A87Q TCGA-HT-7467 TCGA-HT-7470 
       15.02        10.78        36.66         5.72         0.10        40.11 
TCGA-HT-7471 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7480 TCGA-HT-7603 TCGA-HT-7605 
        0.13         3.75        17.42        75.19        23.18         4.57 
TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 
        3.16        56.09         0.10        31.69         6.90        14.53 
TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
       39.09        37.15         0.13         5.33        35.47        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 
       31.43         1.64         0.10        37.87        33.01         0.46 
TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R7 
        5.56        29.59        13.74        15.72        26.04        20.22 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61A TCGA-HT-A74L 
        0.10         2.70         1.81        16.14         6.38        11.05 
TCGA-HW-7486 TCGA-HW-7493 TCGA-HW-7495 TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 
       56.58        69.27        35.44        14.40         7.99         9.44 
TCGA-P5-A5F4 TCGA-P5-A72Z TCGA-P5-A733 TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65V 
        7.59        11.64        13.61         3.45         4.41        12.62 
TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       19.33        13.41         9.17        14.53        16.34        16.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MO TCGA-RY-A843 TCGA-S9-A6TY 
        1.91        16.50        16.70        32.65         2.07        35.38 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7J1 TCGA-S9-A7QZ TCGA-TM-A84R 
       18.64        14.07        36.13         8.19        27.16        18.61 
TCGA-TQ-A7RR TCGA-VM-A8CD 
       25.87         7.89 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  117.50   156.23   211.17   154.36 
subtype1 subtype2 subtype3 subtype4 
  23.560   19.525   24.790   18.625 
[1] "0.0 - 117.5 (23.6)" "0.1 - 156.2 (19.5)" "0.1 - 211.2 (24.8)"
[4] "0.1 - 154.4 (18.6)"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 35 55
  subtype2 52 43
  subtype3 43 83
  subtype4 61 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   55
  subtype2   52   43
  subtype3   43   83
  subtype4   61   56
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       35       52       43       61
  MALE         55       43       83       56
[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"
D5V4, binary
          cls
clus        0  1
  subtype1 37 45
  subtype2 29 57
  subtype3 42 77
  subtype4 44 65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   45
  subtype2   29   57
  subtype3   42   77
  subtype4   44   65
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        37       29       42       44
  YES       45       57       77       65
[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"
D5V5, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          35               30                25
  subtype2          44               15                36
  subtype3          41               37                48
  subtype4          27               32                58
D5V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             35       44       41       27
  OLIGOASTROCYTOMA        30       15       37       32
  OLIGODENDROGLIOMA       25       36       48       58
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         6
  subtype2                                0     4                         3
  subtype3                                0     2                         5
  subtype4                                1     2                         4
          vv
clus       WHITE
  subtype1    82
  subtype2    85
  subtype3   117
  subtype4   109
D5V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                   0        4        2        2
  BLACK OR AFRICAN AMERICAN               6        3        5        4
  WHITE                                  82       85      117      109
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus         0   1
  subtype1   8  76
  subtype2   6  83
  subtype3   7 111
  subtype4   5 107
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   76
  subtype2    6   83
  subtype3    7  111
  subtype4    5  107
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            8        6        7        5
  NOT HISPANIC OR LATINO       76       83      111      107
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  75   8
  subtype2 127  30
  subtype3 124  60
subtype1 subtype2 subtype3 
      83      157      184 
subtype1 subtype2 subtype3 
       8       30       60 
$subtype1
TCGA-CS-6665 TCGA-IK-8125 TCGA-CS-4938 TCGA-CS-4944 TCGA-CS-6186 TCGA-DB-5273 
       51.55        42.77       117.50        60.10        17.69        81.96 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-A4XF TCGA-DB-A64Q TCGA-DB-A64V TCGA-DB-A64X 
       75.25        72.92        33.57         5.98        29.23        18.51 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5143 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       17.88        30.74        46.06        27.81        17.19        17.19 
TCGA-DH-A7US TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-7304 TCGA-DU-8163 TCGA-DU-A5TR 
       23.21       182.33        15.16        23.31        20.68        29.85 
TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5319 TCGA-E1-A7Z3 TCGA-E1-A7Z6 TCGA-FG-6688 
       38.89        50.14        95.57        73.48        32.35        18.77 
TCGA-FG-6691 TCGA-FG-7636 TCGA-FG-8191 TCGA-FG-A4MY TCGA-FG-A60L TCGA-HT-7468 
       41.33        17.88        32.61        23.70        21.53         6.67 
TCGA-HT-7472 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7608 TCGA-HT-7611 
        0.03        40.34       106.95         4.01        22.06        57.60 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7686 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 
       16.24         0.76        42.74        14.96         0.10         2.96 
TCGA-HT-7854 TCGA-HT-7858 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-A5R5 TCGA-HT-A618 
       39.48        50.63         0.23        34.19         0.13        16.83 
TCGA-HT-A74H TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72X TCGA-P5-A731 
        2.43         6.71         2.30         5.88        13.25         9.01 
TCGA-P5-A736 TCGA-P5-A737 TCGA-QH-A65S TCGA-QH-A6CW TCGA-R8-A6ML TCGA-S9-A6TS 
        7.56        12.23         2.53        13.61        94.03        62.17 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6WG TCGA-S9-A6WN TCGA-S9-A7IY TCGA-TM-A84S 
       32.61        35.15        85.55        26.47        23.51        14.93 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RK TCGA-TQ-A7RV TCGA-VM-A8C9 TCGA-VM-A8CA 
       19.69        15.98        44.09        61.41        43.20        13.51 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-W9-A837 TCGA-WY-A85B TCGA-WY-A85D 
       39.16        23.47        51.06        45.80        37.71 

$subtype2
TCGA-CS-6670 TCGA-DU-7300 TCGA-DU-A76O TCGA-FG-8187 TCGA-FG-A713 TCGA-CS-4942 
       46.88        62.01        17.16        20.09        20.45        43.89 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5278 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XE 
       49.12       122.73        91.13        46.42        30.21        37.45 
TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A75P TCGA-DU-5849 
       31.63        25.48        27.81        14.40        16.18        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-6395 TCGA-DU-6403 TCGA-DU-7009 
       17.46         6.74        13.38        49.02        11.64       154.36 
TCGA-DU-7010 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7302 TCGA-DU-7309 
       14.99         7.96        94.32        18.94        60.30         2.76 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       14.60        21.40        16.96        15.48        14.17        33.27 
TCGA-DU-A5TS TCGA-DU-A6S3 TCGA-DU-A76R TCGA-DU-A7TB TCGA-DU-A7TG TCGA-E1-5305 
       31.69        21.57        21.30        51.52        44.42        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-A7YH TCGA-E1-A7YM TCGA-E1-A7YW TCGA-E1-A7YY 
       57.93       134.27        93.21        21.30        36.82       146.14 
TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
        0.23        47.77        25.48        36.82        14.93        42.54 
TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       15.35        22.55        20.61        20.09        28.34        13.68 
TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J3 
       16.01        14.96        22.52        14.76        15.02        22.26 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A87Q TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 
       10.78        36.66         5.72         0.10        40.11         3.75 
TCGA-HT-7475 TCGA-HT-7481 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 
       17.42        95.93        29.85        23.18         4.57         3.16 
TCGA-HT-7610 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 
       56.09        14.27         0.16        44.68         0.10        31.69 
TCGA-HT-7690 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7873 TCGA-HT-7877 
        0.10         6.90        14.53        39.09        23.61         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33        35.47        11.28        31.43         1.64 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 TCGA-HT-8109 
       63.55         0.10        37.87        33.01         0.46         5.56 
TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5RB 
       29.59        13.74        15.72        26.04        20.22         0.10 
TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61A TCGA-HT-A74J TCGA-HT-A74L 
        2.70         1.81        16.14         6.38        10.52        11.05 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8322 
       56.58        45.44        69.27        35.44        39.75        24.92 
TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A72Z 
       14.40         7.99         2.37         9.44         7.59        11.64 
TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65V 
       13.61         9.60        19.20         3.45         4.41        12.62 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 
       14.04        19.33        14.83        13.41         9.17        14.53 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6MO 
       16.73         1.91        16.50        16.70        88.83        32.65 
TCGA-RY-A843 TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6WE TCGA-S9-A6WP TCGA-S9-A6WQ 
        2.07        40.93        35.38       135.22        18.64        14.07 
TCGA-S9-A7IQ TCGA-S9-A7J1 TCGA-S9-A7QZ TCGA-TM-A84R TCGA-TQ-A7RR TCGA-TQ-A7RW 
       36.13         8.19        27.16        18.61        25.87        26.99 
TCGA-VM-A8CD 
        7.89 

$subtype3
TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-E1-A7YN TCGA-FG-A87N TCGA-HT-A619 
       46.72        31.82        42.05        23.90        18.64        21.40 
TCGA-HW-7490 TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 
       45.60        36.36        40.18         0.26        53.62         6.38 
TCGA-CS-6188 TCGA-CS-6666 TCGA-CS-6668 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 
       26.76        46.95        49.94        47.93        50.86        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A64L 
       36.56        78.28        18.84        39.78        72.95        24.20 
TCGA-DB-A64P TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A75K TCGA-DB-A75L TCGA-DH-5140 
       30.12        31.40        27.45        12.10        11.24        19.96 
TCGA-DH-5142 TCGA-DH-5144 TCGA-DU-5847 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 
       63.88        24.59        18.02         8.45         6.81        18.94 
TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       17.49       211.17        52.11        22.42        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 
       65.75         1.22        87.45         7.04       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         2.40        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
       62.96       156.23       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7301 TCGA-DU-7306 
       90.77        30.67        26.30        10.36        25.91        41.98 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
        5.10        23.74        19.13        24.43        26.17        24.99 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 
       33.96        25.55        22.29        11.41        26.76        17.98 
TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5318 
       84.33         7.50         0.56        67.46        41.13        78.21 
TCGA-E1-5322 TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7YS 
      130.78         3.65        19.46        16.18        51.88        15.32 
TCGA-E1-A7YV TCGA-E1-A7Z2 TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5964 TCGA-FG-7637 
       32.45        13.08        39.48         0.20        52.21        40.08 
TCGA-FG-8185 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A70Y 
       14.24        38.27        10.72        18.38        18.71        28.54 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       11.54         0.13        16.54         6.54        24.26         6.38 
TCGA-HT-7480 TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 
       75.19       172.77         5.03       122.47        17.29        45.99 
TCGA-HT-7616 TCGA-HT-7684 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7860 
        0.23         6.05        17.52        19.23         0.23         0.49 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8104 
       37.15         0.33         3.72        16.24         9.40        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A61B 
        6.25         0.10        13.78         0.07        16.93        17.52 
TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ 
        0.10        41.49        68.32        40.01        42.54        31.63 
TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5F2 TCGA-P5-A5F6 
       12.76        20.71        19.00         0.23         7.96         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A730 TCGA-P5-A780 TCGA-QH-A65X TCGA-QH-A6CV 
        0.23        10.42        10.95         2.37        15.85        14.53 
TCGA-QH-A6CX TCGA-QH-A6X5 TCGA-QH-A86X TCGA-QH-A870 TCGA-RY-A83X TCGA-RY-A83Y 
       12.23        16.34        11.08        12.99        30.87         5.46 
TCGA-RY-A83Z TCGA-RY-A845 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6U0 TCGA-S9-A6U1 
        9.90        19.59        87.12        18.77        24.39        25.81 
TCGA-S9-A6U9 TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A7J0 
       95.93        75.25        38.56         7.92        19.99        20.02 
TCGA-S9-A7J2 TCGA-S9-A7QX TCGA-S9-A7R1 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C5 
        2.04        18.54       169.84        30.05        31.59        49.32 
TCGA-TQ-A7RF TCGA-TQ-A7RN TCGA-TQ-A7RQ TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CB 
       21.37        33.73        26.14        31.36        45.93         0.10 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-WY-A85C 
       37.05        16.01        23.21        46.88 

subtype1 subtype2 subtype3 
    0.03     0.10     0.07 
subtype1 subtype2 subtype3 
  182.33   154.36   211.17 
subtype1 subtype2 subtype3 
  23.700   18.640   21.845 
[1] "0.0 - 182.3 (23.7)" "0.1 - 154.4 (18.6)" "0.1 - 211.2 (21.8)"
D6V2, continuous
D6V3, binary
          cls
clus         0   1
  subtype1  32  51
  subtype2  76  84
  subtype3  83 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   51
  subtype2   76   84
  subtype3   83  102
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       32       76       83
  MALE         51       84      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"
D6V4, binary
          cls
clus         0   1
  subtype1  34  44
  subtype2  64  84
  subtype3  54 116
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   44
  subtype2   64   84
  subtype3   54  116
     clus
vv    subtype1 subtype2 subtype3
  NO        34       64       54
  YES       44       84      116
[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"
D6V5, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          40               25                18
  subtype2          33               50                77
  subtype3          74               39                72
D6V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             40       33       74
  OLIGOASTROCYTOMA        25       50       39
  OLIGODENDROGLIOMA       18       77       72
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         4
  subtype2                                1     3                         6
  subtype3                                0     5                         8
          vv
clus       WHITE
  subtype1    76
  subtype2   149
  subtype3   168
D6V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   0        3        5
  BLACK OR AFRICAN AMERICAN               4        6        8
  WHITE                                  76      149      168
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus         0   1
  subtype1   8  67
  subtype2   8 146
  subtype3  10 164
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   67
  subtype2    8  146
  subtype3   10  164
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        8       10
  NOT HISPANIC OR LATINO       67      146      164
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 102  27
  subtype2  59  55
  subtype3  92  12
  subtype4 106  28
  subtype5  27   3
subtype1 subtype2 subtype3 subtype4 subtype5 
     129      114      104      134       30 
subtype1 subtype2 subtype3 subtype4 subtype5 
      27       55       12       28        3 
$subtype1
TCGA-DU-A76O TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-6290 
       17.16        45.60       117.50        43.89        36.36        37.38 
TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5280 TCGA-DB-A4X9 
       46.95        48.30        81.96        47.93        36.56        46.42 
TCGA-DB-A4XD TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5142 
       39.78        27.45        18.51        17.88        30.74        63.88 
TCGA-DH-A66D TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 
       27.81        13.71        18.61        13.38         6.81        18.94 
TCGA-DU-5872 TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 
       17.49        49.02        65.75        87.45        94.52       114.08 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 
      117.40        90.77        44.02        25.91        41.98        20.68 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A7T8 
       16.96        15.48        31.69        24.99        20.98       139.04 
TCGA-DU-A7TA TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5322 TCGA-E1-A7YW 
       84.33        38.89        50.14        67.46       130.78        36.82 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7636 
      145.05        32.35        36.82        42.54        41.33        17.88 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX 
       13.68        14.24        14.96        32.61        38.27        18.71 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A70Y TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 
       14.76        21.53        28.54        27.52         0.03        16.54 
TCGA-HT-7478 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7604 TCGA-HT-7609 TCGA-HT-7611 
        6.38       106.95         4.01       122.47        45.99        57.60 
TCGA-HT-7676 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 
        0.16        17.52        19.23        50.63        23.61         3.68 
TCGA-HT-8013 TCGA-HT-8108 TCGA-HT-8114 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL 
       63.55         2.50        34.19        40.01        42.54        28.87 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5F1 TCGA-P5-A72W 
       20.71        19.00         0.23         6.71         5.88        10.42 
TCGA-P5-A72X TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A780 TCGA-QH-A6CW 
       13.25        13.61         9.60         7.56         2.37        13.61 
TCGA-QH-A6X3 TCGA-QH-A6XA TCGA-QH-A870 TCGA-RY-A845 TCGA-S9-A6TU TCGA-S9-A6TZ 
       10.29        16.50        12.99        19.59        87.12        36.82 
TCGA-S9-A6U1 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WO TCGA-S9-A7QW TCGA-S9-A7QX 
       25.81        98.24        95.93        18.61        15.06        18.54 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84Q 
       99.06        30.05        31.59        30.44        40.83        25.38 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RW 
       23.80        21.37        15.98        40.41        44.09        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CH TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A85A 
       31.36        45.93        23.47        16.01        13.32        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       45.80        46.88        37.71 

$subtype2
TCGA-CS-6665 TCGA-DH-A66B TCGA-E1-A7YN TCGA-FG-A87N TCGA-CS-4941 TCGA-CS-4944 
       51.55        42.05        23.90        18.64         7.69        60.10 
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-DH-5140 TCGA-DH-A669 
       21.01         6.38        17.69        26.76        19.96        30.21 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6396 TCGA-DU-6402 
       18.02         6.74         8.45       211.17        75.16         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7007 
       11.64       133.74        19.89        16.83        11.47        62.96 
TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-8158 TCGA-DU-8161 
       14.99         6.54         8.84        10.36         5.10        23.74 
TCGA-DU-8165 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY 
       19.13        33.27        29.85        24.43        26.17        33.96 
TCGA-DU-A76L TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-A7YD TCGA-E1-A7YE 
       26.76         7.50         0.56        41.13        14.30        29.13 
TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7YV 
        3.65        19.46        12.43        16.18        51.88        32.45 
TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 
       25.48        18.77        18.44        10.72        18.38        22.26 
TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7601 TCGA-HT-7616 
       10.78         5.72        11.54        24.26         5.03         0.23 
TCGA-HT-7680 TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7857 TCGA-HT-7860 
        0.76        42.74         0.10        39.48         0.23         0.49 
TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8563 
        3.72        16.24        12.23         0.10        13.78        28.27 
TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A61B 
        0.23        27.35         5.33        16.14        16.83        17.52 
TCGA-HT-A61C TCGA-HT-A74O TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5EZ 
       17.65         0.10        12.76        14.40         7.99         2.30 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A730 TCGA-QH-A6CV TCGA-QH-A6CX TCGA-RY-A83Z 
        1.28         0.23        10.95        14.53        12.23         9.90 
TCGA-S9-A6TV TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WN 
       18.77        24.39         5.85        85.55        19.86        26.47 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7R2 TCGA-S9-A7R7 TCGA-S9-A89V 
        7.92        26.93        20.02        10.39        98.63        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84I 
       20.48        54.77        24.92        16.18        59.05        28.08 
TCGA-TM-A84J TCGA-TQ-A7RM TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VW-A8FI TCGA-WY-A858 
       24.16        36.69        43.20         7.89         8.05        43.96 

$subtype3
TCGA-DH-5141 TCGA-FG-A60K TCGA-HT-A619 TCGA-R8-A73M TCGA-CS-5394 TCGA-CS-5396 
       31.82        17.82        21.40        59.38         0.26        53.62 
TCGA-CS-6668 TCGA-DB-5274 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A64P TCGA-DB-A64Q 
       49.94        75.25        18.84        72.95        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A75K TCGA-DH-5144 TCGA-DH-A66F TCGA-DH-A7UR 
       31.40        27.81        12.10        24.59        17.19        54.25 
TCGA-DH-A7US TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 
       23.21       182.33        15.16        52.11        22.42        46.06 
TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8164 TCGA-DU-8168 
        1.22         7.96        30.67        94.32        21.40        14.17 
TCGA-DU-A6S8 TCGA-DU-A7T6 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-E1-A7YS 
       22.29        17.98        78.21        95.57        75.02        15.32 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-8186 TCGA-FG-A6IZ 
       39.48         0.23        15.35        40.08        16.01        15.02 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7481 TCGA-HT-7606 
       16.44        36.66         6.67         0.13        95.93        17.29 
TCGA-HT-7677 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-A5R9 
       16.24         0.10         2.96         9.40         6.25         0.07 
TCGA-HT-A615 TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KJ 
       16.93        15.35        11.05        68.32        24.92        31.63 
TCGA-KT-A74X TCGA-P5-A72Z TCGA-P5-A737 TCGA-P5-A77W TCGA-QH-A65R TCGA-QH-A65X 
       14.40        11.64        12.23        19.20        15.16        15.85 
TCGA-QH-A65Z TCGA-QH-A6X4 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML 
       14.04        14.53        16.73        11.08        88.83        94.03 
TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-S9-A6TW TCGA-S9-A6TX 
       32.65        30.87         5.46        28.08        41.10        40.93 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       29.85        32.61       123.65        75.25       135.22        38.56 
TCGA-S9-A6WP TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QZ TCGA-TM-A7C5 
       18.64         8.19         2.04        20.68        27.16        49.32 
TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S TCGA-TQ-A7RG TCGA-TQ-A7RI 
       40.64        24.79        33.24        14.93        19.69         2.04 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-VM-A8CB TCGA-VM-A8CE 
       33.73        31.20        26.14        33.93         0.10        39.16 
TCGA-VV-A829 TCGA-VW-A7QS 
       37.05        23.21 

$subtype4
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DU-7300 TCGA-FG-A713 TCGA-IK-8125 TCGA-CS-5393 
       46.88        46.72        62.01        20.45        42.77        40.18 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
       49.12       122.73        72.92        50.86        91.13        44.52 
TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L 
       78.28        30.21        37.45        33.57        31.63        24.20 
TCGA-DB-A64O TCGA-DB-A64W TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-5143 TCGA-DH-A66G 
       25.48        14.40        11.24        16.18        46.06        17.19 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-6542 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
       14.56        17.46         2.40       156.23       154.36       105.21 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
       26.30         7.96        18.94        60.30        23.31         2.76 
TCGA-DU-8162 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76R 
       14.60        25.55        21.57        95.11        11.41        21.30 
TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-A7YU 
       37.38        44.42        79.99        57.93       134.27         0.76 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 
      146.14        13.08        73.48         0.20        47.77        52.21 
TCGA-FG-6689 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 
       14.93        22.55        20.61        20.09        28.34        22.52 
TCGA-FG-A711 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       48.69         0.10        40.11         3.75        17.42         6.54 
TCGA-HT-7480 TCGA-HT-7483 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 
       75.19       172.77        23.18         4.57         3.16        22.06 
TCGA-HT-7610 TCGA-HT-7681 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7694 TCGA-HT-7695 
       56.09        44.68        31.69         0.10         6.90        14.53 
TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 
       39.09        37.15         0.33         0.13         5.33        35.47 
TCGA-HT-8010 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 TCGA-HT-8109 
        1.64         0.10        37.87        33.01         0.46         5.56 
TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       29.59        13.74        15.72        26.04         0.13        20.22 
TCGA-HT-A5RB TCGA-HT-A616 TCGA-HT-A61A TCGA-HT-A74J TCGA-HW-7487 TCGA-HW-7489 
        0.10         1.81         6.38        10.52        45.44        41.49 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F2 
       69.27        35.44        39.75         2.37         9.44         7.96 
TCGA-P5-A5F4 TCGA-P5-A731 TCGA-P5-A77X TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 
        7.59         9.01         3.45        13.41         9.17         1.91 
TCGA-QH-A6XC TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 
       16.70         2.07        30.67        62.17        35.38        35.15 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A7IQ TCGA-S9-A7IZ TCGA-S9-A7R1 TCGA-TM-A7C4 
       84.99        31.10        36.13        19.99       169.84        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84R TCGA-TQ-A7RV TCGA-VM-A8CA TCGA-W9-A837 
       34.78        65.39        18.61        61.41        13.51        51.06 
TCGA-WY-A859 TCGA-WY-A85E 
       39.88        20.81 

$subtype5
TCGA-FG-8187 TCGA-DB-A64V TCGA-DH-A7UT TCGA-DU-A7TB TCGA-E1-A7YH TCGA-E1-A7YM 
       20.09        29.23        17.46        51.52        93.21        21.30 
TCGA-FG-A4MY TCGA-HT-7479 TCGA-HT-7602 TCGA-HT-7620 TCGA-HT-7684 TCGA-HT-7689 
       23.70        40.34        29.85        14.27         6.05        14.96 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8111 TCGA-HT-A614 TCGA-HT-A74H TCGA-HW-7486 
       11.28        31.43         0.23         2.70         2.43        56.58 
TCGA-P5-A781 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6X5 
        4.41         2.53        12.62        19.33        14.83        16.34 
TCGA-S9-A6WQ TCGA-S9-A7IY TCGA-S9-A7QY TCGA-TQ-A7RP TCGA-TQ-A7RR TCGA-VM-A8CF 
       14.07        23.51        28.37        30.05        25.87        20.02 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.10     0.07     0.10     0.23 
subtype1 subtype2 subtype3 subtype4 subtype5 
  145.05   211.17   182.33   172.77    93.21 
subtype1 subtype2 subtype3 subtype4 subtype5 
  28.870   17.670   22.815   25.515   19.675 
[1] "0.0 - 145.1 (28.9)" "0.1 - 211.2 (17.7)" "0.1 - 182.3 (22.8)"
[4] "0.1 - 172.8 (25.5)" "0.2 - 93.2 (19.7)" 
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 51 78
  subtype2 55 60
  subtype3 50 56
  subtype4 61 74
  subtype5 13 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51   78
  subtype2   55   60
  subtype3   50   56
  subtype4   61   74
  subtype5   13   17
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       51       55       50       61       13
  MALE         78       60       56       74       17
[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 42 81
  subtype2 20 84
  subtype3 57 42
  subtype4 54 73
  subtype5 13 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   81
  subtype2   20   84
  subtype3   57   42
  subtype4   54   73
  subtype5   13   16
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        42       20       57       54       13
  YES       81       84       42       73       16
[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       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          66               40                23
  subtype2          80               17                18
  subtype3           3               21                82
  subtype4          36               39                60
  subtype5           9               13                 8
D7V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4 subtype5
  ASTROCYTOMA             66       80        3       36        9
  OLIGOASTROCYTOMA        40       17       21       39       13
  OLIGODENDROGLIOMA       23       18       82       60        8
[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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         6
  subtype2                                1     2                         6
  subtype3                                0     4                         2
  subtype4                                0     1                         6
  subtype5                                0     1                         1
          vv
clus       WHITE
  subtype1   121
  subtype2   105
  subtype3    96
  subtype4   125
  subtype5    28
D7V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   0        2        4        1        1
  BLACK OR AFRICAN AMERICAN               6        6        2        6        1
  WHITE                                 121      105       96      125       28
[1] 4 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   8 110
  subtype2   3 105
  subtype3  11  87
  subtype4   7 121
  subtype5   3  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  110
  subtype2    3  105
  subtype3   11   87
  subtype4    7  121
  subtype5    3   26
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            8        3       11        7        3
  NOT HISPANIC OR LATINO      110      105       87      121       26
[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 = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 106  28
  subtype2  31  40
  subtype3  30   5
  subtype4  48  20
  subtype5  78  12
  subtype6  29  11
  subtype7  64   9
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
     134       71       35       68       90       40       73 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      28       40        5       20       12       11        9 
$subtype1
TCGA-DU-A76O TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 
       17.16        45.60       117.50        43.89        36.36        60.10 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5280 
       37.38        46.95        48.30        81.96        47.93        36.56 
TCGA-DB-A4XD TCGA-DB-A64S TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-A66D TCGA-DH-A7UT 
       39.78        27.45        17.88        30.74        27.81        17.46 
TCGA-DH-A7UV TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6395 
       18.61        13.38         6.81        18.94        17.49        49.02 
TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7014 
       75.16        65.75        87.45        94.52       114.08       117.40 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 
       90.77        26.30        44.02        25.91        41.98        20.68 
TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A7T8 TCGA-DU-A7TA 
       15.48        31.69        24.99        20.98       139.04        84.33 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5322 TCGA-E1-A7YH TCGA-E1-A7YW TCGA-E1-A7Z4 
       50.14        67.46       130.78        93.21        36.82       145.05 
TCGA-E1-A7Z6 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-8182 TCGA-FG-8185 
       32.35        36.82        42.54        41.33        13.68        14.24 
TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       14.96        32.61        38.27        18.71        23.70        14.76 
TCGA-FG-A60L TCGA-FG-A70Y TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 
       21.53        28.54        27.52         0.03        16.54        40.34 
TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7604 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7676 
      106.95         4.01       122.47        45.99        57.60         0.16 
TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 
        6.05        14.96        17.52        19.23        50.63        23.61 
TCGA-HT-7879 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 
        3.68        31.43        63.55         2.50         0.23        34.19 
TCGA-HT-A614 TCGA-HT-A74O TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL TCGA-HW-A5KM 
        2.70         0.10        40.01        42.54        28.87        20.71 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72W TCGA-P5-A72X 
        0.23         6.71         2.30         5.88        10.42        13.25 
TCGA-P5-A733 TCGA-P5-A736 TCGA-P5-A780 TCGA-QH-A65S TCGA-QH-A6CW TCGA-QH-A6X3 
       13.61         7.56         2.37         2.53        13.61        10.29 
TCGA-QH-A870 TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U8 TCGA-S9-A6U9 
       12.99        87.12        36.82        25.81        98.24        95.93 
TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 
       85.55        18.61        14.07        18.54        99.06        30.05 
TCGA-S9-A7R8 TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RH 
       31.59        30.44        40.83        23.80        21.37        15.98 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RR TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 
       40.41        44.09        25.87        26.99        31.36        45.93 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85B 
       20.02        23.47        16.01        13.32        43.96        45.80 
TCGA-WY-A85C TCGA-WY-A85D 
       46.88        37.71 

$subtype2
TCGA-E1-A7YN TCGA-CS-4941 TCGA-CS-6186 TCGA-CS-6188 TCGA-DB-A64O TCGA-DU-5847 
       23.90         7.69        17.69        26.76        25.48        18.02 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        6.74         8.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-8158 
       16.83        11.47         6.54         8.84        10.36         5.10 
TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A76L TCGA-DU-A7TD 
       23.74        19.13        24.43        33.96        26.76         7.50 
TCGA-DU-A7TJ TCGA-E1-A7YD TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-FG-6688 
        0.56        14.30        19.46        16.18        51.88        18.77 
TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 
       18.44        10.72        18.38        10.78         5.72        11.54 
TCGA-HT-7680 TCGA-HT-7691 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 
        0.76         0.10         0.23         0.49         3.72        16.24 
TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 
       12.23        13.78         0.23        27.35         5.33        16.14 
TCGA-HT-A61C TCGA-HT-A74H TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5F6 
       17.65         2.43        12.76        14.40         7.99         1.28 
TCGA-P5-A72U TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-S9-A6U0 TCGA-S9-A6UA 
        0.23        19.33        14.53        12.23        24.39         5.85 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84B 
       19.86        26.47        10.39        18.71        54.77        24.92 
TCGA-TM-A84C TCGA-TQ-A7RP TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VW-A8FI 
       16.18        30.05        43.20         7.89         8.05 

$subtype3
TCGA-R8-A73M TCGA-CS-6668 TCGA-DB-5279 TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64R 
       59.38        49.94        44.52        72.95        24.20        31.40 
TCGA-DH-5144 TCGA-DH-A7UR TCGA-DU-5874 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7294 
       24.59        54.25        15.16         1.22         7.96        94.32 
TCGA-DU-8168 TCGA-DU-A6S8 TCGA-E1-5311 TCGA-E1-A7YO TCGA-EZ-7264 TCGA-F6-A8O3 
       14.17        22.29       134.27        75.02        39.48         0.23 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-HT-7687 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-A5R9 
       16.44        36.66         0.10         9.40         6.25         0.07 
TCGA-HW-A5KJ TCGA-P5-A77W TCGA-QH-A65R TCGA-QH-A86X TCGA-S9-A6WH TCGA-S9-A6WL 
       31.63        19.20        15.16        11.08        38.56        31.10 
TCGA-S9-A7R1 TCGA-TM-A84G TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-VM-A8CB 
      169.84        40.64        31.20        26.14         0.10 

$subtype4
TCGA-DB-A4XC TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-DB-5270 TCGA-DB-5276 
       46.72        40.18        21.01         6.38       122.73        72.92 
TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DB-A4XF 
       50.86        78.28        46.42        30.21        37.45        33.57 
TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-5143 TCGA-DH-A66G TCGA-DU-6542 
       18.51        11.24        16.18        46.06        17.19         2.40 
TCGA-DU-7008 TCGA-DU-7011 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7304 TCGA-DU-8162 
      156.23       105.21         7.96        18.94        23.31        14.60 
TCGA-DU-8166 TCGA-DU-A76K TCGA-DU-A7TI TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YM 
       16.96        11.41        38.89        79.99        57.93        21.30 
TCGA-E1-A7YU TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-F6-A8O4 TCGA-FG-6689 TCGA-FG-7636 
        0.76        13.08        73.48         0.20        14.93        17.88 
TCGA-FG-7643 TCGA-FG-A711 TCGA-HT-7476 TCGA-HT-7483 TCGA-HT-7690 TCGA-HT-7854 
       20.09        48.69         6.54       172.77         0.10        39.48 
TCGA-HT-7884 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8564 TCGA-HT-A5R5 TCGA-HT-A74J 
       11.28         0.10        37.87        15.72         0.13        10.52 
TCGA-HW-7493 TCGA-P5-A5EY TCGA-P5-A5F2 TCGA-P5-A731 TCGA-P5-A735 TCGA-QH-A6X9 
       69.27         2.37         7.96         9.01         9.60         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6U6 
       16.50        16.70         2.07        19.59        62.17        35.15 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7QW TCGA-TM-A7CA TCGA-TQ-A7RV TCGA-VM-A8CA 
       26.93        19.99        15.06        34.78        61.41        13.51 
TCGA-WY-A85A TCGA-WY-A85E 
       43.40        20.81 

$subtype5
TCGA-DH-5141 TCGA-FG-8187 TCGA-FG-A60K TCGA-HT-A619 TCGA-CS-5394 TCGA-CS-5396 
       31.82        20.09        17.82        21.40         0.26        53.62 
TCGA-DB-5274 TCGA-DB-A4XA TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64U 
       75.25        18.84        31.63        30.12         5.98        27.81 
TCGA-DB-A64V TCGA-DB-A75K TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7US TCGA-DU-5870 
       29.23        12.10        30.21        17.19        23.21       182.33 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-7018 TCGA-DU-A76R TCGA-DU-A7T6 
       52.11        22.42        46.06        30.67        21.30        17.98 
TCGA-DU-A7TB TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YS TCGA-FG-5964 TCGA-FG-7634 
       51.52        78.21        95.57        15.32        52.21        15.35 
TCGA-FG-7637 TCGA-FG-8186 TCGA-FG-A6IZ TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7602 
       40.08        16.01        15.02         6.67         0.13        29.85 
TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7692 TCGA-HT-A4DV 
       22.06         0.23        14.27        16.24         2.96        26.04 
TCGA-HT-A615 TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7491 TCGA-HW-8322 
       16.93        15.35        11.05        56.58        68.32        24.92 
TCGA-KT-A74X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A737 TCGA-P5-A781 TCGA-QH-A65V 
       14.40        11.64        10.95        12.23         4.41        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       15.85        14.04        14.83        14.53        16.34        16.73 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       88.83        94.03        32.65        30.87         5.46        28.08 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD 
       41.10        40.93        29.85        32.61       123.65        75.25 
TCGA-S9-A6WE TCGA-S9-A6WP TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
      135.22        18.64        23.51         8.19         2.04        20.68 
TCGA-S9-A7QY TCGA-TM-A7C5 TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S TCGA-TQ-A7RG 
       28.37        49.32        24.79        33.24        14.93        19.69 
TCGA-TQ-A7RI TCGA-TQ-A7RN TCGA-TQ-A7RU TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS 
        2.04        33.73        33.93        39.16        37.05        23.21 

$subtype6
TCGA-CS-6665 TCGA-DH-A66B TCGA-FG-A87N TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A7UU 
       51.55        42.05        18.64        19.96        63.88        13.71 
TCGA-DU-6392 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU 
      211.17        62.96        14.99        33.27        29.85        26.17 
TCGA-E1-5304 TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YV TCGA-FG-5963 
       41.13        29.13         3.65        12.43        32.45        25.48 
TCGA-FG-A6J3 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7601 TCGA-HT-7606 TCGA-HT-7686 
       22.26        24.26         6.38         5.03        17.29        42.74 
TCGA-HT-8106 TCGA-HT-8563 TCGA-HT-A618 TCGA-HT-A61B TCGA-IK-7675 TCGA-RY-A83Z 
        0.10        28.27        16.83        17.52        19.00         9.90 
TCGA-S9-A6TV TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A84F 
       18.77         7.92        20.02        98.63        20.48        59.05 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84Q TCGA-TQ-A7RM 
       28.08        24.16        25.38        36.69 

$subtype7
TCGA-CS-6670 TCGA-DU-7300 TCGA-FG-A713 TCGA-IK-8125 TCGA-CS-6669 TCGA-DB-5278 
       46.88        62.01        20.45        42.77        49.12        91.13 
TCGA-DB-A64W TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-7009 TCGA-DU-7302 TCGA-DU-7309 
       14.40        14.56        17.46       154.36        60.30         2.76 
TCGA-DU-8164 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A7TC TCGA-DU-A7TG 
       21.40        25.55        21.57        95.11        37.38        44.42 
TCGA-E1-A7YY TCGA-FG-5962 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8189 
      146.14        47.77        22.55        20.61        28.34        22.52 
TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7480 TCGA-HT-7481 
        0.10        40.11         3.75        17.42        75.19        95.93 
TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7681 TCGA-HT-7688 
       23.18         4.57         3.16        56.09        44.68        31.69 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        6.90        14.53        39.09        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8019 TCGA-HT-8107 TCGA-HT-8109 
        5.33        35.47         1.64        33.01         0.46         5.56 
TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HT-A61A 
       29.59        13.74        20.22         0.10         1.81         6.38 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7495 TCGA-HW-8319 TCGA-P5-A5F0 TCGA-P5-A5F4 
       45.44        41.49        35.44        39.75         9.44         7.59 
TCGA-P5-A77X TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-RY-A847 TCGA-S9-A6TY TCGA-S9-A6WI 
        3.45        13.41         9.17        30.67        35.38        84.99 
TCGA-S9-A7IQ TCGA-S9-A7QZ TCGA-TM-A7C4 TCGA-TM-A7CF TCGA-TM-A84R TCGA-W9-A837 
       36.13        27.16        48.33        65.39        18.61        51.06 
TCGA-WY-A859 
       39.88 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.03     0.10     0.07     0.10     0.13     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  145.05   133.74   169.84   172.77   182.33   211.17   154.36 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  29.460   14.300   26.140   19.790   22.815   24.210   27.160 
[1] "0.0 - 145.1 (29.5)" "0.1 - 133.7 (14.3)" "0.1 - 169.8 (26.1)"
[4] "0.1 - 172.8 (19.8)" "0.1 - 182.3 (22.8)" "0.1 - 211.2 (24.2)"
[7] "0.1 - 154.4 (27.2)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 53 81
  subtype2 34 37
  subtype3 22 14
  subtype4 32 36
  subtype5 35 56
  subtype6 19 22
  subtype7 35 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53   81
  subtype2   34   37
  subtype3   22   14
  subtype4   32   36
  subtype5   35   56
  subtype6   19   22
  subtype7   35   39
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       53       34       22       32       35       19       35
  MALE         81       37       14       36       56       22       39
[1] 2 7
[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 42 83
  subtype2 12 51
  subtype3 20 12
  subtype4 22 42
  subtype5 51 37
  subtype6  5 35
  subtype7 34 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   83
  subtype2   12   51
  subtype3   20   12
  subtype4   22   42
  subtype5   51   37
  subtype6    5   35
  subtype7   34   36
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        42       12       20       22       51        5       34
  YES       83       51       12       42       37       35       36
[1] 2 7
[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       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          65               46                23
  subtype2          46               12                13
  subtype3           1                3                32
  subtype4          37               22                 9
  subtype5           3               25                63
  subtype6          33                5                 3
  subtype7           9               17                48
D8V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ASTROCYTOMA             65       46        1       37        3       33
  OLIGOASTROCYTOMA        46       12        3       22       25        5
  OLIGODENDROGLIOMA       23       13       32        9       63        3
                   clus
vv                  subtype7
  ASTROCYTOMA              9
  OLIGOASTROCYTOMA        17
  OLIGODENDROGLIOMA       48
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         6
  subtype2                                1     1                         6
  subtype3                                0     1                         1
  subtype4                                0     1                         3
  subtype5                                0     4                         2
  subtype6                                0     1                         0
  subtype7                                0     0                         3
          vv
clus       WHITE
  subtype1   126
  subtype2    62
  subtype3    31
  subtype4    62
  subtype5    83
  subtype6    40
  subtype7    71
D8V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   0        1        1        1        4
  BLACK OR AFRICAN AMERICAN               6        6        1        3        2
  WHITE                                 126       62       31       62       83
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   1        0
  BLACK OR AFRICAN AMERICAN               0        3
  WHITE                                  40       71
[1] 4 7
[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   9 112
  subtype2   3  64
  subtype3   3  29
  subtype4   4  58
  subtype5   8  78
  subtype6   2  39
  subtype7   3  69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  112
  subtype2    3   64
  subtype3    3   29
  subtype4    4   58
  subtype5    8   78
  subtype6    2   39
  subtype7    3   69
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            9        3        3        4        8        2
  NOT HISPANIC OR LATINO      112       64       29       58       78       39
                        clus
vv                       subtype7
  HISPANIC OR LATINO            3
  NOT HISPANIC OR LATINO       69
[1] 2 7
[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 = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 107  32
  subtype2  68  38
  subtype3  63  18
  subtype4 145  36
subtype1 subtype2 subtype3 subtype4 
     139      106       81      181 
subtype1 subtype2 subtype3 subtype4 
      32       38       18       36 
$subtype1
TCGA-DH-5141 TCGA-E1-A7YN TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       31.82        23.90        45.60       117.50         7.69        43.89 
TCGA-CS-4944 TCGA-CS-5395 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
       60.10        21.01        17.69        37.38        46.95        48.30 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5280 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A64O 
       75.25        72.92        36.56        18.84        39.78        25.48 
TCGA-DB-A64V TCGA-DB-A75O TCGA-DH-A66F TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5854 
       29.23        30.74        17.19        18.61        18.02         8.45 
TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6396 TCGA-DU-6407 TCGA-DU-6542 TCGA-DU-7012 
        6.81        17.49        75.16        94.52         2.40         6.54 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7290 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 
      117.40        90.77        10.36        25.91        41.98         5.10 
TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 
       23.74        19.13        24.43        24.99        33.96        20.98 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YD TCGA-E1-A7YH TCGA-E1-A7YJ TCGA-E1-A7YQ 
       78.21        95.57        14.30        93.21        19.46        51.88 
TCGA-E1-A7Z4 TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-8182 TCGA-FG-8188 
      145.05        18.77        41.33        15.35        13.68        14.96 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MY TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A87Q 
       32.61        38.27        23.70        21.53        28.54         5.72 
TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 
       27.52         0.03        16.54        40.34       106.95         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 
        5.03        29.85       122.47        17.29        22.06        45.99 
TCGA-HT-7611 TCGA-HT-7680 TCGA-HT-7689 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 
       57.60         0.76        14.96        39.48        19.23        50.63 
TCGA-HT-7860 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8563 
        0.49        16.24        63.55        13.78         0.23        28.27 
TCGA-HT-A4DS TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-8320 
        0.23        16.14        17.65        15.35         0.10        40.01 
TCGA-HW-A5KK TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F6 
       12.76         0.23         6.71         2.30         5.88         1.28 
TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A735 TCGA-P5-A736 TCGA-QH-A65S 
       10.42        11.64        10.95         9.60         7.56         2.53 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6X3 TCGA-QH-A870 TCGA-RY-A83X 
       19.33        14.83        14.53        10.29        12.99        30.87 
TCGA-RY-A840 TCGA-S9-A6TU TCGA-S9-A6TX TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 
       28.08        87.12        40.93        29.85        32.61        98.24 
TCGA-S9-A6U9 TCGA-S9-A6WD TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IY 
       95.93        75.25        19.86        18.61        14.07        23.51 
TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A84B TCGA-TM-A84O 
       18.54        10.39        99.06        31.59        24.92        33.24 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RP 
       14.93        23.80        21.37        44.09        36.69        30.05 
TCGA-TQ-A7RW TCGA-VM-A8CF TCGA-VV-A829 TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 
       26.99        20.02        37.05        16.01        13.32        43.96 
TCGA-WY-A85D 
       37.71 

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

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

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

subtype1 subtype2 subtype3 subtype4 
    0.03     0.10     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 
  145.05   211.17   182.33   156.23 
subtype1 subtype2 subtype3 subtype4 
  23.510   21.105   24.920   21.400 
[1] "0.0 - 145.1 (23.5)" "0.1 - 211.2 (21.1)" "0.1 - 182.3 (24.9)"
[4] "0.1 - 156.2 (21.4)"
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1 61 79
  subtype2 43 63
  subtype3 38 45
  subtype4 88 94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61   79
  subtype2   43   63
  subtype3   38   45
  subtype4   88   94
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       61       43       38       88
  MALE         79       63       45       94
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
          cls
clus        0  1
  subtype1 45 84
  subtype2 27 74
  subtype3 39 39
  subtype4 73 97
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   84
  subtype2   27   74
  subtype3   39   39
  subtype4   73   97
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        45       27       39       73
  YES       84       74       39       97
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          69               35                36
  subtype2          66               22                18
  subtype3           5               20                58
  subtype4          53               50                79
D9V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             69       66        5       53
  OLIGOASTROCYTOMA        35       22       20       50
  OLIGODENDROGLIOMA       36       18       58       79
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        10
  subtype2                                0     2                         3
  subtype3                                0     3                         2
  subtype4                                0     2                         6
          vv
clus       WHITE
  subtype1   125
  subtype2   100
  subtype3    75
  subtype4   171
D9V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   1        2        3        2
  BLACK OR AFRICAN AMERICAN              10        3        2        6
  WHITE                                 125      100       75      171
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus         0   1
  subtype1   9 121
  subtype2   3  94
  subtype3   8  67
  subtype4  12 163
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  121
  subtype2    3   94
  subtype3    8   67
  subtype4   12  163
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            9        3        8       12
  NOT HISPANIC OR LATINO      121       94       67      163
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 177  42
  subtype2 149  36
  subtype3  57  46
subtype1 subtype2 subtype3 
     219      185      103 
subtype1 subtype2 subtype3 
      42       36       46 
$subtype1
TCGA-DH-5141 TCGA-DH-A66B TCGA-FG-A60K TCGA-HT-A619 TCGA-HW-7490 TCGA-CS-4938 
       31.82        42.05        17.82        21.40        45.60       117.50 
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-5396 
        7.69        43.89        36.36        60.10         0.26        53.62 
TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-DB-5273 
       17.69        37.38        46.95        48.30        49.94        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-A4X9 
       75.25        47.93        72.92        50.86        36.56        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A64P TCGA-DB-A64Q 
       18.84        30.21        39.78        37.45        30.12         5.98 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A75K TCGA-DB-A75O TCGA-DH-5140 
       27.45        27.81        29.23        12.10        30.74        19.96 
TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UT 
       63.88        24.59        30.21        27.81        17.19        17.46 
TCGA-DH-A7UV TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6394 
       18.61         6.81       182.33        18.94        17.49        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 
       49.02        75.16        46.06        65.75        87.45        94.52 
TCGA-DU-6408 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 
      114.08       117.40        90.77        30.67        94.32        44.02 
TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76R 
       25.91        41.98        20.68        24.99        20.98        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5318 
      139.04        84.33        50.14        67.46        41.13        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YW 
       95.57       130.78        14.30        29.13        93.21        36.82 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
      145.05        32.35        39.48        42.54        41.33        15.35 
TCGA-FG-7637 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       40.08        13.68        14.24        14.96        32.61        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A70Y 
       18.71        23.70        14.76        21.53        15.02        28.54 
TCGA-FN-7833 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 
       27.52         6.67         0.13         0.03        16.54        40.34 
TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 
      106.95         4.01         5.03        29.85       122.47        17.29 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7676 TCGA-HT-7677 
       22.06        45.99        57.60         0.23         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7693 
        0.76         6.05        14.96         0.10         2.96        17.52 
TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8013 TCGA-HT-8111 
       19.23        50.63        23.61         3.68        63.55         0.23 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A614 TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       34.19        28.27         2.70        15.35        11.05         0.10 
TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KL TCGA-KT-A74X TCGA-P5-A5EV 
       68.32        40.01        24.92        28.87        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72W 
        6.71         2.30         5.88         7.96         1.28        10.42 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       11.64        10.95         9.01         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A780 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS 
       19.20         2.37         2.53        12.62        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-QH-A870 
       14.83        10.29        16.34        16.73        11.08        12.99 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 
       94.03        32.65        30.87         5.46        28.08        30.67 
TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 
       87.12        41.10        40.93        36.82        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WO 
       32.61        98.24        95.93       123.65        75.25        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       18.64        14.07        23.51         8.19         2.04        20.68 
TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-TM-A84B TCGA-TM-A84G TCGA-TM-A84H 
       18.54        99.06        30.05        24.92        40.64        30.44 
TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF 
       40.83        33.24        25.38        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       19.69        15.98         2.04        44.09        36.69        33.73 
TCGA-TQ-A7RP TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CE 
       30.05        25.87        33.93        26.99        45.93        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-WH-A86K 
       20.02        23.47        37.05        16.01        23.21        13.32 
TCGA-WY-A858 TCGA-WY-A85B TCGA-WY-A85D 
       43.96        45.80        37.71 

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

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

subtype1 subtype2 subtype3 
    0.03     0.07     0.10 
subtype1 subtype2 subtype3 
  182.33   172.77   211.17 
subtype1 subtype2 subtype3 
   27.45    23.31    17.52 
[1] "0.0 - 182.3 (27.4)" "0.1 - 172.8 (23.3)" "0.1 - 211.2 (17.5)"
D10V2, continuous
D10V3, binary
          cls
clus         0   1
  subtype1  91 131
  subtype2  90  96
  subtype3  49  54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   91  131
  subtype2   90   96
  subtype3   49   54
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       91       90       49
  MALE        131       96       54
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
          cls
clus         0   1
  subtype1  91 119
  subtype2  76  97
  subtype3  17  78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   91  119
  subtype2   76   97
  subtype3   17   78
     clus
vv    subtype1 subtype2 subtype3
  NO        91       76       17
  YES      119       97       78
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          76               67                79
  subtype2          48               44                94
  subtype3          69               16                18
D10V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             76       48       69
  OLIGOASTROCYTOMA        67       44       16
  OLIGODENDROGLIOMA       79       94       18
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         7
  subtype2                                0     3                         8
  subtype3                                1     2                         6
          vv
clus       WHITE
  subtype1   208
  subtype2   170
  subtype3    93
D10V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   3        3        2
  BLACK OR AFRICAN AMERICAN               7        8        6
  WHITE                                 208      170       93
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus         0   1
  subtype1  17 188
  subtype2  12 164
  subtype3   3  93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17  188
  subtype2   12  164
  subtype3    3   93
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           17       12        3
  NOT HISPANIC OR LATINO      188      164       93
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1  90  36
  subtype2  74  44
  subtype3  92  12
  subtype4 123  32
subtype1 subtype2 subtype3 subtype4 
     126      118      104      155 
subtype1 subtype2 subtype3 subtype4 
      36       44       12       32 
$subtype1
TCGA-CS-6665 TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
       51.55        45.60       117.50        17.69        26.76        37.38 
TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5279 TCGA-DB-A75O TCGA-DU-5847 TCGA-DU-5852 
       46.95        48.30        44.52        30.74        18.02         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        46.06        65.75        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
        2.40        11.47        62.96         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 
       90.77        44.02        25.91        41.98         5.10        23.74 
TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A6S7 TCGA-E1-5305 TCGA-E1-5319 
       20.68        19.13        15.48        20.98        79.99        95.57 
TCGA-E1-A7Z6 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-7634 
       32.35        25.48        36.82        18.77        41.33        15.35 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FN-7833 TCGA-HT-7469 
       13.68        14.24        14.96        32.61        27.52        11.54 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        0.03        16.54       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 
       29.85       122.47        22.06        45.99        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 
       14.27         0.16        16.24         0.76         6.05        42.74 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 
       14.96         0.10         0.10        17.52        39.48        19.23 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7882 
        0.23        50.63         0.49        23.61         3.68         3.72 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8111 
       16.24        63.55        12.23         0.10        13.78         0.23 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-8320 
       34.19        28.27        15.35         0.10        56.58        40.01 
TCGA-HW-8321 TCGA-IK-7675 TCGA-P5-A72W TCGA-P5-A730 TCGA-P5-A735 TCGA-P5-A780 
       42.54        19.00        10.42        10.95         9.60         2.37 
TCGA-QH-A6X3 TCGA-QH-A870 TCGA-RY-A83Z TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A7R3 
       10.29        12.99         9.90        87.12        36.82        99.06 
TCGA-S9-A89V TCGA-TM-A84I TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RW 
       18.71        28.08        25.38        23.80        21.37        26.99 
TCGA-VM-A8C8 TCGA-VM-A8CH TCGA-WH-A86K TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       45.93        23.47        13.32        45.80        46.88        37.71 

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

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

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

subtype1 subtype2 subtype3 subtype4 
    0.03     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  182.33   145.05   169.84   211.17 
subtype1 subtype2 subtype3 subtype4 
  21.175   21.895   25.365   21.300 
[1] "0.0 - 182.3 (21.2)" "0.1 - 145.1 (21.9)" "0.1 - 169.8 (25.4)"
[4] "0.1 - 211.2 (21.3)"
D11V2, continuous
D11V3, binary
          cls
clus        0  1
  subtype1 53 73
  subtype2 49 70
  subtype3 50 56
  subtype4 77 79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53   73
  subtype2   49   70
  subtype3   50   56
  subtype4   77   79
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       53       49       50       77
  MALE         73       70       56       79
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
          cls
clus        0  1
  subtype1 38 81
  subtype2 27 81
  subtype3 57 44
  subtype4 61 86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   81
  subtype2   27   81
  subtype3   57   44
  subtype4   61   86
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        38       27       57       61
  YES       81       81       44       86
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          58               36                32
  subtype2          74               23                22
  subtype3          13               26                67
  subtype4          46               41                69
D11V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             58       74       13       46
  OLIGOASTROCYTOMA        36       23       26       41
  OLIGODENDROGLIOMA       32       22       67       69
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         5
  subtype2                                1     2                         7
  subtype3                                0     4                         3
  subtype4                                0     2                         6
          vv
clus       WHITE
  subtype1   119
  subtype2   107
  subtype3    95
  subtype4   146
D11V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   0        2        4        2
  BLACK OR AFRICAN AMERICAN               5        7        3        6
  WHITE                                 119      107       95      146
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus         0   1
  subtype1   5 114
  subtype2   6 102
  subtype3  13  86
  subtype4   8 139
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  114
  subtype2    6  102
  subtype3   13   86
  subtype4    8  139
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        6       13        8
  NOT HISPANIC OR LATINO      114      102       86      139
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 84 13
  subtype2 55 21
  subtype3 95 24
  subtype4 49  7
  subtype5 26 37
  subtype6 70 22
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      97       76      119       56       63       92 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      13       21       24        7       37       22 
$subtype1
TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-4944 TCGA-CS-6186 TCGA-CS-6666 TCGA-CS-6667 
       45.60       117.50        60.10        17.69        46.95        48.30 
TCGA-DB-A4XD TCGA-DB-A64S TCGA-DB-A75O TCGA-DH-A7UV TCGA-DU-6396 TCGA-DU-6542 
       39.78        27.45        30.74        18.61        75.16         2.40 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-A5TP 
      117.40        90.77        44.02        25.91        41.98        33.27 
TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A7TA TCGA-E1-5303 TCGA-E1-A7YD TCGA-E1-A7Z4 
       24.99        20.98        84.33        67.46        14.30       145.05 
TCGA-E1-A7Z6 TCGA-FG-6691 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 
       32.35        41.33        13.68        14.24        14.96        32.61 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 
       38.27        18.71        27.52         0.03        16.54        40.34 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 
      106.95       172.77         4.01         5.03        29.85       122.47 
TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7689 
       17.29        45.99        57.60         0.76         6.05        14.96 
TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8013 
       17.52        19.23        50.63        23.61         3.68        63.55 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A74O TCGA-HW-A5KL TCGA-HW-A5KM 
        0.23        34.19        28.27         0.10        28.87        20.71 
TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72W 
       19.00         0.23         6.71         2.30         5.88        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-QH-A6X3 TCGA-QH-A870 TCGA-RY-A840 
       13.25        11.64        10.95        10.29        12.99        28.08 
TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6WO TCGA-S9-A7QX TCGA-S9-A7R3 
       87.12        36.82        25.81        18.61        18.54        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84Q TCGA-TM-A84T 
       30.05        31.59        24.92        30.44        25.38        23.80 
TCGA-TQ-A7RF TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-VM-A8C8 TCGA-VM-A8CF TCGA-VM-A8CH 
       21.37        44.09        36.69        45.93        20.02        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85B TCGA-WY-A85C 
       37.05        16.01        13.32        43.96        45.80        46.88 
TCGA-WY-A85D 
       37.71 

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

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

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

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

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

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.03     0.07     0.10     0.10     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  172.77   134.27   169.84   123.65   133.74   211.17 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  27.450   25.955   21.570   24.690   15.720   22.355 
[1] "0.0 - 172.8 (27.4)" "0.1 - 134.3 (26.0)" "0.1 - 169.8 (21.6)"
[4] "0.1 - 123.7 (24.7)" "0.1 - 133.7 (15.7)" "0.1 - 211.2 (22.4)"
D12V2, continuous
D12V3, binary
          cls
clus        0  1
  subtype1 34 64
  subtype2 36 41
  subtype3 59 61
  subtype4 23 34
  subtype5 31 32
  subtype6 46 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   64
  subtype2   36   41
  subtype3   59   61
  subtype4   23   34
  subtype5   31   32
  subtype6   46   46
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       34       36       59       23       31       46
  MALE         64       41       61       34       32       46
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
          cls
clus        0  1
  subtype1 34 58
  subtype2 19 55
  subtype3 47 66
  subtype4 37 17
  subtype5 11 45
  subtype6 35 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   58
  subtype2   19   55
  subtype3   47   66
  subtype4   37   17
  subtype5   11   45
  subtype6   35   51
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        34       19       47       37       11       35
  YES       58       55       66       17       45       51
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          55               27                16
  subtype2          35               20                22
  subtype3          35               28                57
  subtype4           2               11                44
  subtype5          41               11                11
  subtype6          23               29                40
D12V6, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ASTROCYTOMA             55       35       35        2       41       23
  OLIGOASTROCYTOMA        27       20       28       11       11       29
  OLIGODENDROGLIOMA       16       22       57       44       11       40
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         2
  subtype2                                0     2                         3
  subtype3                                0     2                         5
  subtype4                                0     3                         2
  subtype5                                1     1                         7
  subtype6                                0     0                         2
          vv
clus       WHITE
  subtype1    94
  subtype2    72
  subtype3   112
  subtype4    50
  subtype5    53
  subtype6    86
D12V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                   0        2        2        3        1
  BLACK OR AFRICAN AMERICAN               2        3        5        2        7
  WHITE                                  94       72      112       50       53
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   0
  BLACK OR AFRICAN AMERICAN               2
  WHITE                                  86
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
          cls
clus         0   1
  subtype1   6  81
  subtype2   4  69
  subtype3   5 110
  subtype4   8  44
  subtype5   3  55
  subtype6   6  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   81
  subtype2    4   69
  subtype3    5  110
  subtype4    8   44
  subtype5    3   55
  subtype6    6   82
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        4        5        8        3        6
  NOT HISPANIC OR LATINO       81       69      110       44       55       82
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
