[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/15082624/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LGG-TP/15115118/LGG-TP.mergedcluster.txt"

nPatients in clinical file=475, in cluster file=516, common to both=475
[1]  12 475
[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 
156 110 206 
  1   2   3 
156 110 206 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
208  72 156  39 
  1   2   3   4 
208  72 156  39 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
52 62 69 75 
 1  2  3  4 
52 62 69 75 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
 67 132  59 
  1   2   3 
 67 132  59 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4   5 
124 100  99 128  24 
  1   2   3   4   5 
124 100  99 128  24 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7 
124  65  33  61  83  37  72 
  1   2   3   4   5   6   7 
124  65  33  61  83  37  72 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
124 103 172  72 
  1   2   3   4 
124 103 172  72 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
202 172  97 
  1   2   3 
202 172  97 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
173 143 152 
  1   2   3 
173 143 152 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 83 125 178  82 
  1   2   3   4 
 83 125 178  82 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "DCC_UPLOAD_DATE"                       
 [7] "GENDER"                                
 [8] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
 [9] "DAYS_TO_LAST_KNOWN_ALIVE"              
[10] "RADIATION_THERAPY"                     
[11] "KARNOFSKY_PERFORMANCE_SCORE"           
[12] "HISTOLOGICAL_TYPE"                     
[13] "RADIATIONS_RADIATION_REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCH_NUMBER"                          

Input Data has 16 rows and 475 columns.

[1] "Batch" "16"   
[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=92,	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=356,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 9:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 10:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH_NUMBER':	nDistinctValues=21,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 475 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"                        
[2] "GENDER"                                
[3] "KARNOFSKY_PERFORMANCE_SCORE"           
[4] "HISTOLOGICAL_TYPE"                     
[5] "RADIATIONS_RADIATION_REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 5 4
  subtype2 7 3
  subtype3 5 3
subtype1 subtype2 subtype3 
       9       10        8 
subtype1 subtype2 subtype3 
       4        3        3 
$subtype1
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-DB-5273 TCGA-DB-5280 TCGA-DH-5142 
       43.89        18.15        10.62        81.96        36.56        30.31 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5322 
       50.14        67.46       130.78 

$subtype2
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-DB-5274 TCGA-DB-5275 TCGA-DH-5140 
       64.64         0.10         9.96        75.25        47.93        19.96 
TCGA-DH-5141 TCGA-DH-5144 TCGA-E1-5304 TCGA-E1-5318 
       31.82         8.02        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        50.17        78.28 
TCGA-DH-5143 TCGA-E1-5311 
       14.40       134.27 

subtype1 subtype2 subtype3 
   10.62     0.10    14.40 
subtype1 subtype2 subtype3 
  130.78    78.21   134.27 
subtype1 subtype2 subtype3 
  43.890   36.475   61.890 
[1] "10.6 - 130.8 (43.9)" "0.1 - 78.2 (36.5)"   "14.4 - 134.3 (61.9)"
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, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1           7                2                 0
  subtype2           2                3                 5
  subtype3           1                4                 3
D1V5, 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"
D1V6, binary
          cls
clus       0 1
  subtype1 7 2
  subtype2 8 2
  subtype3 5 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    2
  subtype2    8    2
  subtype3    5    3
     clus
vv    subtype1 subtype2 subtype3
  NO         7        8        5
  YES        2        2        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       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 3 4
  subtype3 6 1
  subtype4 5 1
subtype1 subtype2 subtype3 subtype4 
       7        7        7        6 
subtype1 subtype2 subtype3 subtype4 
       4        4        1        1 
$subtype1
TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5395 TCGA-DB-5273 TCGA-DB-5280 TCGA-E1-5302 
       43.89        10.62        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 
       18.15        47.93        50.86        19.96        30.31        41.13 
TCGA-E1-5322 
      130.78 

$subtype3
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-DB-5274 TCGA-DH-5141 TCGA-DH-5144 
       64.64         0.10         9.96        75.25        31.82         8.02 
TCGA-E1-5318 
       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        50.17        78.28        14.40       134.27 

subtype1 subtype2 subtype3 subtype4 
   10.62    18.15     0.10    14.40 
subtype1 subtype2 subtype3 subtype4 
   81.96   130.78    78.21   134.27 
subtype1 subtype2 subtype3 subtype4 
   43.89    41.13    31.82    75.60 
[1] "10.6 - 82.0 (43.9)"  "18.1 - 130.8 (41.1)" "0.1 - 78.2 (31.8)"  
[4] "14.4 - 134.3 (75.6)"
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, 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
D2V5, 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"
D2V6, binary
          cls
clus       0 1
  subtype1 6 1
  subtype2 6 1
  subtype3 5 2
  subtype4 3 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2    6    1
  subtype3    5    2
  subtype4    3    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6        6        5        3
  YES        1        1        2        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       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 128  28
  subtype2  66  43
  subtype3 182  23
subtype1 subtype2 subtype3 
     156      109      205 
subtype1 subtype2 subtype3 
      28       43       23 
$subtype1
TCGA-CS-4938 TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
        4.70        18.15        40.18        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XC 
        7.56        47.93        50.86        36.56        78.28        46.72 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64X TCGA-DB-A75O TCGA-DB-A75P 
       39.78        37.45        33.57        18.51        30.74        16.18 
TCGA-DH-5140 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       19.96        14.40        42.05        27.81        17.19        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5853 TCGA-DU-5871 TCGA-DU-6399 TCGA-DU-6401 
        3.45        18.61        13.38        18.94        65.75        87.45 
TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7014 
      114.08        62.96       156.23        14.99       105.21       117.40 
TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A5TU 
       26.30        44.02        23.31        15.48        15.12         3.65 
TCGA-DU-A6S7 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5307 
        7.23         7.13       124.50        50.14        67.46        57.93 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-FG-5963 TCGA-FG-6689 TCGA-FG-6690 
       32.45        36.82        32.35        25.48        14.93        24.99 
TCGA-FG-6691 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MY 
       23.97        13.68        14.24        14.96        32.61        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A70Y TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 
       14.76        16.41        28.54        27.52        11.54        40.11 
TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 
        3.75         6.54        24.26         6.38        40.34       106.95 
TCGA-HT-7485 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7686 
        4.01        23.18       122.47        57.60         0.16        42.74 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7857 
       31.69        14.96         0.10        17.52        19.23         0.23 
TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 
       23.61         3.68        11.28        31.43        63.55        37.87 
TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A5R7 TCGA-HT-A5RB 
        0.10         0.23        34.19        28.27        20.22         0.10 
TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74O TCGA-HW-7489 
        2.70         1.81        16.83        17.52         0.10         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-A5KL TCGA-HW-A5KM 
       19.23        35.90        21.70        19.59        20.81        20.71 
TCGA-IK-7675 TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F4 TCGA-P5-A5F6 
       19.00         6.71         2.30         5.88         0.76         1.28 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A733 TCGA-QH-A65S TCGA-QH-A6CW TCGA-QH-A6X3 
       10.42        13.25        13.61         2.53        13.61        10.29 
TCGA-QH-A6XA TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6UA 
       16.50        62.17        87.12        17.62        16.08         5.85 
TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A7QX 
       80.12        18.61        14.07         7.92        20.02        13.12 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 
       99.06        30.05        98.63        18.71        11.97        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       34.78        48.39        59.05        30.44        28.08        24.16 
TCGA-TM-A84L TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CH TCGA-VV-A86M TCGA-WH-A86K 
       40.83        26.99        43.04        23.47        16.01        13.32 
TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        39.88        43.40        45.80        46.88        37.71 

$subtype2
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        7.69        43.89        21.01         6.38        17.69        23.84 
TCGA-DB-5270 TCGA-DB-A4X9 TCGA-DB-A64O TCGA-DH-A669 TCGA-DU-5847 TCGA-DU-5852 
      122.73        46.42        25.48        30.21        18.02         6.74 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6402 
        8.45         6.81        17.49       211.17        49.02         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 
       11.64       133.74        19.89        16.83        94.52         7.96 
TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7290 TCGA-DU-7292 
       11.47         6.54         8.84        90.77        10.36         7.96 
TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       18.94        25.91        41.98         5.10        23.74        14.60 
TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TW 
       20.68        19.13        16.96        12.59         4.96         5.65 
TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ 
       12.20        11.41        26.76        77.88         7.50         0.56 
TCGA-E1-5304 TCGA-F6-A8O4 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 
       41.13         0.20        36.82        18.77        18.44        20.09 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87Q 
       10.72        18.38        22.26        10.78        48.69         5.72 
TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7606 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 
       16.54        17.42        17.29         0.49         3.72        16.24 
TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 
       12.23         2.50        13.78        15.72         0.23         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A619 TCGA-HT-A61C 
        0.07        27.35         5.33        16.14        21.40        17.65 
TCGA-HT-A74H TCGA-HT-A74J TCGA-HW-8322 TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EV 
        2.43        10.52        17.82        12.76        14.40         0.23 
TCGA-P5-A5F0 TCGA-P5-A72U TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X9 
        4.11         0.16        19.33        14.53        12.23         1.91 
TCGA-QH-A6XC TCGA-QH-A870 TCGA-RY-A83Z TCGA-RY-A845 TCGA-S9-A6TY TCGA-S9-A6U0 
        5.03        12.99         9.90        19.59        31.33        22.95 
TCGA-S9-A6WM TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7QW TCGA-S9-A7R1 
       19.86        36.13        22.32         7.13        15.06       169.84 
TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TQ-A7RH TCGA-VM-A8CD TCGA-VW-A8FI 
       10.39        49.45        24.92        15.98         7.89         8.05 
TCGA-WY-A85E 
       20.81 

$subtype3
TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6669 
       10.62        64.64         0.10         9.96         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
        6.61        81.96        75.25        72.92        50.17        44.52 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P 
       18.84        30.21        72.95        31.63        24.20        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        31.40        27.45        27.81        29.23        14.40 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 
       12.10        11.24        17.88        31.82        30.31         8.02 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5870 
       17.19        54.25        13.12        14.56        17.46       182.33 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 
       15.16        52.11        22.42        75.16        46.06         1.22 
TCGA-DU-6542 TCGA-DU-7009 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 
        7.73       138.28        30.67        94.32        62.01        60.30 
TCGA-DU-7309 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A6S2 TCGA-DU-A6S3 
        2.76        21.40        14.17        14.24         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC 
       77.98         5.98        21.30        17.98        42.31        23.51 
TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       44.42        79.99       134.27        78.21        95.57       130.78 
TCGA-E1-A7YO TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 
       75.02        14.33         0.23        47.77        34.36        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 
       17.88        22.55        20.61        12.95        16.01        20.09 
TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
       22.52        38.27        18.71        17.82        15.02        16.44 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FG-A87N TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 
       36.66        20.45        13.58         0.10         6.67         0.13 
TCGA-HT-7472 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7602 
        0.03        75.19        95.93       172.77         5.03        29.85 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 
        4.57         3.16        22.06        45.99        56.09         0.23 
TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 
       14.27        16.24         0.76        44.68         6.05         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        0.10         2.96         6.90        14.53        39.48        39.09 
TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 
       50.63        37.15         0.33         0.13         5.33        35.47 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 
        1.64         9.40         0.10        33.01         6.25         0.46 
TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-A4DV TCGA-HT-A615 TCGA-HT-A74K TCGA-HT-A74L 
        5.56        29.59        26.04        16.93        15.35        11.05 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-A5KJ 
       29.92        19.89        40.18         4.31        21.60        20.35 
TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F2 TCGA-P5-A72Z 
       42.77        14.40         1.64         2.37         7.63        11.64 
TCGA-P5-A730 TCGA-P5-A731 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        0.20         9.01        15.16        12.62        15.85        14.04 
TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       14.83         2.20         9.17        14.53        16.34        16.73 
TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       11.08        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TV TCGA-S9-A6TW 
        5.46        28.08         2.07        30.67        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 
       34.49        28.70        23.64        32.61        98.24        95.93 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
      106.39        69.50        72.59        32.45        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       15.91        15.16        23.51         8.19         2.04        17.03 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A84C TCGA-TM-A84G 
       28.37        13.02        31.59        49.32        16.18        40.64 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS 
       30.08        13.51         0.10        35.93        37.05        23.21 
TCGA-W9-A837 
       51.06 

subtype1 subtype2 subtype3 
    0.10     0.07     0.03 
subtype1 subtype2 subtype3 
  156.23   211.17   182.33 
subtype1 subtype2 subtype3 
  20.465   15.980   20.350 
[1] "0.1 - 156.2 (20.5)" "0.1 - 211.2 (16.0)" "0.0 - 182.3 (20.4)"
D3V2, continuous
D3V3, binary
          cls
clus         0   1
  subtype1  62  94
  subtype2  56  54
  subtype3  88 118
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   62   94
  subtype2   56   54
  subtype3   88  118
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       62       56       88
  MALE         94       54      118
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          90               41                25
  subtype2          52               31                27
  subtype3          34               46               126
D3V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             90       52       34
  OLIGOASTROCYTOMA        41       31       46
  OLIGODENDROGLIOMA       25       27      126
[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"
D3V6, binary
          cls
clus         0   1
  subtype1  34 122
  subtype2  24  86
  subtype3  34 172
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34  122
  subtype2   24   86
  subtype3   34  172
     clus
vv    subtype1 subtype2 subtype3
  NO        34       24       34
  YES      122       86      172
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         2
  subtype2                                1     3                         9
  subtype3                                0     5                         4
          vv
clus       WHITE
  subtype1   151
  subtype2    96
  subtype3   190
D3V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   0        3        5
  BLACK OR AFRICAN AMERICAN               2        9        4
  WHITE                                 151       96      190
[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   6 136
  subtype2   5  99
  subtype3   7 184
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  136
  subtype2    5   99
  subtype3    7  184
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        5        7
  NOT HISPANIC OR LATINO      136       99      184
[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 173  34
  subtype2  36  36
  subtype3 138  17
  subtype4  32   7
subtype1 subtype2 subtype3 subtype4 
     207       72      155       39 
subtype1 subtype2 subtype3 subtype4 
      34       36       17        7 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6290 TCGA-CS-6665 
        4.70        43.89        18.15        40.18        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5280 
        8.48         7.56        81.96        47.93        50.86        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       78.28        46.42        30.21        46.72        39.78        37.45 
TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       33.57        27.45        18.51        11.24        17.88        30.74 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       30.31        14.40        42.05        27.81        17.19        13.38 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 
        3.45        18.61        17.46        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-7010 TCGA-DU-7011 
      114.08         7.73        62.96       156.23        14.99       105.21 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 
      117.40        90.77        26.30        44.02        25.91        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP 
       41.98         2.76        20.68        16.96        15.48        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76O 
       12.59        15.12         3.65         5.65         7.23         7.13 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-DU-A7TC TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
      124.50        77.88        23.51        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5322 TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-F6-A8O4 
       79.99        57.93       130.78        36.82        32.35         0.20 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-8188 
       36.82        14.93        24.99        17.88        14.24        14.96 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
       32.61        38.27        18.71        23.70        14.76        16.41 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A711 TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7472 
       22.26        28.54        48.69        27.52        40.11         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7603 TCGA-HT-7604 
      106.95       172.77         4.01         5.03        23.18       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-8563 TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 
        0.23        34.19        28.27        20.22         0.10         2.70 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7489 
        1.81        16.83        17.52        10.52         0.10         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL 
       19.23        35.90        21.70        21.60        19.59        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 
       20.71        19.00         0.23         6.71         2.30         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A731 TCGA-P5-A733 
        7.63         0.76        10.42        13.25         9.01        13.61 
TCGA-QH-A65S TCGA-QH-A6CW TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A870 
        2.53        13.61        10.29         1.91        16.50        12.99 
TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        9.90         2.07        19.59        62.17        87.12        18.77 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WO 
       28.70        17.62        16.08        98.24        95.93        18.61 
TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX 
       14.07         7.92         7.13        20.02        15.06        13.12 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 
       99.06        30.05        98.63        31.59        11.97        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L 
       34.78        48.39        59.05        30.44        28.08        40.83 
TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CH 
       25.38        23.80        15.98        26.99        43.04        23.47 
TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B 
       16.01        13.32        43.96        39.88        43.40        45.80 
TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E 
       46.88        37.71        20.81 

$subtype2
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-DH-5140 
        7.69        21.01         6.38        17.69        23.84        19.96 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6402 TCGA-DU-6403 
       18.02         6.74         8.45       211.17         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 
      133.74        19.89        16.83        11.47         6.54         8.84 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT 
       10.36         7.96         5.10        23.74        19.13         4.96 
TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7TB TCGA-DU-A7TD TCGA-DU-A7TJ 
       12.20        11.41        26.76        42.31         7.50         0.56 
TCGA-E1-A7YV TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z 
       32.45        18.77        18.44        10.72        18.38        10.78 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 
       13.58         5.72        11.54         0.23         0.49         3.72 
TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS 
       16.24        12.23         0.10        13.78        15.72         0.23 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HW-A5KK 
       27.35         5.33        16.14        17.65         2.43        12.76 
TCGA-KT-A7W1 TCGA-P5-A72U TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XC TCGA-S9-A6U0 
       14.40         0.16        14.53        12.23         5.03        22.95 
TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-S9-A89V 
        5.85        19.86        15.91        22.32        10.39        18.71 
TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84J TCGA-VM-A8CD TCGA-VW-A8FI 
       49.45        24.92        16.18        24.16         7.89         8.05 

$subtype3
TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 
       10.62        64.64         0.10         9.96         8.02         6.61 
TCGA-DB-5274 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH 
       75.25        50.17        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-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F 
       14.40        12.10        31.82         8.02        30.21        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 
       54.25        13.12        14.56       182.33        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7018 
       22.42        46.06         1.22         7.96       138.28        30.67 
TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A6S2 
       94.32        62.01        60.30        21.40        14.17         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-E1-5311 
        2.70        77.98         5.98        21.30        17.98       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 
       78.21        95.57        75.02        14.33         0.23        47.77 
TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8186 
       34.36        15.35        40.08        22.55        20.61        16.01 
TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-HT-7467 
       20.09        17.82        15.02        16.44        36.66         0.10 
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-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 
        0.23        14.27        16.24        44.68         0.10         2.96 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 
        6.90        14.53        37.15         0.33         0.13        35.47 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-A4DV TCGA-HT-A5R9 
        1.64         9.40         6.25         5.56        26.04         0.07 
TCGA-HT-A615 TCGA-HT-A619 TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 
       16.93        21.40        15.35        11.05        29.92        19.89 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X 
       40.18         4.31        17.82        20.35        42.77        14.40 
TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-P5-A72Z TCGA-P5-A730 TCGA-QH-A65R TCGA-QH-A65V 
        1.64         4.11        11.64         0.20        15.16        12.62 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 
       15.85        14.04        14.83         2.20         9.17        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-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 TCGA-S9-A6TW 
       59.38        30.87         5.46        28.08        30.67        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD 
       34.49        31.33        23.64        32.61       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IY 
       72.59        32.45        31.10        15.16        36.13        23.51 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.19         2.04        17.03        28.37        13.02       169.84 
TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S TCGA-VM-A8CA 
       49.32        40.64        24.79        33.24        14.93        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 
        0.10        35.93        37.05        23.21        51.06 

$subtype4
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-A64O TCGA-DB-A75P TCGA-DU-7298 
        7.40       122.73        72.92        25.48        16.18        18.94 
TCGA-DU-8162 TCGA-DU-A7TG TCGA-FG-5963 TCGA-FG-6691 TCGA-FG-7643 TCGA-FG-8181 
       14.60        44.42        25.48        23.97        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8189 TCGA-FG-A713 TCGA-HT-7479 TCGA-HT-7602 TCGA-HT-7607 
       13.68        22.52        20.45        40.34        29.85         3.16 
TCGA-HT-7680 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7880 TCGA-HT-7902 
        0.76         0.10        39.48        39.09         5.33        31.43 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 TCGA-HT-8113 TCGA-HT-8558 
        0.10        37.87        33.01         0.46        29.59        13.74 
TCGA-HT-A5R5 TCGA-HT-A61A TCGA-P5-A5EY TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-S9-A6WG 
        0.13         6.38         2.37         1.28        19.33        80.12 
TCGA-S9-A6WI TCGA-TM-A84R TCGA-VM-A8C9 
       84.99        18.61        30.08 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.10     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 
  172.77   211.17   182.33   122.73 
subtype1 subtype2 subtype3 subtype4 
  20.680   12.495   20.090   20.090 
[1] "0.0 - 172.8 (20.7)" "0.1 - 211.2 (12.5)" "0.1 - 182.3 (20.1)"
[4] "0.1 - 122.7 (20.1)"
D4V2, continuous
D4V3, binary
          cls
clus         0   1
  subtype1  87 121
  subtype2  33  39
  subtype3  67  89
  subtype4  21  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   87  121
  subtype2   33   39
  subtype3   67   89
  subtype4   21   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       87       33       67       21
  MALE        121       39       89       18
[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, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1         112               65                31
  subtype2          46               12                14
  subtype3           4               31               121
  subtype4          14               11                14
D4V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA            112       46        4       14
  OLIGOASTROCYTOMA        65       12       31       11
  OLIGODENDROGLIOMA       31       14      121       14
[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"
D4V6, binary
          cls
clus         0   1
  subtype1  51 157
  subtype2  15  57
  subtype3  21 135
  subtype4   5  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51  157
  subtype2   15   57
  subtype3   21  135
  subtype4    5   34
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        51       15       21        5
  YES      157       57      135       34
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         5
  subtype2                                1     3                         5
  subtype3                                0     4                         3
  subtype4                                0     0                         2
          vv
clus       WHITE
  subtype1   199
  subtype2    63
  subtype3   143
  subtype4    35
D4V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   1        3        4        0
  BLACK OR AFRICAN AMERICAN               5        5        3        2
  WHITE                                 199       63      143       35
[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   8 185
  subtype2   2  66
  subtype3   6 137
  subtype4   2  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  185
  subtype2    2   66
  subtype3    6  137
  subtype4    2   34
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            8        2        6        2
  NOT HISPANIC OR LATINO      185       66      137       34
[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 45  6
  subtype2 31 30
  subtype3 59 10
  subtype4 62 13
subtype1 subtype2 subtype3 subtype4 
      51       61       69       75 
subtype1 subtype2 subtype3 subtype4 
       6       30       10       13 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-5273 
        4.70        43.89        17.69        23.84        12.43        81.96 
TCGA-DB-5276 TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DH-5143 TCGA-DU-5874 TCGA-DU-6395 
       72.92        33.57        31.63        14.40        15.16        49.02 
TCGA-DU-7304 TCGA-DU-8163 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-E1-5302 TCGA-FG-6688 
       23.31        20.68        12.59        15.12        50.14        18.77 
TCGA-FG-6691 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8191 
       23.97        13.68        16.01        20.09        14.96        32.61 
TCGA-FG-A4MW TCGA-FG-A60J TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7602 
       18.38        14.76        40.34       106.95         4.01        29.85 
TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7691 
       57.60        14.27         0.16         0.76        44.68         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8111 
        2.96        17.52        39.48        23.61         3.68         0.23 
TCGA-HT-8114 TCGA-HT-A5R5 TCGA-HW-8319 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ 
       34.19         0.13        21.70         6.71         2.37         2.30 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 
        5.88         7.63         1.28 

$subtype2
TCGA-CS-4943 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-A4XG TCGA-DH-5140 
       18.15         6.38         8.48        50.86        72.95        19.96 
TCGA-DH-5142 TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-6393 
       30.31        18.02         6.74         8.45         6.81        52.11 
TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       22.42        75.16         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7301 
      156.23        14.99         6.54         8.84        10.36        25.91 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TT TCGA-DU-A5TU 
        5.10        23.74        19.13        14.17         4.96         3.65 
TCGA-DU-A5TY TCGA-E1-5304 TCGA-E1-5318 TCGA-E1-5322 TCGA-FG-7636 TCGA-FG-8185 
       12.20        41.13        78.21       130.78        17.88        14.24 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7606 
       38.27        10.72        11.54        24.26       122.47        17.29 
TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        0.23         0.49         3.72        16.24         9.40        63.55 
TCGA-HT-8104 TCGA-HT-A5R9 TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KK TCGA-HW-A5KM 
       12.23         0.07        40.18        17.82        12.76        20.71 
TCGA-IK-7675 
       19.00 

$subtype3
TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 
       10.62        40.18         0.10         9.96         8.02         6.61 
TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XC 
       47.93        44.52        36.56        78.28        18.84        46.72 
TCGA-DB-A4XD TCGA-DH-5141 TCGA-DH-5144 TCGA-DU-5853 TCGA-DU-5870 TCGA-DU-5871 
       39.78        31.82         8.02        13.38       182.33        18.94 
TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 
       17.49       211.17        46.06        65.75        87.45        94.52 
TCGA-DU-7011 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7306 
      105.21       117.40        90.77        30.67        26.30        41.98 
TCGA-DU-8167 TCGA-DU-A5TW TCGA-E1-5303 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5964 
       15.48         5.65        67.46        95.57        14.33        34.36 
TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-A4MX TCGA-FG-A4MY 
       15.35        40.08        22.55        20.61        18.71        23.70 
TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7483 
        6.67         0.03        16.54         6.54         6.38       172.77 
TCGA-HT-7601 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7684 
        5.03        22.06        45.99         0.23        16.24         6.05 
TCGA-HT-7686 TCGA-HT-7689 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7875 TCGA-HT-8105 
       42.74        14.96        19.23        50.63         0.33         6.25 
TCGA-HT-8106 TCGA-HT-8110 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-8321 
        0.10        13.78         8.32        19.23        21.60        19.59 
TCGA-HW-A5KJ TCGA-IK-8125 TCGA-P5-A5EV 
       20.35        42.77         0.23 

$subtype4
TCGA-CS-5390 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5274 TCGA-DB-5278 TCGA-DB-A4X9 
       64.64         7.40       122.73        75.25        50.17        46.42 
TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-6400 TCGA-DU-7009 
       30.21        37.45        14.56        17.46         1.22       138.28 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 
        7.96        94.32        18.94        62.01        60.30         2.76 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TP TCGA-E1-5305 TCGA-E1-5307 
       14.60        21.40        16.96        14.24        79.99        57.93 
TCGA-E1-5311 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
      134.27        47.77        25.48        36.82        14.93        24.99 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7471 
       20.09        12.95        22.52         0.10        40.11         0.13 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 
        3.75        17.42        75.19        95.93        23.18         4.57 
TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7694 
        3.16        56.09         0.10        31.69         0.10         6.90 
TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 
       14.53        39.09        37.15         0.13         5.33        35.47 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       11.28        31.43         1.64         0.10        37.87        33.01 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV 
        0.46         5.56        29.59        13.74        15.72        26.04 
TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7493 TCGA-HW-7495 
       20.22         0.10        29.92        19.89        35.90         4.31 
TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-P5-A5F4 
        1.64         4.11         0.76 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.07     0.03     0.10 
subtype1 subtype2 subtype3 subtype4 
  106.95   156.23   211.17   138.28 
subtype1 subtype2 subtype3 subtype4 
   17.52    16.83    20.35    20.09 
[1] "0.1 - 107.0 (17.5)" "0.1 - 156.2 (16.8)" "0.0 - 211.2 (20.4)"
[4] "0.1 - 138.3 (20.1)"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 19 33
  subtype2 33 29
  subtype3 20 49
  subtype4 39 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   33
  subtype2   33   29
  subtype3   20   49
  subtype4   39   36
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19       33       20       39
  MALE         33       29       49       36
[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, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          20               21                11
  subtype2          31               11                20
  subtype3          20               21                28
  subtype4          15               17                43
D5V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             20       31       20       15
  OLIGOASTROCYTOMA        21       11       21       17
  OLIGODENDROGLIOMA       11       20       28       43
[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"
D5V6, binary
          cls
clus        0  1
  subtype1 16 36
  subtype2 22 40
  subtype3 30 39
  subtype4 19 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   36
  subtype2   22   40
  subtype3   30   39
  subtype4   19   56
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        16       22       30       19
  YES       36       40       39       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"
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         3    49
  subtype2                         2    60
  subtype3                         3    65
  subtype4                         3    72
D5V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  BLACK OR AFRICAN AMERICAN        3        2        3        3
  WHITE                           49       60       65       72
[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"
D5V8, binary
          cls
clus        0  1
  subtype1  3 48
  subtype2  2 56
  subtype3  4 60
  subtype4  4 69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   48
  subtype2    2   56
  subtype3    4   60
  subtype4    4   69
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        4        4
  NOT HISPANIC OR LATINO       48       56       60       69
[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 57  9
  subtype2 92 39
  subtype3 48 11
subtype1 subtype2 subtype3 
      66      131       59 
subtype1 subtype2 subtype3 
       9       39       11 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-5390 TCGA-CS-6186 TCGA-CS-6665 TCGA-CS-6670 
        4.70        43.89        64.64        17.69        12.43         6.61 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DH-5143 
       75.25        72.92        37.45        33.57        31.63        14.40 
TCGA-DU-5853 TCGA-DU-6395 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7294 TCGA-DU-7298 
       13.38        49.02       138.28        14.99        94.32        18.94 
TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-A5TS TCGA-E1-5302 TCGA-E1-5319 TCGA-FG-5963 
       20.68        16.96        15.12        50.14        95.57        25.48 
TCGA-FG-6688 TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 
       18.77        15.35        20.61        13.68        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A60J TCGA-HT-7467 TCGA-HT-7472 TCGA-HT-7479 
       14.96        32.61        14.76         0.10         0.03        40.34 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7611 TCGA-HT-7620 
       95.93       106.95         4.01        29.85        57.60        14.27 
TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7854 
        0.16         0.76        44.68        14.96         2.96        39.48 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
       50.63        23.61         3.68         5.33        35.47        11.28 
TCGA-HT-8010 TCGA-HT-8013 TCGA-HT-8111 TCGA-HT-A5R5 TCGA-HW-7486 TCGA-HW-7487 
        1.64        63.55         0.23         0.13        29.92        19.89 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8322 TCGA-P5-A5EW TCGA-P5-A5F0 TCGA-P5-A5F1 
        4.31        21.70        17.82         6.71         4.11         5.88 

$subtype2
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 
       18.15        10.62        40.18         0.10         9.96         6.38 
TCGA-CS-6188 TCGA-CS-6666 TCGA-CS-6668 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5277 
       23.84         8.48         8.02        81.96        47.93        50.86 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XD 
       44.52        36.56        78.28        18.84        46.72        39.78 
TCGA-DB-A4XG TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DU-5847 
       72.95        19.96        31.82        30.31         8.02        18.02 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
        6.74         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       15.16       211.17        52.11        22.42        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       11.47        62.96       156.23       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7301 
      117.40        90.77        30.67        26.30        10.36        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TR 
       23.31        41.98         5.10        23.74        19.13        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-E1-5303 TCGA-E1-5318 
        4.96         3.65         5.65        12.20        67.46        78.21 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5964 TCGA-FG-6691 TCGA-FG-7637 TCGA-FG-8185 
      130.78        14.33        34.36        23.97        40.08        14.24 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-HT-7468 
       38.27        10.72        18.38        18.71        23.70         6.67 
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-7608 
       75.19       172.77         5.03       122.47        17.29        22.06 
TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7691 
       45.99         0.23        16.24         6.05        42.74         0.10 
TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 
       17.52        19.23         0.23         0.49        37.15         0.33 
TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        3.72        16.24         9.40        12.23         6.25         0.10 
TCGA-HT-8110 TCGA-HT-8114 TCGA-HT-A5R9 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
       13.78        34.19         0.07         8.32        19.23        40.18 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 
       21.60        19.59        20.35        12.76        20.71        19.00 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F6 
       42.77         0.23         2.30         7.63         1.28 

$subtype3
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5278 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DU-5849 
        7.40       122.73        50.17        46.42        30.21        14.56 
TCGA-DU-5851 TCGA-DU-7292 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8162 
       17.46         7.96        62.01        60.30         2.76        14.60 
TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-E1-5304 TCGA-E1-5305 
       21.40        15.48        14.17        14.24        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-FG-5962 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 
       57.93       134.27        47.77        36.82        14.93        24.99 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-HT-7470 
       17.88        22.55        20.09        12.95        22.52        40.11 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 
        3.75        17.42        23.18         4.57         3.16        56.09 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 
        0.10        31.69         0.10         6.90        14.53        39.09 
TCGA-HT-7877 TCGA-HT-7902 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 
        0.13        31.43         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-HW-7493 TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F4 
        0.10        35.90         1.64         2.37         0.76 

subtype1 subtype2 subtype3 
    0.03     0.07     0.10 
subtype1 subtype2 subtype3 
  138.28   211.17   134.27 
subtype1 subtype2 subtype3 
  18.295   18.840   17.880 
[1] "0.0 - 138.3 (18.3)" "0.1 - 211.2 (18.8)" "0.1 - 134.3 (17.9)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 28 39
  subtype2 54 78
  subtype3 29 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   39
  subtype2   54   78
  subtype3   29   30
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       28       54       29
  MALE         39       78       30
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          18               23                26
  subtype2          53               33                46
  subtype3          15               14                30
D6V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             18       53       15
  OLIGOASTROCYTOMA        23       33       14
  OLIGODENDROGLIOMA       26       46       30
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 20 47
  subtype2 51 81
  subtype3 16 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   47
  subtype2   51   81
  subtype3   16   43
     clus
vv    subtype1 subtype2 subtype3
  NO        20       51       16
  YES       47       81       43
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       BLACK OR AFRICAN AMERICAN WHITE
  subtype1                         5    62
  subtype2                         5   126
  subtype3                         1    58
D6V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  BLACK OR AFRICAN AMERICAN        5        5        1
  WHITE                           62      126       58
[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"
D6V8, binary
          cls
clus         0   1
  subtype1   4  61
  subtype2   6 117
  subtype3   3  55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   61
  subtype2    6  117
  subtype3    3   55
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        6        3
  NOT HISPANIC OR LATINO       61      117       55
[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 104  20
  subtype2  59  40
  subtype3  87  12
  subtype4 107  20
  subtype5  22   2
subtype1 subtype2 subtype3 subtype4 subtype5 
     124       99       99      127       24 
subtype1 subtype2 subtype3 subtype4 subtype5 
      20       40       12       20        2 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
        4.70        43.89        18.15        17.95         8.48         7.56 
TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XD TCGA-DB-A64S 
       81.96        47.93        36.56        46.42        39.78        27.45 
TCGA-DB-A64X TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5142 TCGA-DH-A66D TCGA-DH-A7UU 
       18.51        17.88        30.74        30.31        27.81         3.45 
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-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7014 TCGA-DU-7015 
       65.75        87.45        94.52       114.08       117.40        90.77 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 
       44.02        25.91        41.98        20.68        16.96        15.48 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TA 
       15.12         5.65         7.23         7.13       124.50        77.88 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5322 TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-FG-5965 
       50.14        67.46       130.78        36.82        32.35        36.82 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7636 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 
       24.99        23.97        17.88        13.68        14.24        14.96 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A70Y 
       32.61        38.27        18.71        14.76        16.41        28.54 
TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7478 TCGA-HT-7482 TCGA-HT-7485 
       27.52         0.03        16.54         6.38       106.95         4.01 
TCGA-HT-7604 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7693 TCGA-HT-7855 
      122.47        45.99        57.60         0.16        17.52        19.23 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8013 TCGA-HT-8108 TCGA-HT-8111 
       50.63        23.61         3.68        63.55         2.50         0.23 
TCGA-HT-8114 TCGA-HT-A74O TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL 
       34.19         0.10        19.23        21.60        19.59        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 
       20.71        19.00         0.23         6.71         2.30         5.88 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A733 TCGA-QH-A6CW TCGA-QH-A6X3 TCGA-QH-A6XA 
       10.42        13.25        13.61        13.61        10.29        16.50 
TCGA-QH-A870 TCGA-RY-A845 TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U9 
       12.99        19.59        87.12        28.70        17.62        95.93 
TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 
       80.12        18.61        15.06        13.12        99.06        30.05 
TCGA-S9-A7R8 TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RH 
       31.59        30.44        40.83        25.38        23.80        15.98 
TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CH TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 
       26.99        43.04        23.47        16.01        13.32        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.40        45.80        46.88        37.71 

$subtype2
TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        7.69        10.62        21.01         6.38        17.69        23.84 
TCGA-CS-6665 TCGA-DH-5140 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 
       12.43        19.96        42.05        18.02         6.74         8.45 
TCGA-DU-6392 TCGA-DU-6396 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
      211.17        75.16         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 
       16.83        11.47        62.96        14.99         6.54         8.84 
TCGA-DU-7290 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TP TCGA-DU-A5TR 
       10.36         5.10        23.74        19.13        14.24        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A76L TCGA-DU-A7TD TCGA-DU-A7TJ 
        4.96         3.65        12.20        26.76         7.50         0.56 
TCGA-E1-5304 TCGA-E1-A7YV TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-A4MU 
       41.13        32.45        25.48        18.77        18.44        10.72 
TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A87N TCGA-FG-A87Q TCGA-HT-7469 
       18.38        22.26        10.78        13.58         5.72        11.54 
TCGA-HT-7477 TCGA-HT-7601 TCGA-HT-7680 TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7854 
       24.26         5.03         0.76        42.74         0.10        39.48 
TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8106 
        0.23         0.49         3.72        16.24        12.23         0.10 
TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 
       13.78        28.27         0.23        27.35         5.33        16.14 
TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A61C TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EX 
       16.83        17.52        17.65        12.76        14.40         1.64 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A730 TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX 
        1.28         0.16         0.20        19.33        14.53        12.23 
TCGA-RY-A83Z TCGA-S9-A6TV TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN 
        9.90        18.77        22.95         5.85        19.86        15.91 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z 
        7.92        22.32        10.39        98.63        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84J 
       49.45        24.92        16.18        59.05        28.08        24.16 
TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VW-A8FI 
       30.08         7.89         8.05 

$subtype3
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5274 TCGA-DB-A4XA 
       64.64         0.10         9.96         8.02        75.25        18.84 
TCGA-DB-A4XG TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A75K 
       72.95        30.12         5.98        31.40        27.81        12.10 
TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US 
       31.82         8.02        30.21        17.19        54.25        13.12 
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-7018 TCGA-DU-7294 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A6S8 
        7.96        30.67        94.32        21.40        14.17         5.98 
TCGA-DU-A7T6 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YO TCGA-EZ-7264 TCGA-F6-A8O3 
       17.98        78.21        95.57        75.02        14.33         0.23 
TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-8186 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
       15.35        40.08        16.01        17.82        15.02        16.44 
TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7481 TCGA-HT-7606 TCGA-HT-7616 
       36.66         6.67         0.13        95.93        17.29         0.23 
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-A619 TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7491 TCGA-HW-8322 
       16.93        21.40        15.35        11.05        40.18        17.82 
TCGA-HW-A5KJ TCGA-KT-A74X TCGA-P5-A72Z TCGA-QH-A65R TCGA-QH-A65X TCGA-QH-A65Z 
       20.35        14.40        11.64        15.16        15.85        14.04 
TCGA-QH-A6X4 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       14.53        16.73        11.08        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        30.87         5.46        28.08        37.84        34.49 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       23.64        32.61       106.39        69.50        72.59        32.45 
TCGA-S9-A6WP TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QZ 
       15.16        20.02         8.19         2.04        17.03        13.02 
TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S TCGA-VM-A8CB 
       49.32        40.64        24.79        33.24        14.93         0.10 
TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS 
       35.93        37.05        23.21 

$subtype4
TCGA-CS-5393 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5277 
       40.18         7.40         6.61       122.73        72.92        50.86 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE 
       50.17        44.52        78.28        30.21        46.72        37.45 
TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64W TCGA-DB-A75L TCGA-DB-A75P 
       33.57        31.63        24.20        14.40        11.24        16.18 
TCGA-DH-5143 TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-6542 TCGA-DU-7008 
       14.40        17.19        14.56        17.46         7.73       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 
      138.28       105.21        26.30         7.96        18.94        62.01 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-A6S2 TCGA-DU-A6S3 
       60.30        23.31         2.76        14.60         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76R TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5305 
       77.98        11.41        21.30        23.51        44.42        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6689 
       57.93       134.27         0.20        47.77        34.36        14.93 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A711 
       22.55        20.61        20.09        12.95        22.52        48.69 
TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       20.45         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        19.89         8.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-IK-8125 TCGA-P5-A5EY TCGA-P5-A5F0 
       35.90         4.31        21.70        42.77         2.37         4.11 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A731 TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 
        7.63         0.76         9.01         2.20         9.17         1.91 
TCGA-QH-A6XC TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 
        5.03         2.07        30.67        62.17        31.33        16.08 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A7IQ TCGA-S9-A7IZ TCGA-S9-A7R1 TCGA-TM-A7C4 
       84.99        31.10        36.13         7.13       169.84        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84R TCGA-VM-A8CA TCGA-W9-A837 TCGA-WY-A859 
       34.78        48.39        18.61        13.51        51.06        39.88 
TCGA-WY-A85E 
       20.81 

$subtype5
TCGA-DB-A64O TCGA-DB-A64V TCGA-DH-A7UT TCGA-DU-A7TB TCGA-FG-8187 TCGA-FG-A4MY 
       25.48        29.23        13.38        42.31        20.09        23.70 
TCGA-HT-7479 TCGA-HT-7602 TCGA-HT-7620 TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7884 
       40.34        29.85        14.27         6.05        14.96        11.28 
TCGA-HT-7902 TCGA-HT-A614 TCGA-HT-A74H TCGA-HW-7486 TCGA-QH-A65S TCGA-QH-A65V 
       31.43         2.70         2.43        29.92         2.53        12.62 
TCGA-QH-A6CU TCGA-QH-A6X5 TCGA-S9-A6U8 TCGA-S9-A6WQ TCGA-S9-A7IY TCGA-S9-A7QY 
       14.83        16.34        98.24        14.07        23.51        28.37 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.10     0.07     0.10     2.43 
subtype1 subtype2 subtype3 subtype4 subtype5 
  130.78   211.17   182.33   172.77    98.24 
subtype1 subtype2 subtype3 subtype4 subtype5 
  21.205   14.400   17.820   20.610   18.215 
[1] "0.0 - 130.8 (21.2)" "0.1 - 211.2 (14.4)" "0.1 - 182.3 (17.8)"
[4] "0.1 - 172.8 (20.6)" "2.4 - 98.2 (18.2)" 
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 46 78
  subtype2 48 52
  subtype3 47 52
  subtype4 57 71
  subtype5 10 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   78
  subtype2   48   52
  subtype3   47   52
  subtype4   57   71
  subtype5   10   14
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       46       48       47       57       10
  MALE         78       52       52       71       14
[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, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          64               39                21
  subtype2          70               16                14
  subtype3           3               17                79
  subtype4          34               36                58
  subtype5           5               11                 8
D7V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4 subtype5
  ASTROCYTOMA             64       70        3       34        5
  OLIGOASTROCYTOMA        39       16       17       36       11
  OLIGODENDROGLIOMA       21       14       79       58        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"
D7V6, binary
          cls
clus         0   1
  subtype1  31  93
  subtype2  23  77
  subtype3  11  88
  subtype4  25 103
  subtype5   2  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   93
  subtype2   23   77
  subtype3   11   88
  subtype4   25  103
  subtype5    2   22
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        31       23       11       25        2
  YES       93       77       88      103       22
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         5
  subtype2                                1     2                         5
  subtype3                                0     4                         0
  subtype4                                0     1                         5
  subtype5                                0     1                         0
          vv
clus       WHITE
  subtype1   116
  subtype2    91
  subtype3    91
  subtype4   119
  subtype5    23
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               5        5        0        5        0
  WHITE                                 116       91       91      119       23
[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   5 107
  subtype2   2  92
  subtype3   4  85
  subtype4   6 115
  subtype5   1  23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  107
  subtype2    2   92
  subtype3    4   85
  subtype4    6  115
  subtype5    1   23
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            5        2        4        6        1
  NOT HISPANIC OR LATINO      107       92       85      115       23
[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 103  21
  subtype2  34  31
  subtype3  29   4
  subtype4  47  14
  subtype5  72  11
  subtype6  28   8
  subtype7  66   5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
     124       65       33       61       83       36       71 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      21       31        4       14       11        8        5 
$subtype1
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-6290 TCGA-CS-6666 
        4.70        43.89        18.15        10.62        17.95         8.48 
TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5280 TCGA-DB-A4XD TCGA-DB-A64S 
        7.56        81.96        47.93        36.56        39.78        27.45 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-A66D TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5853 
       17.88        30.74        27.81        13.38        18.61        13.38 
TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
        6.81        18.94        17.49        49.02        75.16        65.75 
TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 
       87.45        94.52       114.08       117.40        90.77        26.30 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-8167 TCGA-DU-A5TS 
       44.02        25.91        41.98        20.68        15.48        15.12 
TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 
        5.65         7.23         7.13       124.50        77.88        50.14 
TCGA-E1-5303 TCGA-E1-5322 TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-FG-5965 TCGA-FG-6690 
       67.46       130.78        36.82        32.35        36.82        24.99 
TCGA-FG-6691 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       23.97        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-FN-7833 
       18.71        23.70        14.76        16.41        28.54        27.52 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7604 
        0.03        16.54        40.34       106.95         4.01       122.47 
TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7693 
       45.99        57.60         0.16         6.05        14.96        17.52 
TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7902 TCGA-HT-8013 
       19.23        50.63        23.61         3.68        31.43        63.55 
TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-A614 TCGA-HT-A74O TCGA-HW-7490 
        2.50         0.23        34.19         2.70         0.10        19.23 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-P5-A5EV TCGA-P5-A5EW 
       21.60        19.59        20.81        20.71         0.23         6.71 
TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A733 TCGA-QH-A65S 
        2.30         5.88        10.42        13.25        13.61         2.53 
TCGA-QH-A6CW TCGA-QH-A6X3 TCGA-QH-A870 TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A6U1 
       13.61        10.29        12.99        87.12        28.70        17.62 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WG TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7QX 
       98.24        95.93        80.12        18.61        14.07        13.12 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84T 
       99.06        30.05        31.59        30.44        40.83        23.80 
TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CH TCGA-VV-A86M TCGA-WH-A86K 
       15.98        26.99        43.04        23.47        16.01        13.32 
TCGA-WY-A858 TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.96        45.80        46.88        37.71 

$subtype2
TCGA-CS-4941 TCGA-CS-6186 TCGA-CS-6188 TCGA-DB-A64O TCGA-DU-5847 TCGA-DU-5852 
        7.69        17.69        23.84        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         4.96        12.20        26.76         7.50         0.56 
TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q 
       18.77        18.44        10.72        18.38        10.78         5.72 
TCGA-HT-7469 TCGA-HT-7680 TCGA-HT-7691 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 
       11.54         0.76         0.10         0.23         0.49         3.72 
TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC 
       16.24        12.23        13.78         0.23        27.35         5.33 
TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74H TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EX 
       16.14        17.65         2.43        12.76        14.40         1.64 
TCGA-P5-A5F6 TCGA-P5-A72U TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-S9-A6U0 
        1.28         0.16        19.33        14.53        12.23        22.95 
TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A7C3 
        5.85        19.86        15.91        10.39        18.71        49.45 
TCGA-TM-A84B TCGA-TM-A84C TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VW-A8FI 
       24.92        16.18        30.08         7.89         8.05 

$subtype3
TCGA-CS-5390 TCGA-CS-6668 TCGA-DB-5279 TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64R 
       64.64         8.02        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 
        8.02        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         5.98       134.27        75.02        14.33         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-QH-A65R TCGA-QH-A86X TCGA-R8-A73M TCGA-S9-A6WH TCGA-S9-A6WL 
       20.35        15.16        11.08        59.38        32.45        31.10 
TCGA-S9-A7R1 TCGA-TM-A84G TCGA-VM-A8CB 
      169.84        40.64         0.10 

$subtype4
TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5277 
       40.18        21.01         6.38       122.73        72.92        50.86 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF 
       78.28        46.42        30.21        46.72        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        14.40        17.19         7.73 
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-E1-5305 TCGA-E1-5307 TCGA-F6-A8O4 TCGA-FG-6689 
       16.96        11.41        79.99        57.93         0.20        14.93 
TCGA-FG-7636 TCGA-FG-7643 TCGA-FG-A711 TCGA-HT-7476 TCGA-HT-7483 TCGA-HT-7690 
       17.88        20.09        48.69         6.54       172.77         0.10 
TCGA-HT-7854 TCGA-HT-7884 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8564 TCGA-HT-A5R5 
       39.48        11.28         0.10        37.87        15.72         0.13 
TCGA-HT-A74J TCGA-HW-7493 TCGA-P5-A5EY TCGA-P5-A5F2 TCGA-P5-A731 TCGA-QH-A6X9 
       10.52        35.90         2.37         7.63         9.01         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6U6 
       16.50         5.03         2.07        19.59        62.17        16.08 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7QW TCGA-TM-A7CA TCGA-VM-A8CA TCGA-WY-A85A 
       22.32         7.13        15.06        34.78        13.51        43.40 
TCGA-WY-A85E 
       20.81 

$subtype5
TCGA-CS-5394 TCGA-CS-5396 TCGA-DB-5274 TCGA-DB-A4XA TCGA-DB-A4XH TCGA-DB-A64P 
        0.10         9.96        75.25        18.84        31.63        30.12 
TCGA-DB-A64Q TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A75K TCGA-DH-5141 TCGA-DH-A669 
        5.98        27.81        29.23        12.10        31.82        30.21 
TCGA-DH-A66F TCGA-DH-A7US TCGA-DU-5870 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 
       17.19        13.12       182.33        52.11        22.42        46.06 
TCGA-DU-7018 TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-E1-5318 TCGA-E1-5319 
       30.67        21.30        17.98        42.31        78.21        95.57 
TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-A60K 
       34.36        15.35        40.08        16.01        20.09        17.82 
TCGA-FG-A6IZ TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7602 TCGA-HT-7608 TCGA-HT-7616 
       15.02         6.67         0.13        29.85        22.06         0.23 
TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7692 TCGA-HT-A4DV TCGA-HT-A615 TCGA-HT-A619 
       14.27        16.24         2.96        26.04        16.93        21.40 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7491 TCGA-HW-8322 TCGA-KT-A74X 
       15.35        11.05        29.92        40.18        17.82        14.40 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
       11.64         0.20        12.62        15.85        14.04        14.83 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       14.53        16.34        16.73        88.83        94.03        32.65 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6U2 
       30.87         5.46        28.08        37.84        34.49        23.64 
TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WP TCGA-S9-A7IY 
       32.61       106.39        69.50        72.59        15.16        23.51 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-TM-A7C5 TCGA-TM-A84M 
        8.19         2.04        17.03        28.37        49.32        24.79 
TCGA-TM-A84O TCGA-TM-A84S TCGA-VM-A8CE TCGA-VV-A829 TCGA-VW-A7QS 
       33.24        14.93        35.93        37.05        23.21 

$subtype6
TCGA-CS-6665 TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A66B TCGA-DH-A7UU TCGA-DU-6392 
       12.43        19.96        30.31        42.05         3.45       211.17 
TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU TCGA-E1-5304 
       62.96        14.99        14.24        12.59         3.65        41.13 
TCGA-E1-A7YV TCGA-FG-5963 TCGA-FG-A6J3 TCGA-FG-A87N TCGA-HT-7477 TCGA-HT-7478 
       32.45        25.48        22.26        13.58        24.26         6.38 
TCGA-HT-7601 TCGA-HT-7606 TCGA-HT-7686 TCGA-HT-8106 TCGA-HT-8563 TCGA-HT-A618 
        5.03        17.29        42.74         0.10        28.27        16.83 
TCGA-HT-A61B TCGA-IK-7675 TCGA-RY-A83Z TCGA-S9-A6TV TCGA-S9-A7IS TCGA-S9-A7J0 
       17.52        19.00         9.90        18.77         7.92        20.02 
TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84Q 
       98.63        11.97        59.05        28.08        24.16        25.38 

$subtype7
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5278 TCGA-DB-A64W TCGA-DU-5849 TCGA-DU-5851 
        7.40         6.61        50.17        14.40        14.56        17.46 
TCGA-DU-7009 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8164 TCGA-DU-A6S2 
      138.28        62.01        60.30         2.76        21.40         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A7TC TCGA-DU-A7TG TCGA-FG-5962 TCGA-FG-7638 
        2.70        77.98        23.51        44.42        47.77        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7470 
       20.61        12.95        22.52        20.45         0.10        40.11 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 
        3.75        17.42        75.19        95.93        23.18         4.57 
TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7681 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 
        3.16        56.09        44.68        31.69         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-8019 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 
        1.64        33.01         0.46         5.56        29.59        13.74 
TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HT-A61A TCGA-HW-7487 TCGA-HW-7489 
       20.22         0.10         1.81         6.38        19.89         8.32 
TCGA-HW-7495 TCGA-HW-8319 TCGA-IK-8125 TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-QH-A6CY 
        4.31        21.70        42.77         4.11         0.76         2.20 
TCGA-QH-A6CZ TCGA-RY-A847 TCGA-S9-A6TY TCGA-S9-A6WI TCGA-S9-A7IQ TCGA-S9-A7QZ 
        9.17        30.67        31.33        84.99        36.13        13.02 
TCGA-TM-A7C4 TCGA-TM-A7CF TCGA-TM-A84R TCGA-W9-A837 TCGA-WY-A859 
       48.33        48.39        18.61        51.06        39.88 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.03     0.10     0.07     0.10     0.10     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  130.78   133.74   169.84   172.77   182.33   211.17   138.28 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   23.54    12.20    16.44    17.88    22.06    19.48    20.22 
[1] "0.0 - 130.8 (23.5)" "0.1 - 133.7 (12.2)" "0.1 - 169.8 (16.4)"
[4] "0.1 - 172.8 (17.9)" "0.1 - 182.3 (22.1)" "0.1 - 211.2 (19.5)"
[7] "0.1 - 138.3 (20.2)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 46 78
  subtype2 32 33
  subtype3 20 13
  subtype4 29 32
  subtype5 32 51
  subtype6 16 21
  subtype7 33 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   78
  subtype2   32   33
  subtype3   20   13
  subtype4   29   32
  subtype5   32   51
  subtype6   16   21
  subtype7   33   39
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       46       32       20       29       32       16       33
  MALE         78       33       13       32       51       21       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, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          60               43                21
  subtype2          42               11                12
  subtype3           1                1                31
  subtype4          32               21                 8
  subtype5           2               23                58
  subtype6          30                4                 3
  subtype7           9               16                47
D8V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ASTROCYTOMA             60       42        1       32        2       30
  OLIGOASTROCYTOMA        43       11        1       21       23        4
  OLIGODENDROGLIOMA       21       12       31        8       58        3
                   clus
vv                  subtype7
  ASTROCYTOMA              9
  OLIGOASTROCYTOMA        16
  OLIGODENDROGLIOMA       47
[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"
D8V6, binary
          cls
clus        0  1
  subtype1 31 93
  subtype2 11 54
  subtype3  2 31
  subtype4 12 49
  subtype5 10 73
  subtype6 11 26
  subtype7 15 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   93
  subtype2   11   54
  subtype3    2   31
  subtype4   12   49
  subtype5   10   73
  subtype6   11   26
  subtype7   15   57
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        31       11        2       12       10       11       15
  YES       93       54       31       49       73       26       57
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         5
  subtype2                                1     1                         4
  subtype3                                0     1                         0
  subtype4                                0     1                         2
  subtype5                                0     4                         1
  subtype6                                0     1                         0
  subtype7                                0     0                         3
          vv
clus       WHITE
  subtype1   116
  subtype2    58
  subtype3    29
  subtype4    56
  subtype5    76
  subtype6    36
  subtype7    69
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               5        4        0        2        1
  WHITE                                 116       58       29       56       76
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   1        0
  BLACK OR AFRICAN AMERICAN               0        3
  WHITE                                  36       69
[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   5 107
  subtype2   2  59
  subtype3   1  27
  subtype4   3  52
  subtype5   3  74
  subtype6   1  36
  subtype7   3  67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  107
  subtype2    2   59
  subtype3    1   27
  subtype4    3   52
  subtype5    3   74
  subtype6    1   36
  subtype7    3   67
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            5        2        1        3        3        1
  NOT HISPANIC OR LATINO      107       59       27       52       74       36
                        clus
vv                       subtype7
  HISPANIC OR LATINO            3
  NOT HISPANIC OR LATINO       67
[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 100  23
  subtype2  71  32
  subtype3 145  26
  subtype4  60  12
subtype1 subtype2 subtype3 subtype4 
     123      103      171       72 
subtype1 subtype2 subtype3 subtype4 
      23       32       26       12 
$subtype1
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5395 TCGA-CS-6186 
        4.70         7.69        43.89        10.62        21.01        17.69 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5280 
       17.95         8.48         7.56        75.25        72.92        36.56 
TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A64O TCGA-DB-A64V TCGA-DB-A75O TCGA-DH-5140 
       18.84        39.78        25.48        29.23        30.74        19.96 
TCGA-DH-5141 TCGA-DH-A66F TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5854 TCGA-DU-5855 
       31.82        17.19        18.61        18.02         8.45         6.81 
TCGA-DU-5872 TCGA-DU-6396 TCGA-DU-6407 TCGA-DU-6542 TCGA-DU-7012 TCGA-DU-7014 
       17.49        75.16        94.52         7.73         6.54       117.40 
TCGA-DU-7290 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 
       10.36        25.91        41.98         5.10        23.74        19.13 
TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-E1-5318 TCGA-E1-5319 
        4.96         5.65        12.20         7.23        78.21        95.57 
TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-8182 TCGA-FG-8188 TCGA-FG-8191 
       18.77        23.97        15.35        13.68        14.96        32.61 
TCGA-FG-A4MT TCGA-FG-A4MY TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A87Q TCGA-FN-7833 
       38.27        23.70        16.41        28.54         5.72        27.52 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 
        0.03        16.54        40.34       106.95         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 
       29.85       122.47        17.29        22.06        45.99        57.60 
TCGA-HT-7680 TCGA-HT-7689 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 
        0.76        14.96        39.48        19.23        50.63         0.49 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8563 TCGA-HT-A4DS 
       16.24        63.55        13.78         0.23        28.27         0.23 
TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7490 TCGA-HW-8320 
       16.14        17.65        15.35         0.10        19.23        21.60 
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-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CU 
       10.42        11.64         0.20         2.53        19.33        14.83 
TCGA-QH-A6CV TCGA-QH-A6X3 TCGA-QH-A870 TCGA-RY-A83X TCGA-RY-A840 TCGA-S9-A6TU 
       14.53        10.29        12.99        30.87        28.08        87.12 
TCGA-S9-A6TX TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WD TCGA-S9-A6WM 
       34.49        32.61        98.24        95.93        69.50        19.86 
TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IY TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 
       18.61        14.07        23.51        13.12        10.39        99.06 
TCGA-S9-A7R8 TCGA-TM-A84B TCGA-TM-A84S TCGA-TM-A84T TCGA-VV-A829 TCGA-VV-A86M 
       31.59        24.92        14.93        23.80        37.05        16.01 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85D 
       13.32        43.96        37.71 

$subtype2
TCGA-CS-4943 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-5273 TCGA-DB-A4XE TCGA-DB-A4XF 
       18.15        23.84        12.43        81.96        37.45        33.57 
TCGA-DB-A64S TCGA-DB-A64X TCGA-DH-5142 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G 
       27.45        18.51        30.31        42.05        27.81        17.19 
TCGA-DH-A7UU TCGA-DU-6392 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 
        3.45       211.17        65.75        87.45         7.04       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7013 
       19.89        16.83       114.08        11.47        62.96         8.84 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A76L TCGA-DU-A7T8 TCGA-DU-A7TD 
       14.24        12.59         3.65        26.76       124.50         7.50 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5322 TCGA-E1-A7YV 
        0.56        50.14        67.46        41.13       130.78        32.45 
TCGA-E1-A7YW TCGA-FG-5963 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MU 
       36.82        25.48        18.44        17.88        14.24        10.72 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A87N TCGA-HT-7468 
       18.71        14.76        22.26        10.78        13.58         6.67 
TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 
       11.54        24.26         6.38         6.05        42.74         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7857 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7882 
        0.10        17.52         0.23        23.61         3.68         3.72 
TCGA-HT-8106 TCGA-HT-8114 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A618 TCGA-HT-A619 
        0.10        34.19        27.35         5.33        16.83        21.40 
TCGA-HT-A61B TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EX 
       17.52        20.81        20.71        19.00        14.40         1.64 
TCGA-P5-A72U TCGA-QH-A6CX TCGA-RY-A845 TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 
        0.16        12.23        19.59        18.77        28.70        22.95 
TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7R4 
       17.62         5.85        80.12        15.91         7.92        30.05 
TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84C TCGA-TM-A84I 
       98.63        18.71        11.97        49.45        16.18        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TQ-A7RH TCGA-TQ-A7RW 
       24.16        40.83        33.24        25.38        15.98        26.99 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CH TCGA-VW-A8FI TCGA-WY-A85B TCGA-WY-A85C 
       43.04        30.08        23.47         8.05        45.80        46.88 
TCGA-WY-A85E 
       20.81 

$subtype3
TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       64.64        40.18         6.38         7.40         6.61       122.73 
TCGA-DB-5278 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XG TCGA-DB-A4XH 
       50.17        78.28        30.21        46.72        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A75L TCGA-DB-A75P 
       24.20        31.40        27.81        14.40        11.24        16.18 
TCGA-DH-5143 TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DU-5849 TCGA-DU-5851 
       14.40        54.25        13.12        13.38        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5871 TCGA-DU-6393 TCGA-DU-6403 TCGA-DU-6410 
        6.74        13.38        18.94        52.11        11.64         7.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 
      156.23       138.28        14.99        26.30         7.96        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8162 
       44.02        62.01        60.30        23.31         2.76        14.60 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A6S2 
       20.68        21.40        16.96        15.48        15.12         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A7T6 
        2.70        77.98         5.98        11.41         7.13        17.98 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       42.31        23.51        44.42        79.99        57.93       134.27 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-7638 
        0.20        47.77        34.36        36.82        14.93        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 
       20.61        20.09        12.95        16.01        20.09        22.52 
TCGA-FG-A4MW TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7470 
       18.38        36.66        48.69        20.45         0.10        40.11 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7603 
        3.75        17.42         6.54        75.19        95.93        23.18 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7620 TCGA-HT-7681 TCGA-HT-7687 
        4.57         3.16        56.09        14.27        44.68         0.10 
TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7875 
       31.69         6.90        14.53        39.09        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        0.13         5.33        35.47        11.28        31.43         1.64 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
        0.10        37.87        33.01        12.23         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-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
        0.13        20.22         0.10         2.70        16.93         1.81 
TCGA-HT-A61A TCGA-HT-A74H TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 
        6.38         2.43        29.92        19.89         8.32        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-IK-8125 TCGA-P5-A5EY TCGA-P5-A5F0 
        4.31        21.70        19.59        42.77         2.37         4.11 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72X TCGA-P5-A731 TCGA-P5-A733 TCGA-QH-A65V 
        7.63         0.76        13.25         9.01        13.61        12.62 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA 
        2.20         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 
        5.03        88.83         2.07        30.67        62.17        31.33 
TCGA-S9-A6U6 TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IX 
       16.08        84.99        31.10        15.16        36.13        22.32 
TCGA-S9-A7IZ TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-TM-A7C4 
        7.13        17.03        15.06        28.37        13.02        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84R TCGA-VM-A8CA TCGA-VM-A8CD 
       34.78        48.39        59.05        18.61        13.51         7.89 
TCGA-W9-A837 TCGA-WY-A859 TCGA-WY-A85A 
       51.06        39.88        43.40 

$subtype4
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 
        0.10         9.96         8.02        47.93        50.86        44.52 
TCGA-DB-A4X9 TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A75K TCGA-DH-5144 TCGA-DH-A669 
       46.42        30.12         5.98        12.10         8.02        30.21 
TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6400 
      182.33        15.16        22.42        49.02        46.06         1.22 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8168 TCGA-DU-A76R TCGA-DU-A7TA 
       90.77        30.67        94.32        14.17        21.30        77.88 
TCGA-E1-A7YO TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-6690 TCGA-FG-7637 
       75.02        32.35        14.33         0.23        24.99        40.08 
TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-HT-7471 TCGA-HT-7483 TCGA-HT-7616 
       17.82        15.02        16.44         0.13       172.77         0.23 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7692 TCGA-HT-8012 TCGA-HT-A5R9 TCGA-HT-A74L 
        0.16        16.24         2.96         9.40         0.07        11.05 
TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X TCGA-QH-A65R TCGA-QH-A65X 
       40.18        17.82        20.35        14.40        15.16        15.85 
TCGA-QH-A65Z TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
       14.04        16.73        11.08        94.03        32.65        59.38 
TCGA-RY-A83Y TCGA-RY-A83Z TCGA-S9-A6TW TCGA-S9-A6U2 TCGA-S9-A6UB TCGA-S9-A6WE 
        5.46         9.90        37.84        23.64       106.39        72.59 
TCGA-S9-A6WH TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7R1 TCGA-TM-A7C5 
       32.45        20.02         8.19         2.04       169.84        49.32 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84M TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VW-A7QS 
       40.64        30.44        24.79         0.10        35.93        23.21 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.10     0.10     0.07 
subtype1 subtype2 subtype3 subtype4 
  122.47   211.17   156.23   182.33 
subtype1 subtype2 subtype3 subtype4 
  18.610   19.590   17.420   20.825 
[1] "0.0 - 122.5 (18.6)" "0.1 - 211.2 (19.6)" "0.1 - 156.2 (17.4)"
[4] "0.1 - 182.3 (20.8)"
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1 51 73
  subtype2 43 60
  subtype3 81 91
  subtype4 33 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51   73
  subtype2   43   60
  subtype3   81   91
  subtype4   33   39
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       51       43       81       33
  MALE         73       60       91       39
[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, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          61               33                30
  subtype2          62               22                19
  subtype3          48               46                78
  subtype4           4               15                53
D9V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             61       62       48        4
  OLIGOASTROCYTOMA        33       22       46       15
  OLIGODENDROGLIOMA       30       19       78       53
[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"
D9V6, binary
          cls
clus         0   1
  subtype1  26  98
  subtype2  25  78
  subtype3  30 142
  subtype4  10  62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   98
  subtype2   25   78
  subtype3   30  142
  subtype4   10   62
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        26       25       30       10
  YES       98       78      142       62
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                         8
  subtype2                                0     2                         2
  subtype3                                0     2                         5
  subtype4                                0     3                         0
          vv
clus       WHITE
  subtype1   111
  subtype2    97
  subtype3   162
  subtype4    66
D9V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   1        2        2        3
  BLACK OR AFRICAN AMERICAN               8        2        5        0
  WHITE                                 111       97      162       66
[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   5 110
  subtype2   4  90
  subtype3   8 156
  subtype4   1  62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  110
  subtype2    4   90
  subtype3    8  156
  subtype4    1   62
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        4        8        1
  NOT HISPANIC OR LATINO      110       90      156       62
[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 167  34
  subtype2 148  23
  subtype3  61  36
subtype1 subtype2 subtype3 
     201      171       97 
subtype1 subtype2 subtype3 
      34       23       36 
$subtype1
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
        0.10         9.96        17.69        17.95         8.48         7.56 
TCGA-CS-6668 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        8.02        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE 
       36.56        46.42        18.84        30.21        39.78        37.45 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A75K 
       30.12         5.98        27.45        27.81        29.23        12.10 
TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 
       30.74        19.96        31.82        30.31         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5855 
       42.05        27.81        17.19        13.38        18.61         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
      182.33        18.94        17.49        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7014 
       46.06        65.75        87.45        94.52       114.08       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 
       90.77        30.67        94.32        44.02        25.91        41.98 
TCGA-DU-8163 TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TA 
       20.68         5.65         7.23        21.30       124.50        77.88 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       50.14        67.46        41.13        78.21        95.57       130.78 
TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
       36.82        32.35        14.33        24.99        23.97        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-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A70Y TCGA-FN-7833 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
       28.54        27.52         6.67         0.13         0.03        16.54 
TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 
       40.34       106.95         4.01         5.03        29.85       122.47 
TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7676 
       17.29        22.06        45.99        57.60         0.23         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 
       16.24         0.76         6.05        14.96         0.10         2.96 
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-A614 TCGA-HT-A619 TCGA-HT-A74K 
        0.23        34.19        28.27         2.70        21.40        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-8322 
       11.05         0.10        19.23        40.18        21.60        17.82 
TCGA-HW-A5KL TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 
       20.81        14.40         0.23         6.71         2.30         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 
        7.63         1.28        10.42        11.64         0.20         9.01 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6X3 
        2.53        12.62        14.04        19.33        14.83        10.29 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6ML TCGA-R8-A6MO 
       16.34        16.73        11.08        12.99        94.03        32.65 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 TCGA-S9-A6TU TCGA-S9-A6TW 
       30.87         5.46        28.08        30.67        87.12        37.84 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 
       34.49        28.70        17.62        23.64        32.61        98.24 
TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       95.93       106.39        69.50        18.61        15.16        14.07 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7R3 
       23.51         8.19         2.04        17.03        13.12        99.06 
TCGA-S9-A7R4 TCGA-TM-A84B TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84O 
       30.05        24.92        40.64        30.44        40.83        33.24 
TCGA-TM-A84Q TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RH TCGA-TQ-A7RW TCGA-VM-A8C8 
       25.38        14.93        23.80        15.98        26.99        43.04 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-WH-A86K 
       35.93        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-5393 TCGA-CS-5397 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5278 
       40.18         6.38         7.40         6.61       122.73        50.17 
TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XC TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       44.52        78.28        46.72        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        14.40 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
       17.19        54.25        13.12        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       138.28 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 
       26.30         7.96        18.94        62.01        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TS 
        2.76        14.60        21.40        16.96        14.17        15.12 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A7T6 
        8.65         2.70        77.98         5.98         7.13        17.98 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       42.31        23.51        44.42        79.99        57.93       134.27 
TCGA-E1-A7YO TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 
       75.02         0.23         0.20        47.77        34.36        36.82 
TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       14.93        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A711 
       16.01        20.09        22.52        16.44        36.66        48.69 
TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
       20.45         0.10        40.11         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7603 TCGA-HT-7605 
       24.26        75.19        95.93       172.77        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-8012 
        5.33        35.47        11.28        31.43         1.64         9.40 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 
        0.10        37.87        33.01         6.25         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
        5.56        29.59        13.74        26.04         0.13        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61A 
        0.07         0.10        16.93         1.81        16.83         6.38 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       29.92        19.89         8.32        35.90         4.31        21.70 
TCGA-HW-A5KJ TCGA-IK-8125 TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A72X 
       20.35        42.77         2.37         4.11         0.76        13.25 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A65X TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 
       13.61        15.16        15.85         2.20         9.17        14.53 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-R8-A73M TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS 
        1.91        16.50        59.38         2.07        19.59        62.17 
TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
       31.33        16.08        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7QW TCGA-S9-A7QY 
       31.10        36.13        22.32         7.13        15.06        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       13.02       169.84        48.33        49.32        34.78        48.39 
TCGA-TM-A84F TCGA-TM-A84M TCGA-TM-A84R TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       59.05        24.79        18.61        13.51         0.10         7.89 
TCGA-W9-A837 TCGA-WY-A859 TCGA-WY-A85A 
       51.06        39.88        43.40 

$subtype3
TCGA-CS-5395 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-A64O TCGA-DB-A64X TCGA-DH-A7UU 
       21.01        23.84        12.43        25.48        18.51         3.45 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6402 TCGA-DU-6403 
       18.02         6.74         8.45       211.17         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
      133.74        19.89        16.83         7.73        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-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       19.13        15.48        14.24        12.59         4.96         3.65 
TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-A7YV 
       12.20        11.41        26.76         7.50         0.56        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-A87N TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7478 TCGA-HT-7686 
       10.78        13.58         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        19.59 
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         1.64         0.16 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XC TCGA-R8-A6MK TCGA-RY-A83Z TCGA-S9-A6TV 
       14.53        12.23         5.03        88.83         9.90        18.77 
TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7J0 
       22.95         5.85        19.86        15.91         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        11.97        49.45 
TCGA-TM-A84C TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8C9 TCGA-VW-A8FI TCGA-WY-A85C 
       16.18        28.08        24.16        30.08         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 
   23.21    18.94    14.53 
[1] "0.0 - 182.3 (23.2)" "0.1 - 172.8 (18.9)" "0.1 - 211.2 (14.5)"
D10V2, continuous
D10V3, binary
          cls
clus         0   1
  subtype1  80 122
  subtype2  82  90
  subtype3  46  51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   80  122
  subtype2   82   90
  subtype3   46   51
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       80       82       46
  MALE        122       90       51
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          68               60                74
  subtype2          43               40                89
  subtype3          64               16                17
D10V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             68       43       64
  OLIGOASTROCYTOMA        60       40       16
  OLIGODENDROGLIOMA       74       89       17
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus         0   1
  subtype1  44 158
  subtype2  28 144
  subtype3  19  78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44  158
  subtype2   28  144
  subtype3   19   78
     clus
vv    subtype1 subtype2 subtype3
  NO        44       28       19
  YES      158      144       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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         5
  subtype2                                0     3                         5
  subtype3                                1     2                         5
          vv
clus       WHITE
  subtype1   189
  subtype2   159
  subtype3    88
D10V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   3        3        2
  BLACK OR AFRICAN AMERICAN               5        5        5
  WHITE                                 189      159       88
[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   8 177
  subtype2   7 154
  subtype3   3  87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  177
  subtype2    7  154
  subtype3    3   87
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        7        3
  NOT HISPANIC OR LATINO      177      154       87
[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 123  50
  subtype2 124  18
  subtype3 126  25
subtype1 subtype2 subtype3 
     173      142      151 
subtype1 subtype2 subtype3 
      50       18       25 
$subtype1
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5395 TCGA-CS-6186 TCGA-CS-6188 
        4.70         7.69        10.62        21.01        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-5279 
       17.95         8.48         7.56        81.96        72.92        44.52 
TCGA-DB-A64O TCGA-DB-A75O TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 
       25.48        30.74        18.02         6.74         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
      182.33        18.94        17.49        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7290 TCGA-DU-7301 
       62.96         6.54         8.84       117.40        10.36        25.91 
TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8167 
       41.98         5.10        23.74        20.68        19.13        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76L 
       14.24        12.59         4.96        12.20         7.23        26.76 
TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5319 TCGA-E1-A7Z6 TCGA-FG-5963 TCGA-FG-6688 
        7.50         0.56        95.57        32.35        25.48        18.77 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-8182 TCGA-FG-8185 
       24.99        23.97        18.44        15.35        13.68        14.24 
TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       14.96        32.61        10.72        13.58         5.72        27.52 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 TCGA-HT-7482 
       11.54         0.13         0.03        16.54        40.34       106.95 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 
      172.77         4.01         5.03        29.85       122.47        17.29 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       22.06        45.99        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7689 TCGA-HT-7690 
       16.24         0.76         6.05        42.74        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 
        0.10         2.96        17.52        39.48        19.23         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7882 TCGA-HT-8011 
       50.63         0.49        23.61         3.68         3.72        16.24 
TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8114 
       63.55        12.23         0.10        13.78         0.23        34.19 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C 
       28.27         0.23        27.35         5.33        16.14        17.65 
TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-8321 
       15.35         0.10        29.92        19.23        21.60        19.59 
TCGA-HW-A5KK TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5F1 TCGA-P5-A72U 
       12.76        19.00        14.40         1.64         5.88         0.16 
TCGA-P5-A72X TCGA-P5-A730 TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X3 
       13.25         0.20        19.33        14.53        12.23        10.29 
TCGA-QH-A870 TCGA-RY-A83Z TCGA-RY-A840 TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       12.99         9.90        28.08        87.12        18.77        37.84 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U5 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM 
       28.70        22.95        32.61         5.85        80.12        19.86 
TCGA-S9-A6WN TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z 
       15.91        10.39        99.06        98.63        18.71        11.97 
TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84I TCGA-TM-A84O TCGA-TM-A84Q 
       49.45        24.92        16.18        28.08        33.24        25.38 
TCGA-TM-A84S TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VV-A829 
       14.93        26.99        43.04        30.08         7.89        37.05 
TCGA-VW-A8FI TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85B TCGA-WY-A85D 
        8.05        13.32        43.96        45.80        37.71 

$subtype2
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 
       43.89        18.15        64.64         0.10         9.96         8.02 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       75.25        47.93        50.86        78.28        46.42        18.84 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       30.21        46.72        39.78        37.45        33.57        72.95 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       30.12         5.98        31.40        27.45        27.81        29.23 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       18.51        12.10        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7US 
        8.02        30.21        42.05        27.81        17.19        13.12 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-6393 TCGA-DU-7008 TCGA-DU-7015 
       13.38         3.45        18.61        52.11       156.23        90.77 
TCGA-DU-7018 TCGA-DU-7299 TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S8 
       30.67        44.02        15.12         3.65         5.65         5.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
      124.50        77.88        50.14        67.46        41.13        79.99 
TCGA-E1-5318 TCGA-E1-5322 TCGA-E1-A7YO TCGA-E1-A7YW TCGA-EZ-7264 TCGA-F6-A8O3 
       78.21       130.78        75.02        36.82        14.33         0.23 
TCGA-FG-7637 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       40.08        38.27        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 
       16.41        15.02        16.44        22.26        28.54        36.66 
TCGA-HT-7468 TCGA-HT-7477 TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 
        6.67        24.26         0.13         0.07         0.10         2.70 
TCGA-HT-A615 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A74L TCGA-HW-7491 TCGA-HW-A5KJ 
       16.93        21.40        17.52        11.05        40.18        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ 
       20.81        20.71        14.40         0.23         6.71         2.30 
TCGA-P5-A5F2 TCGA-P5-A72W TCGA-P5-A72Z TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        7.63        10.42        11.64        15.16         2.53        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-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X 
       11.08        88.83        94.03        32.65        59.38        30.87 
TCGA-RY-A83Y TCGA-RY-A843 TCGA-S9-A6TX TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U8 
        5.46         2.07        34.49        17.62        23.64        98.24 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WO TCGA-S9-A6WP 
      106.39        69.50        72.59        32.45        18.61        15.16 
TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       23.51        20.02         8.19         2.04        17.03        15.06 
TCGA-S9-A7QX TCGA-S9-A7R1 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A84G 
       13.12       169.84        30.05        31.59        49.32        40.64 
TCGA-TM-A84H TCGA-TM-A84M TCGA-TM-A84T TCGA-TQ-A7RH TCGA-VM-A8CB TCGA-VM-A8CE 
       30.44        24.79        23.80        15.98         0.10        35.93 
TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS TCGA-WY-A85C 
       23.47        16.01        23.21        46.88 

$subtype3
TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6665 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       40.18         6.38        12.43         7.40         6.61       122.73 
TCGA-DB-5278 TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64W TCGA-DB-A75L TCGA-DB-A75P 
       50.17        31.63        24.20        14.40        11.24        16.18 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5874 
       17.19        54.25        14.56        17.46        13.38        15.16 
TCGA-DU-6392 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7019 
      211.17         1.22         7.96       138.28        14.99        26.30 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 
        7.96        94.32        18.94        62.01        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A6S2 
        2.76        14.60        21.40        16.96        14.17         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T6 
        2.70        77.98        11.41         7.13        21.30        17.98 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-A7YV 
       42.31        23.51        44.42        57.93       134.27        32.45 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-7636 
        0.20        47.77        34.36        36.82        14.93        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8187 
       22.55        20.61        20.09        12.95        16.01        20.09 
TCGA-FG-8189 TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A713 TCGA-HT-7467 
       22.52        18.38        10.78        48.69        20.45         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-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
        1.64         9.40         0.10        37.87        33.01         6.25 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 
        0.46         2.50         5.56        29.59        13.74        15.72 
TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61A TCGA-HT-A74H 
       26.04        20.22         1.81        16.83         6.38         2.43 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8322 
       19.89         8.32        35.90         4.31        21.70        17.82 
TCGA-IK-8125 TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A731 TCGA-P5-A733 
       42.77         2.37         4.11         0.76         9.01        13.61 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-RY-A845 
        2.20         9.17         1.91        16.50         5.03        19.59 
TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WI TCGA-S9-A6WL 
       30.67        62.17        31.33        16.08        84.99        31.10 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7QY 
       14.07        36.13         7.92        22.32         7.13        28.37 
TCGA-S9-A7QZ TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84J 
       13.02        48.33        34.78        48.39        59.05        24.16 
TCGA-TM-A84L TCGA-TM-A84R TCGA-VM-A8CA TCGA-W9-A837 TCGA-WY-A859 TCGA-WY-A85A 
       40.83        18.61        13.51        51.06        39.88        43.40 
TCGA-WY-A85E 
       20.81 

subtype1 subtype2 subtype3 
    0.03     0.07     0.10 
subtype1 subtype2 subtype3 
  182.33   169.84   211.17 
subtype1 subtype2 subtype3 
   17.65    21.83    17.88 
[1] "0.0 - 182.3 (17.6)" "0.1 - 169.8 (21.8)" "0.1 - 211.2 (17.9)"
D11V2, continuous
D11V3, binary
          cls
clus         0   1
  subtype1  64 109
  subtype2  66  77
  subtype3  78  74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64  109
  subtype2   66   77
  subtype3   78   74
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       64       66       78
  MALE        109       77       74
[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"
D11V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          86               42                45
  subtype2          46               34                63
  subtype3          42               39                71
D11V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             86       46       42
  OLIGOASTROCYTOMA        42       34       39
  OLIGODENDROGLIOMA       45       63       71
[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"
D11V6, binary
          cls
clus         0   1
  subtype1  46 127
  subtype2  18 125
  subtype3  27 125
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46  127
  subtype2   18  125
  subtype3   27  125
     clus
vv    subtype1 subtype2 subtype3
  NO        46       18       27
  YES      127      125      125
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                         7
  subtype2                                0     4                         3
  subtype3                                0     2                         5
          vv
clus       WHITE
  subtype1   159
  subtype2   131
  subtype3   143
D11V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   2        4        2
  BLACK OR AFRICAN AMERICAN               7        3        5
  WHITE                                 159      131      143
[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"
D11V8, binary
          cls
clus         0   1
  subtype1   5 155
  subtype2   8 120
  subtype3   5 140
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  155
  subtype2    8  120
  subtype3    5  140
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        8        5
  NOT HISPANIC OR LATINO      155      120      140
[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(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1  70  12
  subtype2 109  16
  subtype3 150  27
  subtype4  44  38
subtype1 subtype2 subtype3 subtype4 
      82      125      177       82 
subtype1 subtype2 subtype3 subtype4 
      12       16       27       38 
$subtype1
TCGA-CS-4938 TCGA-CS-4944 TCGA-CS-6186 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-A4XD 
        4.70        10.62        17.69         8.48         7.56        39.78 
TCGA-DB-A64S TCGA-DB-A75O TCGA-DH-A7UV TCGA-DU-6396 TCGA-DU-6542 TCGA-DU-7014 
       27.45        30.74        18.61        75.16         7.73       117.40 
TCGA-DU-7015 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-A5TW TCGA-DU-A6S7 
       90.77        44.02        25.91        41.98         5.65         7.23 
TCGA-DU-A7TA TCGA-E1-5303 TCGA-E1-A7YW TCGA-E1-A7Z6 TCGA-FG-6691 TCGA-FG-8185 
       77.88        67.46        36.82        32.35        23.97        14.24 
TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MY TCGA-FN-7833 TCGA-HT-7472 
       14.96        32.61        38.27        23.70        27.52         0.03 
TCGA-HT-7473 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       16.54        40.34       106.95         4.01         5.03        29.85 
TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7680 TCGA-HT-7684 
      122.47        17.29        45.99        57.60         0.76         6.05 
TCGA-HT-7689 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 
       14.96        17.52        19.23        50.63        23.61         3.68 
TCGA-HT-8013 TCGA-HT-8111 TCGA-HT-8563 TCGA-HT-A74O TCGA-HW-A5KL TCGA-HW-A5KM 
       63.55         0.23        28.27         0.10        20.81        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-A72Z TCGA-P5-A730 TCGA-QH-A6X3 TCGA-QH-A870 TCGA-RY-A840 TCGA-S9-A6TU 
       11.64         0.20        10.29        12.99        28.08        87.12 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6WO TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R8 
       28.70        17.62        18.61        13.12        99.06        31.59 
TCGA-TM-A84B TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
       24.92        23.80        43.04        23.47        37.05        16.01 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85B TCGA-WY-A85D 
       13.32        43.96        45.80        37.71 

$subtype2
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 
        7.69        43.89        18.15        64.64         0.10         9.96 
TCGA-CS-6668 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
        8.02        81.96        75.25        47.93        72.92        50.86 
TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A64P TCGA-DB-A64Q 
       78.28        18.84        30.21        46.72        30.12         5.98 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K TCGA-DH-5140 TCGA-DH-5141 
       27.81        29.23        18.51        12.10        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DU-7018 TCGA-DU-A5TP TCGA-DU-A5TR 
       13.12        13.38         3.45        30.67        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5311 
       15.12         3.65       124.50        50.14        41.13       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-6690 
       78.21        95.57       130.78        14.33         0.23        24.99 
TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       15.35        40.08        18.71        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A70Y TCGA-HT-7468 TCGA-HT-7477 TCGA-HT-7483 TCGA-HT-7608 
       15.02        28.54         6.67        24.26       172.77        22.06 
TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7692 TCGA-HT-8114 TCGA-HT-A4DV TCGA-HT-A5R9 
        0.23        16.24         2.96        34.19        26.04         0.07 
TCGA-HT-A615 TCGA-HT-A619 TCGA-HT-A61B TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7490 
       16.93        21.40        17.52        15.35        11.05        19.23 
TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-A5KJ TCGA-KT-A74X TCGA-P5-A5F2 TCGA-P5-A72X 
       40.18        21.60        20.35        14.40         7.63        13.25 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53        12.62        15.85        14.04        19.33        14.83 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML 
       14.53        16.34        16.73        11.08        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-RY-A83X TCGA-RY-A83Y TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        30.87         5.46        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6UB TCGA-S9-A6WD 
       34.49        23.64        32.61        98.24       106.39        69.50 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IY TCGA-S9-A7J0 
       72.59        80.12        15.16        14.07        23.51        20.02 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7R4 TCGA-TM-A7C5 TCGA-TM-A84G 
        8.19         2.04        15.06        30.05        49.32        40.64 
TCGA-TM-A84H TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-TQ-A7RW 
       30.44        24.79        33.24        25.38        14.93        26.99 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VW-A7QS TCGA-WY-A85C TCGA-WY-A85E 
        0.10        35.93        23.21        46.88        20.81 

$subtype3
TCGA-CS-5393 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       40.18        17.95        12.43         7.40         6.61       122.73 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4X9 TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       50.17        44.52        46.42        37.45        33.57        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64R TCGA-DB-A64W TCGA-DB-A75L TCGA-DH-5143 
       31.63        24.20        31.40        14.40        11.24        14.40 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 
       17.19        54.25        14.56        17.46        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-7009 TCGA-DU-7019 
       94.52       114.08         7.96       156.23       138.28        26.30 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
       94.32        18.94        62.01        60.30        23.31         2.76 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       14.60        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R 
        8.65         2.70        77.98         5.98         7.13        21.30 
TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YO 
       42.31        23.51        44.42        79.99        57.93        75.02 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-7636 
        0.20        47.77        34.36        36.82        14.93        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 
       22.55        20.61        20.09        12.95        13.68        16.01 
TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       20.09        22.52        16.44        36.66        48.69        20.45 
TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.10        40.11         0.13         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 
        6.38        75.19        95.93        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-7874 TCGA-HT-7875 
        0.10         6.90        14.53        39.09        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        0.13         5.33        35.47        11.28        31.43         1.64 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 
        9.40         0.10        37.87        33.01         6.25         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-A5R5 TCGA-HT-A5R7 
        2.50         5.56        29.59        13.74         0.13        20.22 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 
        0.10         2.70         1.81        16.83         6.38        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 
       19.89         8.32        35.90         4.31        21.70        19.59 
TCGA-HW-8322 TCGA-IK-8125 TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A731 
       17.82        42.77         2.37         4.11         0.76         9.01 
TCGA-P5-A733 TCGA-QH-A65R TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XA 
       13.61        15.16         2.20         9.17         1.91        16.50 
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        31.33        16.08 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ 
       32.45        84.99        31.10        36.13        22.32         7.13 
TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C4 TCGA-TM-A7CA 
       17.03        28.37        13.02       169.84        48.33        34.78 
TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84L TCGA-TM-A84R TCGA-TQ-A7RH TCGA-VM-A8CA 
       48.39        59.05        40.83        18.61        15.98        13.51 
TCGA-W9-A837 TCGA-WY-A859 TCGA-WY-A85A 
       51.06        39.88        43.40 

$subtype4
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6188 TCGA-DB-A64O TCGA-DB-A75P TCGA-DU-5847 
       21.01         6.38        23.84        25.48        16.18        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-7007 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 
       16.83        11.47        62.96        14.99         6.54         8.84 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT 
       10.36         7.96         5.10        23.74        19.13         4.96 
TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 TCGA-DU-A7TD TCGA-DU-A7TJ 
       12.20        11.41        26.76        17.98         7.50         0.56 
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-A87N TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7686 
       22.26        10.78        13.58         5.72        11.54        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-A61C TCGA-HT-A74H TCGA-HW-A5KK TCGA-KT-A7W1 
        5.33        16.14        17.65         2.43        12.76        14.40 
TCGA-P5-A5EX TCGA-P5-A72U TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XC TCGA-RY-A83Z 
        1.64         0.16        14.53        12.23         5.03         9.90 
TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7R2 
       22.95         5.85        19.86        15.91         7.92        10.39 
TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84C TCGA-TM-A84I 
       98.63        18.71        11.97        49.45        16.18        28.08 
TCGA-TM-A84J TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VW-A8FI 
       24.16        30.08         7.89         8.05 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  122.47   172.77   211.17   133.74 
subtype1 subtype2 subtype3 subtype4 
   22.14    21.40    19.59    13.17 
[1] "0.0 - 122.5 (22.1)" "0.1 - 172.8 (21.4)" "0.1 - 211.2 (19.6)"
[4] "0.1 - 133.7 (13.2)"
D12V2, continuous
D12V3, binary
          cls
clus        0  1
  subtype1 31 52
  subtype2 47 78
  subtype3 89 89
  subtype4 41 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   52
  subtype2   47   78
  subtype3   89   89
  subtype4   41   41
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       31       47       89       41
  MALE         52       78       89       41
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          45               24                14
  subtype2          33               33                59
  subtype3          40               47                91
  subtype4          56               11                15
D12V5, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             45       33       40       56
  OLIGOASTROCYTOMA        24       33       47       11
  OLIGODENDROGLIOMA       14       59       91       15
[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"
D12V6, binary
          cls
clus         0   1
  subtype1  18  65
  subtype2  20 105
  subtype3  37 141
  subtype4  16  66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   65
  subtype2   20  105
  subtype3   37  141
  subtype4   16   66
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        18       20       37       16
  YES       65      105      141       66
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         2
  subtype2                                0     4                         3
  subtype3                                0     2                         5
  subtype4                                1     2                         5
          vv
clus       WHITE
  subtype1    79
  subtype2   116
  subtype3   166
  subtype4    72
D12V7, 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               2        3        5        5
  WHITE                                  79      116      166       72
[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"
D12V8, binary
          cls
clus         0   1
  subtype1   5  69
  subtype2   3 109
  subtype3   8 163
  subtype4   2  74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   69
  subtype2    3  109
  subtype3    8  163
  subtype4    2   74
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        3        8        2
  NOT HISPANIC OR LATINO       69      109      163       74
[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"
