[1] "ofn"        "-oTSARC-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/SARC-TP/15087563/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/15111074/SARC-TP.mergedcluster.txt"

nPatients in clinical file=250, in cluster file=260, common to both=250
[1]  10 250
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
66 83 72 25 
 1  2  3  4 
66 83 72 25 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6  7 
48 46 60 32 44 15  5 
 1  2  3  4  5  6  7 
48 46 60 32 44 15  5 
[1] "RPPA_CNMF"
[1] 3
  1   2   3 
 57 100  59 
  1   2   3 
 57 100  59 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
23 28 38 66 39 22 
 1  2  3  4  5  6 
23 28 38 66 39 22 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
113  74  61 
  1   2   3 
113  74  61 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
45 22 50 46 27 26 32 
 1  2  3  4  5  6  7 
45 22 50 46 27 26 32 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
104  49  95 
  1   2   3 
104  49  95 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
76 51 98 23 
 1  2  3  4 
76 51 98 23 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
80 62 47 
 1  2  3 
80 62 47 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8 
21 33 37 24 10 20 22 22 
 1  2  3  4  5  6  7  8 
21 33 37 24 10 20 22 22 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "DCC_UPLOAD_DATE"                       
 [6] "GENDER"                                
 [7] "RADIATION_THERAPY"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCH_NUMBER"                          

Input Data has 11 rows and 250 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=79,	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=166,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              26-3-2015 29-1-2015 31-12-2014
freq.values   "248"     "1"       "1"       
freq.contrast "2"       "249"     "249"     
both >= 3     "FALSE"   "FALSE"   "FALSE"   
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'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 8:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "1"     "249"  
freq.contrast "249"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 9:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'BATCH_NUMBER':	nDistinctValues=17,	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 250 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 43 23
  subtype2 58 24
  subtype3 44 28
  subtype4 17  7
subtype1 subtype2 subtype3 subtype4 
      66       82       72       24 
subtype1 subtype2 subtype3 subtype4 
      23       24       28        7 
$subtype1
TCGA-3B-A9HR TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-DX-A1KY TCGA-DX-A3UC TCGA-DX-A3UE 
       88.57        42.84        31.00        12.85        39.35        34.88 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BB 
       19.30        24.26        27.22        26.47        15.95        23.44 
TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A7EM TCGA-DX-A7ET 
        3.06        67.20        23.54        50.50        48.36         7.04 
TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR 
       17.95        59.87        33.07        44.68        38.17       124.37 
TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2T 
       27.95        36.69        60.66        86.10        12.07        71.57 
TCGA-HB-A3L4 TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       34.88        12.62        23.97        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       21.37        19.89        13.58        16.41         1.05         3.91 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JK TCGA-N1-A6IA 
       10.85         4.08        11.70        13.35         4.34         4.08 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-AA9N TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B 
        6.35        18.08         9.83        18.94        17.92         5.06 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 
        0.72        10.72        72.72        22.62         9.04        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X9-A971 
       29.92        18.08        18.35        25.71        15.95        15.58 

$subtype2
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9I0 
       36.30        53.49        54.74        25.25        10.32        36.03 
TCGA-3B-A9I3 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       26.56        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3U6 TCGA-DX-A3U8 
       27.81        60.30        59.47        54.77        17.75         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       10.68        44.45         9.73        14.96        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BK TCGA-DX-A6Z2 TCGA-DX-A7EL 
       25.15        11.47        28.96        16.18        88.31        75.32 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BZ 
      135.48        29.49        48.20        14.07         9.34         6.58 
TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       40.60         9.21        50.40        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO 
       84.66        50.89        71.31         0.10         0.07         2.07 
TCGA-IE-A4EK TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-K1-A3PN 
        1.38        40.08       143.41       116.88        73.28        71.70 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       36.39       123.78         9.04         8.28         0.49        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       17.98        15.65         7.46       120.20        37.55        38.63 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
        5.03         1.84        48.59        30.90       130.32        62.20 
TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ 
        0.72         6.58         9.93        13.22        11.93         4.80 
TCGA-WK-A8XT TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       41.49        38.96        17.72        36.43 

$subtype3
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX 
       19.69        68.55        18.64         0.56        14.04        38.24 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LY 
       36.69        54.21        59.24         6.28         9.04        17.10 
TCGA-DX-A3M2 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A6BA 
       34.68        42.77        14.99        28.80        64.18        66.05 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF 
       34.55        66.31        16.87        74.10        64.21        21.30 
TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A8BH TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BT 
       34.49        15.62        14.43        35.77        14.07        35.54 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W 
       19.43         1.15        12.99        49.18        96.89       106.45 
TCGA-DX-AB2X TCGA-DX-AB3A TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A2OT 
       13.28        32.15         0.07        20.32         0.07        48.30 
TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3K6 
       15.91         0.10        19.53         3.22        25.22        28.21 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-K1-A42W TCGA-MB-A5Y8 TCGA-MJ-A68H TCGA-MO-A47R 
        5.92        22.62        27.29         8.32        14.99        10.45 
TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VB 
       81.01        20.94        46.82        18.08        35.90       188.15 
TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q TCGA-VT-A80J 
       98.27        10.52        11.18        19.82        27.22        26.17 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C6 
       38.27        65.46        57.80        36.82        16.83        35.08 

$subtype4
TCGA-3B-A9HS TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A2J0 
       44.91        32.71        18.54        74.66         8.58         9.70 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A48N 
       23.08        70.49       108.13        20.05        15.06        12.26 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
        9.11        17.79        21.63         8.75         4.67        12.39 
TCGA-DX-AB35 TCGA-FX-A2QS TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-LI-A67I TCGA-SG-A6Z7 
       19.20         0.46         4.57        37.12        22.03         3.88 

subtype1 subtype2 subtype3 subtype4 
    0.72     0.07     0.07     0.46 
subtype1 subtype2 subtype3 subtype4 
  124.37   143.41   188.15   108.13 
subtype1 subtype2 subtype3 subtype4 
  20.630   30.195   25.695   18.165 
[1] "0.7 - 124.4 (20.6)" "0.1 - 143.4 (30.2)" "0.1 - 188.2 (25.7)"
[4] "0.5 - 108.1 (18.2)"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 43 23
  subtype2 41 42
  subtype3 40 32
  subtype4  8 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   23
  subtype2   41   42
  subtype3   40   32
  subtype4    8   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       43       41       40        8
  MALE         23       42       32       17
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         8    51
  subtype2     2                         6    65
  subtype3     2                         4    58
  subtype4     0                         0    20
D1V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        2        2        0
  BLACK OR AFRICAN AMERICAN        8        6        4        0
  WHITE                           51       65       58       20
[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"
D1V5, binary
          cls
clus        0  1
  subtype1  1 58
  subtype2  2 58
  subtype3  2 55
  subtype4  0 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   58
  subtype2    2   58
  subtype3    2   55
  subtype4    0   20
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        2        0
  NOT HISPANIC OR LATINO       58       58       55       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 32 16
  subtype2 35 10
  subtype3 41 19
  subtype4 16 16
  subtype5 25 19
  subtype6 12  2
  subtype7  4  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      48       45       60       32       44       14        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      16       10       19       16       19        2        1 
$subtype1
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 
       19.69        44.91        32.71        38.24        36.69        18.54 
TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       59.24         6.28         9.70       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS 
       15.06        12.26         9.11        21.63        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EU 
       67.20        23.54        50.50        74.10        64.21        12.20 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX 
       44.68        38.17       124.37        35.54        60.66        19.43 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB35 
        8.75         4.67        86.10        71.57        96.89        19.20 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-K1-A6RU 
       84.66        32.15         4.57        19.89        37.12        10.85 
TCGA-LI-A9QH TCGA-MB-A8JK TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-X6-A8C6 
       13.35         4.34        20.94         9.83        46.82        35.08 

$subtype2
TCGA-3B-A9HJ TCGA-3B-A9HT TCGA-DX-A1KU TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.30        54.74        14.04        54.21        33.53        42.54 
TCGA-DX-A23T TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3M2 
        5.26        59.47        54.77         9.04        70.49        34.68 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BK TCGA-DX-A7ES 
       17.75         4.54        28.96        17.79        16.18        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BP 
        7.04        17.95        14.43        59.87        35.77        14.07 
TCGA-DX-A8BQ TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-HB-A2OT TCGA-IE-A4EJ 
       42.44         9.21        50.40       101.98        48.30         3.22 
TCGA-K1-A3PO TCGA-K1-A6RT TCGA-MB-A5Y9 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VG 
       36.39         9.04         8.28         1.84        18.08        62.20 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71P TCGA-UE-A6QT TCGA-UE-A6QU 
        0.72        11.18         6.58        19.82        13.22         0.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-X9-A973 
       26.17        11.93        36.43 

$subtype3
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       53.49        68.55        88.57        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A3U7 TCGA-DX-A3U9 
       31.00        36.03        18.64        26.56        42.77        14.99 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       66.05        23.44        88.31        75.32        48.36        15.62 
TCGA-FX-A3NJ TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
        0.10        12.62        23.97         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-JV-A5VE 
       19.53         1.38        25.22        40.08        28.21        16.41 
TCGA-K1-A3PN TCGA-K1-A42W TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL 
       71.70        27.29         0.49        14.99       120.20        37.55 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
       81.01        18.08        72.72        38.27        65.46        56.61 
TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X9-A971 
        9.04        29.92        18.08        18.35        38.96        15.58 

$subtype4
TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3UA TCGA-DX-A7EI TCGA-DX-A7EO 
       12.85        74.66         8.58        10.68        34.49       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB3B 
       29.49        48.20        12.39        40.60        22.85        50.89 
TCGA-DX-AB3C TCGA-FX-A3RE TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N8 TCGA-IW-A3M5 
       71.31         0.07         2.07        34.88         0.10         5.92 
TCGA-JV-A75J TCGA-LI-A67I TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DN 
        3.91        22.03        19.73        15.65        10.45        38.63 
TCGA-PT-A8TR TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XQ 
       16.96        10.52         3.88        27.22         9.93         4.80 
TCGA-WK-A8XT TCGA-X6-A8C7 
       41.49        17.72 

$subtype5
TCGA-3R-A8YX TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A3LT TCGA-DX-A48K TCGA-DX-A6B8 
        0.56        76.41        60.30        23.08        19.30        15.95 
TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BS 
        3.06        16.87        21.30         9.34        33.07        27.95 
TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2P TCGA-DX-AB2Q 
       36.69         6.58         1.15        12.99        12.07        49.18 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB36 TCGA-FX-A3TO TCGA-IS-A3K7 TCGA-JV-A5VF 
      106.45        13.28        60.00        20.32       143.41         1.05 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QC-A7B5 
        4.08        11.70         8.32         4.08         6.35         5.03 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-SG-A6Z4 TCGA-SI-A71O 
       48.59        35.90       130.32        98.27        18.94        17.92 
TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 
        5.06        10.72        22.62        26.43        36.82        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 
       15.95        16.83 

$subtype6
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A3UB TCGA-DX-A6B9 TCGA-FX-A48G TCGA-FX-A76Y 
       66.87        27.81        44.45        11.47         0.07         0.07 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-K1-A42X TCGA-MJ-A68J TCGA-MO-A47P 
      116.88        73.28        22.62       123.78        17.98         7.46 
TCGA-QQ-A5VD TCGA-X2-A95T 
       30.90        57.80 

$subtype7
TCGA-FX-A2QS TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IS-A3KA TCGA-QQ-A8VB 
        0.46        15.91        41.33        13.58       188.15 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    4.34     0.72     0.10     0.07     0.56     0.07     0.46 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  124.37   101.98   120.20   135.48   143.41   123.78   188.15 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  32.430   17.950   27.255   17.340   18.430   29.355   15.910 
[1] "4.3 - 124.4 (32.4)" "0.7 - 102.0 (17.9)" "0.1 - 120.2 (27.3)"
[4] "0.1 - 135.5 (17.3)" "0.6 - 143.4 (18.4)" "0.1 - 123.8 (29.4)"
[7] "0.5 - 188.2 (15.9)"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 18 30
  subtype2 19 27
  subtype3 38 22
  subtype4 25  7
  subtype5 19 25
  subtype6 11  4
  subtype7  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   30
  subtype2   19   27
  subtype3   38   22
  subtype4   25    7
  subtype5   19   25
  subtype6   11    4
  subtype7    5    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       18       19       38       25       19       11        5
  MALE         30       27       22        7       25        4        0
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    39
  subtype2     2                         2    35
  subtype3     0                         7    51
  subtype4     1                         1    26
  subtype5     1                         4    34
  subtype6     2                         2     9
  subtype7     0                         0     4
D2V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        2        0        1        1
  BLACK OR AFRICAN AMERICAN        2        2        7        1        4
  WHITE                           39       35       51       26       34
                           clus
vv                          subtype6 subtype7
  ASIAN                            2        0
  BLACK OR AFRICAN AMERICAN        2        0
  WHITE                            9        4
[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"
D2V5, binary
          cls
clus        0  1
  subtype1  1 38
  subtype2  1 36
  subtype3  0 54
  subtype4  2 19
  subtype5  1 35
  subtype6  0  9
  subtype7  0  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   38
  subtype2    1   36
  subtype3    0   54
  subtype4    2   19
  subtype5    1   35
  subtype6    0    9
  subtype7    0    3
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        1        0        2        1        0
  NOT HISPANIC OR LATINO       38       36       54       19       35        9
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO        3
[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(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 41 16
  subtype2 59 41
  subtype3 44 15
subtype1 subtype2 subtype3 
      57      100       59 
subtype1 subtype2 subtype3 
      16       41       15 
$subtype1
TCGA-3B-A9HJ TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 
       36.30        14.04        32.71        38.24        18.54        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M2 
       27.81        60.30        54.77        23.08       108.13        34.68 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS 
        9.73        12.26        28.96        17.79        21.63        66.31 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7ES 
       67.20        23.54        50.50        74.10        64.21        14.07 
TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2F TCGA-DX-AB2H 
       12.20        17.95        60.66        19.43         8.75        12.39 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB30 
       86.10         9.21        71.57        96.89       106.45        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB3A TCGA-IE-A6BZ TCGA-K1-A6RT TCGA-MB-A8JK 
      101.98        19.20        32.15        19.89         9.04         4.34 
TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QQ-A5VD TCGA-RN-AAAQ TCGA-SI-A71Q TCGA-SI-AA8B 
       38.63        16.96        30.90        11.18        27.22         5.06 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80J 
        9.93        13.22        26.17 

$subtype2
TCGA-3B-A9HL TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       19.69        18.64         0.56        12.85        36.69        54.21 
TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LS TCGA-DX-A3LU 
        6.28         8.58         9.70        59.47         9.04        70.49 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A48K 
       20.05        15.06        17.75         4.54        10.68        19.30 
TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7EF 
       15.95         9.11        16.18         3.06        16.87        21.30 
TCGA-DX-A7EI TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ 
       34.49        29.49        48.20         7.04        14.43         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP 
       59.87        33.07        44.68        38.17        35.77        14.07 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BZ 
       42.44       124.37        27.95        35.54        36.69         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2X 
        1.15        12.99         4.67        12.07        49.18        13.28 
TCGA-DX-AB2Z TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       50.40        60.00        84.66        50.89        71.31         0.46 
TCGA-FX-A3TO TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IS-A3KA 
       20.32         0.10        41.33         3.22       143.41        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH 
        5.92         1.05        10.85         4.08        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM 
        8.32         8.28        19.73        10.45         4.08         6.35 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       20.94         5.03         9.83         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       48.59        35.90        98.27        62.20        10.52         0.72 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-UE-A6QU 
       18.94         3.88         6.58        17.92        19.82         0.72 
TCGA-VT-A80G TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 
       10.72        22.62        26.43        36.82        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       16.83        35.08        17.72        36.43 

$subtype3
TCGA-3B-A9I3 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       26.56        42.77        14.99        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       34.88        64.18        24.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        25.15        11.47        66.05        23.44 
TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-AB2J TCGA-FX-A3NJ 
       88.31        75.32        48.36        15.62        40.60         0.10 
TCGA-FX-A3RE TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        34.88         4.57        15.91        12.62        23.97 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IS-A3K6 
        9.80        80.48        21.37        19.53         1.38        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO 
      116.88        73.28        22.62        16.41        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-KF-A41W TCGA-MB-A5YA TCGA-MO-A47P TCGA-PC-A5DK 
       27.29       123.78        11.70         0.49         7.46       120.20 
TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-WK-A8XX TCGA-WP-A9GB 
       37.55        81.01        18.08       188.15        38.27         9.04 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X9-A971 
       29.92        18.08        18.35        38.96        15.58 

subtype1 subtype2 subtype3 
    4.34     0.10     0.07 
subtype1 subtype2 subtype3 
  108.13   143.41   188.15 
subtype1 subtype2 subtype3 
  27.810   17.735   26.560 
[1] "4.3 - 108.1 (27.8)" "0.1 - 143.4 (17.7)" "0.1 - 188.2 (26.6)"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1 26 31
  subtype2 49 51
  subtype3 39 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   31
  subtype2   49   51
  subtype3   39   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       26       49       39
  MALE         31       51       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    40
  subtype2     3                         7    77
  subtype3     2                         3    52
D3V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        3        2
  BLACK OR AFRICAN AMERICAN        3        7        3
  WHITE                           40       77       52
[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"
D3V5, binary
          cls
clus        0  1
  subtype1  2 39
  subtype2  1 77
  subtype3  0 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   39
  subtype2    1   77
  subtype3    0   49
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        0
  NOT HISPANIC OR LATINO       39       77       49
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 17  6
  subtype2 21  7
  subtype3 21 17
  subtype4 48 18
  subtype5 25 14
  subtype6 12 10
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      23       28       38       66       39       22 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       6        7       17       18       14       10 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A6YT 
       32.71        59.24       108.13        15.06        12.26        67.20 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A8BG TCGA-DX-A8BV 
       23.54        50.50        74.10        64.21        17.95        60.66 
TCGA-DX-AB2F TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB35 TCGA-DX-AB3A 
        8.75         9.21        71.57        96.89        19.20        32.15 
TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-MB-A8JK TCGA-PT-A8TR TCGA-SI-AA8B 
        4.57        19.89         4.34        16.96         5.06 

$subtype2
TCGA-3B-A9HJ TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23T 
       36.30        14.04        38.24        54.21        42.54         5.26 
TCGA-DX-A23U TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       76.41        27.81        60.30        59.47        54.77        23.08 
TCGA-DX-A3M2 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A8BK TCGA-DX-A8BO 
       34.68        28.96        17.79        21.63        59.87        35.77 
TCGA-DX-A8BR TCGA-DX-AB2H TCGA-DX-AB32 TCGA-DX-AB37 TCGA-K1-A6RU TCGA-MB-A5Y9 
      124.37        12.39       101.98        84.66        10.85         8.28 
TCGA-QQ-A5VA TCGA-RN-AAAQ TCGA-VT-A80J TCGA-X6-A8C3 
       18.08        11.18        26.17        15.95 

$subtype3
TCGA-3B-A9HL TCGA-3R-A8YX TCGA-DX-A3U8 TCGA-DX-A48K TCGA-DX-A6YX TCGA-DX-A7EF 
       19.69         0.56         4.54        19.30        16.87        21.30 
TCGA-DX-A7EI TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BP TCGA-DX-A8BS 
       34.49         7.04        14.43         9.34        14.07        27.95 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
       19.43         6.58        12.99        86.10        12.07        49.18 
TCGA-DX-AB2X TCGA-DX-AB36 TCGA-FX-A3TO TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-K1-A6RV 
       13.28        60.00        20.32         3.22       143.41         4.08 
TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A5VC 
       11.70         8.32         4.08         6.35        20.94        35.90 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-SG-A849 TCGA-SI-A71O TCGA-X6-A7W8 TCGA-X6-A7WC 
      188.15        98.27         6.58        17.92        26.43        36.82 
TCGA-X6-A8C4 TCGA-X6-A8C6 
       16.83        35.08 

$subtype4
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A23V TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB 
       18.64        26.56        66.87        42.77        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM 
       11.47        66.05        23.44        88.31        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7ES TCGA-DX-AB2W TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A3L4 
       15.62        14.07       106.45         0.10         0.07        34.88 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       15.91        12.62        23.97        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
       21.37        19.53         1.38        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       73.28        22.62        16.41        71.70        36.39        27.29 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-MB-A5YA TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL 
      123.78         9.04         0.49         7.46       120.20        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-WK-A8XX 
       38.63        81.01        18.08        30.90        13.22        38.27 
TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X9-A971 
        9.04        29.92        18.08        18.35        38.96        15.58 

$subtype5
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23Y 
       12.85        36.69        18.54        33.53        74.66         6.28 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3M1 TCGA-DX-A3U6 
        8.58         9.70         9.04        70.49        20.05        17.75 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A7EU TCGA-DX-A8BL 
        9.11        16.18         3.06        66.31        12.20        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BQ TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-AATS 
       44.68        38.17        42.44        35.54        36.69         1.15 
TCGA-DX-AB2G TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-LI-A9QH TCGA-MB-A8JL TCGA-MO-A47R 
        4.67        50.40        50.89        13.35        19.73        10.45 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-SG-A6Z4 TCGA-UE-A6QU TCGA-VT-A80G 
        9.83        46.82        48.59        18.94         0.72        10.72 
TCGA-WK-A8Y0 TCGA-X6-A8C2 TCGA-X9-A973 
       22.62        25.71        36.43 

$subtype6
TCGA-DX-A3UA TCGA-DX-A6B8 TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-AB2J TCGA-DX-AB30 
       10.68        15.95        29.49        48.20        40.60        22.85 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-HS-A5N8 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-LI-A67I 
       71.31         0.46         0.10         5.92         1.05        22.03 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
        5.03         1.84        62.20        10.52         0.72         3.88 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-X6-A8C7 
       19.82        27.22         9.93        17.72 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    4.34     5.26     0.56     0.07     0.72     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  108.13   124.37   188.15   123.78    74.66    71.31 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  23.540   31.820   17.395   26.515   19.730   13.315 
[1] "4.3 - 108.1 (23.5)" "5.3 - 124.4 (31.8)" "0.6 - 188.2 (17.4)"
[4] "0.1 - 123.8 (26.5)" "0.7 - 74.7 (19.7)"  "0.1 - 71.3 (13.3)" 
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 10 13
  subtype2 11 17
  subtype3 16 22
  subtype4 44 22
  subtype5 19 20
  subtype6 14  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   13
  subtype2   11   17
  subtype3   16   22
  subtype4   44   22
  subtype5   19   20
  subtype6   14    8
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       10       11       16       44       19       14
  MALE         13       17       22       22       20        8
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    20
  subtype2     1                         0    18
  subtype3     0                         4    31
  subtype4     3                         5    54
  subtype5     2                         1    27
  subtype6     0                         2    19
D4V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        1        0        3        2
  BLACK OR AFRICAN AMERICAN        1        0        4        5        1
  WHITE                           20       18       31       54       27
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        2
  WHITE                           19
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1  1 19
  subtype2  0 18
  subtype3  2 30
  subtype4  0 56
  subtype5  0 26
  subtype6  0 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   19
  subtype2    0   18
  subtype3    2   30
  subtype4    0   56
  subtype5    0   26
  subtype6    0   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        2        0        0        0
  NOT HISPANIC OR LATINO       19       18       30       56       26       16
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 76 36
  subtype2 53 21
  subtype3 35 25
subtype1 subtype2 subtype3 
     112       74       60 
subtype1 subtype2 subtype3 
      36       21       25 
$subtype1
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3R-A8YX TCGA-DX-A1KU 
       36.30        19.69        44.91        54.74         0.56        14.04 
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       38.24        36.69        18.54        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       42.54         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY 
        9.70        59.47        54.77        23.08        70.49        17.10 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A48K TCGA-DX-A6BE 
       34.68        15.06        17.75         4.54        19.30        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
        9.11        17.79        21.63         3.06        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       67.20        23.54        50.50        16.87        74.10        64.21 
TCGA-DX-A7EF TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH 
       21.30        14.07         7.04        12.20        17.95        14.43 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP 
       59.87        33.07        44.68        38.17        35.77        14.07 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       42.44       124.37        27.95        35.54        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O 
       19.43         6.58        12.99         8.75         4.67        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W 
       12.07        49.18         9.21        71.57        96.89       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-FX-A3TO 
       13.28        50.40       101.98        19.20        84.66        20.32 
TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-K1-A6RT 
       48.30         3.22        19.89        37.12       143.41         9.04 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JK 
       10.85         4.08        13.35         8.32         8.28         4.34 
TCGA-MJ-A68J TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       17.98         6.35        20.94         5.03         1.84        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-UE-A6QT 
       48.59        35.90        18.94         6.58        17.92        13.22 
TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC 
        0.72        26.17        11.93        22.62        26.43        36.82 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C6 
       25.71        15.95        16.83        35.08 

$subtype2
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       53.49        68.55        88.57        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A3U7 TCGA-DX-A3U9 
       31.00        36.03        18.64        26.56        42.77        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 
       24.26        27.22        14.96        26.47        72.72        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM 
       11.47        66.05        23.44        88.31        75.32        48.36 
TCGA-DX-A7EN TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HB-A43Z 
       15.62         0.10         0.07         0.07        34.88        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       19.53         1.38        25.22        40.08        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A42W 
       13.58        73.28        22.62        16.41        71.70        27.29 
TCGA-K1-A42X TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL 
      123.78         0.49        14.99         7.46       120.20        37.55 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5VD TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       81.01        18.08        30.90        72.72        38.27        65.46 
TCGA-WK-A8XZ TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       56.61         9.04        57.80        29.92        18.08        18.35 
TCGA-X6-A8C5 TCGA-X9-A971 
       38.96        15.58 

$subtype3
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A3LS 
       32.71        12.85        74.66        60.30         8.58         9.04 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A7EI 
      108.13        20.05        10.68        12.26        15.95        34.49 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BJ TCGA-DX-AATS TCGA-DX-AB2H 
      135.48        29.49        48.20         9.34         1.15        12.39 
TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       40.60        22.85        60.00        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A8OO TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IW-A3M5 
        0.46         0.07         2.07         4.57         0.10         5.92 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A8JL 
        1.05         3.91        36.39        11.70        22.03        19.73 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QC-AA9N 
       15.65        10.45         4.08        38.63        16.96         9.83 
TCGA-QQ-A5VA TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       18.08       188.15       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
        0.72        11.18         3.88        19.82        27.22         5.06 
TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 TCGA-X9-A973 
        9.93        10.72         4.80        41.49        17.72        36.43 

subtype1 subtype2 subtype3 
    0.56     0.07     0.07 
subtype1 subtype2 subtype3 
  143.41   123.78   188.15 
subtype1 subtype2 subtype3 
  22.125   27.750   16.455 
[1] "0.6 - 143.4 (22.1)" "0.1 - 123.8 (27.8)" "0.1 - 188.2 (16.5)"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 49 64
  subtype2 51 23
  subtype3 34 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49   64
  subtype2   51   23
  subtype3   34   27
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       49       51       34
  MALE         64       23       27
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         6    85
  subtype2     2                         8    61
  subtype3     1                         4    50
D5V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        2        1
  BLACK OR AFRICAN AMERICAN        6        8        4
  WHITE                           85       61       50
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1  3 86
  subtype2  0 63
  subtype3  2 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   86
  subtype2    0   63
  subtype3    2   44
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        0        2
  NOT HISPANIC OR LATINO       86       63       44
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 29 16
  subtype2 19  2
  subtype3 35 15
  subtype4 27 18
  subtype5 16 11
  subtype6 20  6
  subtype7 18 14
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      45       21       50       45       27       26       32 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      16        2       15       18       11        6       14 
$subtype1
TCGA-3B-A9HL TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       19.69        32.71        38.24        18.54        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2J0 TCGA-DX-A3LU 
       33.53        66.87         6.28        27.81         9.70        70.49 
TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A6BF TCGA-DX-A6YR TCGA-DX-A6YS 
       17.10        34.68        15.06         9.11        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EU 
       67.20        23.54        50.50        74.10        64.21        12.20 
TCGA-DX-A8BG TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX 
       17.95        38.17       124.37        35.54        60.66        19.43 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB35 
        8.75         4.67        86.10        71.57        96.89        19.20 
TCGA-FX-A3TO TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-K1-A6RU TCGA-LI-A9QH 
       20.32         3.22        19.89        37.12        10.85        13.35 
TCGA-QQ-A5V9 TCGA-UE-A6QU TCGA-X6-A8C6 
       46.82         0.72        35.08 

$subtype2
TCGA-3B-A9HJ TCGA-DX-A1KZ TCGA-DX-A23T TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       36.30        36.69         5.26        59.47        54.77        23.08 
TCGA-DX-A3U6 TCGA-DX-A6BE TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BL 
       17.75        28.96        14.07         7.04        59.87        33.07 
TCGA-DX-A8BO TCGA-DX-AB2S TCGA-DX-AB32 TCGA-DX-AB37 TCGA-MB-A5Y9 TCGA-MB-A8JK 
       35.77         9.21       101.98        84.66         8.28         4.34 
TCGA-MJ-A68J TCGA-QC-A6FX TCGA-UE-A6QT 
       17.98        20.94        13.22 

$subtype3
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ 
       53.49        68.55        88.57        25.25        10.32        31.00 
TCGA-3B-A9I0 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       36.03        42.77        14.99        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       64.18         9.73        24.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EL 
       72.72        25.15        66.05        23.44        88.31        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-FX-A3NJ TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A3OV 
       48.36        15.62         0.10        12.62        23.97        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-K1-A3PN TCGA-K1-A42W 
       19.53         1.38        25.22        40.08        71.70        27.29 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP 
        0.49        14.99       120.20        37.55        81.01        18.08 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-X6-A7WA TCGA-X6-A7WD 
       72.72        38.27        65.46        56.61        29.92        18.35 
TCGA-X6-A8C5 TCGA-X9-A971 
       38.96        15.58 

$subtype4
TCGA-3B-A9HS TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3LW 
       44.91        14.04        12.85        74.66         8.58       108.13 
TCGA-DX-A3M1 TCGA-DX-A48N TCGA-DX-A6BH TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ 
       20.05        12.26        21.63        34.49       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A8BM TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB3A 
       48.20        44.68        12.39        40.60        22.85        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A8OO TCGA-HB-A3YV TCGA-HS-A5N8 
       50.89        71.31         0.46         2.07         4.57         0.10 
TCGA-IW-A3M5 TCGA-JV-A75J TCGA-LI-A67I TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DN 
        5.92         3.91        22.03        15.65        10.45        38.63 
TCGA-PT-A8TR TCGA-QC-AA9N TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       16.96         9.83       188.15        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XQ 
       11.18         3.88        19.82        27.22         9.93         4.80 
TCGA-WK-A8XT TCGA-X6-A8C7 TCGA-X9-A973 
       41.49        17.72        36.43 

$subtype5
TCGA-3B-A9HT TCGA-3R-A8YX TCGA-DX-A3U8 TCGA-DX-A48K TCGA-DX-A6YQ TCGA-DX-A6YX 
       54.74         0.56         4.54        19.30         3.06        16.87 
TCGA-DX-A7EF TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BU TCGA-DX-AB2E 
       21.30        14.43        14.07        42.44        36.69        12.99 
TCGA-DX-AB2Q TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB36 TCGA-K1-A6RT 
       49.18       106.45        13.28        50.40        60.00         9.04 
TCGA-KF-A41W TCGA-PC-A5DM TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SG-A849 TCGA-VT-A80J 
       11.70         6.35        35.90        98.27         6.58        26.17 
TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-X6-A8C4 
       26.43        15.95        16.83 

$subtype6
TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A3UB TCGA-DX-A6B9 TCGA-FX-A3RE 
       42.84        18.64        26.56        44.45        11.47         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-HS-A5NA 
        0.07         0.07        34.88        15.91        41.33         9.80 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 
       21.37        28.21       116.88        13.58        73.28        22.62 
TCGA-JV-A5VE TCGA-K1-A3PO TCGA-K1-A42X TCGA-MO-A47P TCGA-QQ-A5VD TCGA-WP-A9GB 
       16.41        36.39       123.78         7.46        30.90         9.04 
TCGA-X2-A95T TCGA-X6-A7WB 
       57.80        18.08 

$subtype7
TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A3LS TCGA-DX-A3UA TCGA-DX-A6B8 
       42.54        76.41        60.30         9.04        10.68        15.95 
TCGA-DX-A6BG TCGA-DX-A8BJ TCGA-DX-A8BS TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2P 
       17.79         9.34        27.95         6.58         1.15        12.07 
TCGA-HB-A2OT TCGA-IS-A3K7 TCGA-JV-A5VF TCGA-K1-A6RV TCGA-MB-A5Y8 TCGA-MB-A8JL 
       48.30       143.41         1.05         4.08         8.32        19.73 
TCGA-N1-A6IA TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A8VD 
        4.08         5.03         1.84        18.08        48.59       130.32 
TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8Y0 
       18.94        17.92         5.06        10.72        11.93        22.62 
TCGA-X6-A7WC TCGA-X6-A8C2 
       36.82        25.71 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.72     4.34     0.10     0.10     0.56     0.07     1.05 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  124.37   101.98   120.20   188.15   106.45   123.78   143.41 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  33.530   23.080   30.460   19.820   16.870   21.995   16.870 
[1] "0.7 - 124.4 (33.5)" "4.3 - 102.0 (23.1)" "0.1 - 120.2 (30.5)"
[4] "0.1 - 188.2 (19.8)" "0.6 - 106.5 (16.9)" "0.1 - 123.8 (22.0)"
[7] "1.1 - 143.4 (16.9)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 21 24
  subtype2  9 13
  subtype3 30 20
  subtype4 25 21
  subtype5 12 15
  subtype6 22  4
  subtype7 15 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   24
  subtype2    9   13
  subtype3   30   20
  subtype4   25   21
  subtype5   12   15
  subtype6   22    4
  subtype7   15   17
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       21        9       30       25       12       22       15
  MALE         24       13       20       21       15        4       17
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    33
  subtype2     1                         2    15
  subtype3     0                         5    44
  subtype4     1                         2    39
  subtype5     1                         0    22
  subtype6     2                         3    19
  subtype7     0                         5    24
D6V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        0        1        1
  BLACK OR AFRICAN AMERICAN        1        2        5        2        0
  WHITE                           33       15       44       39       22
                           clus
vv                          subtype6 subtype7
  ASIAN                            2        0
  BLACK OR AFRICAN AMERICAN        3        5
  WHITE                           19       24
[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"
D6V5, binary
          cls
clus        0  1
  subtype1  1 32
  subtype2  1 16
  subtype3  0 46
  subtype4  2 33
  subtype5  1 22
  subtype6  0 19
  subtype7  0 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   32
  subtype2    1   16
  subtype3    0   46
  subtype4    2   33
  subtype5    1   22
  subtype6    0   19
  subtype7    0   25
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        1        0        2        1        0
  NOT HISPANIC OR LATINO       32       16       46       33       22       19
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO       25
[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(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 63 40
  subtype2 35 13
  subtype3 65 30
subtype1 subtype2 subtype3 
     103       48       95 
subtype1 subtype2 subtype3 
      40       13       30 
$subtype1
TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 
       44.91         0.56        32.71        38.24        18.54        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U6 
        9.04        23.08       108.13        20.05        34.68        17.75 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS 
       19.30        12.26        17.79        21.63        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ 
       67.20        50.50        21.30        34.49       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BT 
       48.20         7.04        12.20        33.07        38.17        35.54 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
       19.43         1.15         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB36 
       86.10        12.07        96.89        13.28        19.20        60.00 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A8OO 
       32.15        50.89        71.31         0.46        20.32         2.07 
TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE 
        4.57        19.89        37.12       143.41         5.92        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 
        1.05         3.91         4.08        11.70        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM 
        8.28        19.73        15.65        10.45         4.08         6.35 
TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       38.63        16.96        20.94         9.83        46.82        48.59 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 
      188.15       130.32        10.52         0.72        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-WK-A8XO 
        6.58        19.82        27.22         5.06         9.93        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C6 TCGA-X6-A8C7 
        4.80        41.49        26.43        36.82        35.08        17.72 
TCGA-X9-A973 
       36.43 

$subtype2
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LU 
       36.30        19.69        36.69        54.21         6.28        70.49 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3UA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BK 
       17.10        15.06        10.68        28.96         9.11        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7ES TCGA-DX-A8BH 
        3.06        23.54        16.87        74.10        14.07        14.43 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR 
       59.87        44.68        35.77        14.07        42.44       124.37 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W 
       60.66         6.58        49.18         9.21        71.57       106.45 
TCGA-DX-AB2Z TCGA-DX-AB37 TCGA-HB-A2OT TCGA-K1-A6RT TCGA-K1-A6RU TCGA-MB-A8JK 
       50.40        84.66        48.30         9.04        10.85         4.34 
TCGA-MJ-A68J TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       17.98         5.03        18.08        30.90        98.27        62.20 
TCGA-RN-AAAQ TCGA-SI-A71O TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8Y0 TCGA-X6-A8C2 
       11.18        17.92         0.72        26.17        22.62        25.71 

$subtype3
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       53.49        68.55        88.57        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       10.32        31.00        36.03        18.64        26.56        14.04 
TCGA-DX-A1KY TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       12.85        42.77         4.54        14.99        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O 
       28.80        34.88        64.18         9.73        24.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       14.96        26.47        72.72        25.08        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL 
       11.47        66.05        23.44        64.21        88.31        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BS TCGA-DX-A8BU 
       48.36        15.62        17.95         9.34        27.95        36.69 
TCGA-DX-AB2E TCGA-DX-AB30 TCGA-DX-AB32 TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       12.99        22.85       101.98         0.10         0.07         0.07 
TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07        34.88        15.91        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37        19.53         3.22         1.38 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        40.08        28.21       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-LI-A67I 
       22.62        71.70        36.39        27.29       123.78        22.03 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO 
        0.49        14.99         7.46       120.20        37.55        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XS 
       18.08         1.84        35.90        13.22        10.72        72.72 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       38.27        65.46        56.61         9.04        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X9-A971 
       18.08        18.35        15.95        38.96        15.58 

subtype1 subtype2 subtype3 
    0.46     0.72     0.07 
subtype1 subtype2 subtype3 
  188.15   124.37   123.78 
subtype1 subtype2 subtype3 
   20.05    23.08    25.22 
[1] "0.5 - 188.2 (20.1)" "0.7 - 124.4 (23.1)" "0.1 - 123.8 (25.2)"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 49 55
  subtype2 24 25
  subtype3 60 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49   55
  subtype2   24   25
  subtype3   60   35
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       49       24       60
  MALE         55       25       35
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         6    80
  subtype2     1                         4    39
  subtype3     4                         8    78
D7V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        4
  BLACK OR AFRICAN AMERICAN        6        4        8
  WHITE                           80       39       78
[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"
D7V5, binary
          cls
clus        0  1
  subtype1  3 73
  subtype2  2 42
  subtype3  0 78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   73
  subtype2    2   42
  subtype3    0   78
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        2        0
  NOT HISPANIC OR LATINO       73       42       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"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 46 29
  subtype2 36 14
  subtype3 68 30
  subtype4 13 10
subtype1 subtype2 subtype3 subtype4 
      75       50       98       23 
subtype1 subtype2 subtype3 subtype4 
      29       14       30       10 
$subtype1
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       19.69        44.91         0.56        32.71        38.24        18.54 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        33.53        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3UA TCGA-DX-A48N 
       23.08       108.13        20.05        34.68        10.68        12.26 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT 
        9.11        17.79        21.63        34.55        66.31        67.20 
TCGA-DX-A6YX TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN 
       16.87         7.04        12.20        59.87        33.07        38.17 
TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O 
       35.54        19.43         1.15         8.75         4.67        86.10 
TCGA-DX-AB2P TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB35 TCGA-DX-AB3A 
       12.07        96.89        13.28        50.40        19.20        32.15 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 
        0.46        20.32         4.57        19.89        37.12       143.41 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MO-A47R TCGA-N1-A6IA 
       10.85         4.08        11.70        13.35        10.45         4.08 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V9 
        6.35        38.63        16.96        20.94         5.03        46.82 
TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-AA8B TCGA-WK-A8XO 
       48.59       130.32        18.94         6.58         5.06        11.93 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C6 
       26.43        36.82        35.08 

$subtype2
TCGA-3B-A9HJ TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23Y TCGA-DX-A3LU 
       36.30        36.69        54.21        42.54         6.28        70.49 
TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A48K TCGA-DX-A6BE TCGA-DX-A6BK TCGA-DX-A6YQ 
       17.10        17.75        19.30        28.96        16.18         3.06 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7ES TCGA-DX-A8BH 
       50.50        74.10        21.30        34.49        14.07        14.43 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BZ 
       44.68        35.77        42.44       124.37        60.66         6.58 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB36 TCGA-DX-AB37 
       49.18         9.21        71.57       106.45        60.00        84.66 
TCGA-FX-A3RE TCGA-HB-A2OT TCGA-K1-A6RT TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JK 
        0.07        48.30         9.04         8.32         8.28         4.34 
TCGA-MJ-A68J TCGA-QC-AA9N TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VG 
       17.98         9.83        18.08        35.90        98.27        62.20 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71O TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-A80J 
        0.72        11.18        17.92        19.82         0.72        26.17 
TCGA-WK-A8Y0 TCGA-X6-A8C2 
       22.62        25.71 

$subtype3
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       53.49        68.55        88.57        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       10.32        31.00        36.03        18.64        26.56        14.04 
TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       12.85        15.06        42.77         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YU TCGA-DX-A6Z0 
       15.95        11.47        66.05        23.44        23.54        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BG TCGA-DX-A8BJ 
       88.31        75.32        48.36        15.62        17.95         9.34 
TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB30 TCGA-DX-AB32 
       14.07        27.95        36.69        12.99        22.85       101.98 
TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 
        0.10         0.07         0.07        34.88        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
       23.97         0.10         9.80        80.48        21.37        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        3.22         1.38        25.22        40.08        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        73.28        22.62        16.41        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MO-A47P 
       27.29       123.78        22.03         0.49        14.99         7.46 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VD 
      120.20        37.55        81.01        18.08         1.84        30.90 
TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
       13.22        10.72        72.72        38.27        65.46        56.61 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 
        9.04        57.80        29.92        18.08        18.35        15.95 
TCGA-X6-A8C5 TCGA-X9-A971 
       38.96        15.58 

$subtype4
TCGA-DX-A2IZ TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-AB2H TCGA-DX-AB2J 
        8.58       135.48        29.49        48.20        12.39        40.60 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A8OO TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J 
       50.89        71.31         2.07         5.92         1.05         3.91 
TCGA-MB-A8JL TCGA-MJ-A850 TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71Q 
       19.73        15.65       188.15        10.52         3.88        27.22 
TCGA-SI-AA8C TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 TCGA-X9-A973 
        9.93         4.80        41.49        17.72        36.43 

subtype1 subtype2 subtype3 subtype4 
    0.46     0.07     0.07     1.05 
subtype1 subtype2 subtype3 subtype4 
  143.41   124.37   123.78   188.15 
subtype1 subtype2 subtype3 subtype4 
  20.320   24.165   25.115   17.720 
[1] "0.5 - 143.4 (20.3)" "0.1 - 124.4 (24.2)" "0.1 - 123.8 (25.1)"
[4] "1.1 - 188.2 (17.7)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 32 44
  subtype2 25 26
  subtype3 60 38
  subtype4 16  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   44
  subtype2   25   26
  subtype3   60   38
  subtype4   16    7
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       32       25       60       16
  MALE         44       26       38        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    57
  subtype2     1                         5    40
  subtype3     4                         9    80
  subtype4     0                         2    20
D8V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        4        0
  BLACK OR AFRICAN AMERICAN        2        5        9        2
  WHITE                           57       40       80       20
[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"
D8V5, binary
          cls
clus        0  1
  subtype1  1 56
  subtype2  2 43
  subtype3  0 81
  subtype4  2 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   56
  subtype2    2   43
  subtype3    0   81
  subtype4    2   13
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        0        2
  NOT HISPANIC OR LATINO       56       43       81       13
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 47 32
  subtype2 40 22
  subtype3 35 11
subtype1 subtype2 subtype3 
      79       62       46 
subtype1 subtype2 subtype3 
      32       22       11 
$subtype1
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       19.69        44.91         0.56        32.71        38.24        18.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       74.66         5.26        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 
        9.70        59.47         9.04       108.13        20.05        34.68 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6YR TCGA-DX-A6YS 
       19.30        12.26        28.96         9.11        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A7EI TCGA-DX-A7EQ TCGA-DX-A7EU TCGA-DX-A8BN TCGA-DX-A8BT 
       67.20        34.49        29.49        12.20        38.17        35.54 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
       19.43         1.15         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2V TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3A 
       86.10        12.07        96.89        19.20        60.00        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A8OO 
       50.89        71.31         0.46         0.07        20.32         2.07 
TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J 
        4.57        37.12       143.41         5.92         1.05         3.91 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R 
        4.08        11.70        13.35        19.73        15.65        10.45 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QC-AA9N TCGA-QQ-A8VB TCGA-QQ-A8VD 
        6.35        38.63        16.96         9.83       188.15       130.32 
TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
       10.52        18.94         3.88        27.22         5.06         9.93 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A7WC TCGA-X6-A8C6 TCGA-X6-A8C7 
       11.93         4.80        41.49        36.82        35.08        17.72 
TCGA-X9-A973 
       36.43 

$subtype2
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       53.49        68.55        88.57        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 
       31.00        18.64        26.56        14.04        12.85        15.06 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A6BA TCGA-DX-A6BB 
       42.77        14.99        24.26        27.22        66.05        23.44 
TCGA-DX-A6YU TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BU TCGA-DX-A8BV 
       23.54        14.07        17.95         9.34        36.69        60.66 
TCGA-DX-AB30 TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       22.85         0.10         0.07        15.91        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IF-A4AJ 
        0.10         9.80        80.48        21.37        19.53        25.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
       40.08        13.58        73.28        22.62        16.41        71.70 
TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-PC-A5DK 
       36.39        22.03         0.49         4.34        14.99       120.20 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5VD TCGA-SI-A71O TCGA-WK-A8XS TCGA-WK-A8XX 
       81.01        18.08        30.90        17.92        72.72        38.27 
TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46        56.61         9.04        57.80        29.92        18.08 
TCGA-X6-A8C5 TCGA-X9-A971 
       38.96        15.58 

$subtype3
TCGA-DX-A1KZ TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A6YQ 
       36.69        17.10        17.75         4.54        10.68         3.06 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL 
       16.87        74.10         7.04        14.43        59.87        33.07 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS 
       44.68        35.77        14.07        42.44       124.37        27.95 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
       49.18         9.21        71.57       106.45        13.28        50.40 
TCGA-DX-AB32 TCGA-DX-AB37 TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-K1-A6RT TCGA-K1-A6RU 
      101.98        84.66        48.30         3.22         9.04        10.85 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-QQ-A5VC 
        8.32         8.28        20.94         5.03        48.59        35.90 
TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-A80J 
       62.20        11.18         6.58        19.82         0.72        26.17 
TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C3 
       22.62        26.43        25.71        15.95 

subtype1 subtype2 subtype3 
    0.07     0.07     0.72 
subtype1 subtype2 subtype3 
  188.15   120.20   124.37 
subtype1 subtype2 subtype3 
   19.43    23.49    21.78 
[1] "0.1 - 188.2 (19.4)" "0.1 - 120.2 (23.5)" "0.7 - 124.4 (21.8)"
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1 40 40
  subtype2 40 22
  subtype3 25 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   40
  subtype2   40   22
  subtype3   25   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       40       40       25
  MALE         40       22       22
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    64
  subtype2     1                         6    51
  subtype3     2                         4    37
D9V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        2
  BLACK OR AFRICAN AMERICAN        3        6        4
  WHITE                           64       51       37
[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"
D9V5, binary
          cls
clus        0  1
  subtype1  2 57
  subtype2  0 55
  subtype3  2 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   57
  subtype2    0   55
  subtype3    2   40
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        0        2
  NOT HISPANIC OR LATINO       57       55       40
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 17  4
  subtype2 20 12
  subtype3 23 14
  subtype4 14 10
  subtype5  9  1
  subtype6 10 10
  subtype7 17  4
  subtype8 12 10
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      21       32       37       24       10       20       21       22 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       4       12       14       10        1       10        4       10 
$subtype1
TCGA-DX-A1KZ TCGA-DX-A3LY TCGA-DX-A3UA TCGA-DX-A6BE TCGA-DX-A6YZ TCGA-DX-A8BK 
       36.69        17.10        10.68        28.96        74.10        59.87 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-AB2T 
       33.07        44.68        38.17       124.37        60.66        71.57 
TCGA-DX-AB37 TCGA-FX-A3RE TCGA-K1-A6RU TCGA-LI-A9QH TCGA-MB-A8JK TCGA-QC-AA9N 
       84.66         0.07        10.85        13.35         4.34         9.83 
TCGA-SI-A71O TCGA-WK-A8XQ TCGA-X9-A973 
       17.92         4.80        36.43 

$subtype2
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R 
       19.69        44.91        32.71        38.24        18.54        74.66 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LW 
       66.87        27.81        60.30         9.70        59.47       108.13 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6YR TCGA-DX-A6YS 
       20.05        34.68        12.26         9.11        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A7EU TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F 
       67.20        12.20        35.54        19.43         1.15         8.75 
TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A2QS 
        4.67        86.10        96.89        19.20        32.15         0.46 
TCGA-HB-A3YV TCGA-IF-A3RQ 
        4.57        37.12 

$subtype3
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ 
       53.49        68.55        88.57        25.25        10.32        31.00 
TCGA-3B-A9I1 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A6BA 
       18.64        42.77        14.99        24.26        27.22        66.05 
TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA 
        0.10         0.07        15.91        12.62        23.97         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IW-A3M4 TCGA-K1-A3PN 
       80.48        19.53        25.22        40.08        73.28        71.70 
TCGA-MB-A5YA TCGA-PC-A5DK TCGA-PC-A5DO TCGA-PC-A5DP TCGA-WK-A8XS TCGA-WK-A8XX 
        0.49       120.20        81.01        18.08        72.72        38.27 
TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C5 
       65.46        56.61        57.80        29.92        18.08        38.96 
TCGA-X9-A971 
       15.58 

$subtype4
TCGA-3B-A9HX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U8 TCGA-DX-A6YU 
       42.84        14.04        12.85        15.06         4.54        23.54 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS 
       17.95        14.43         9.34        35.77        14.07        27.95 
TCGA-DX-A8BU TCGA-DX-AB30 TCGA-DX-AB32 TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EJ 
       36.69        22.85       101.98        48.30         0.10         3.22 
TCGA-IS-A3KA TCGA-LI-A67I TCGA-QQ-A5VC TCGA-WK-A8Y0 TCGA-X6-A8C2 TCGA-X6-A8C3 
       13.58        22.03        35.90        22.62        25.71        15.95 

$subtype5
TCGA-3B-A9I3 TCGA-DX-A6BB TCGA-DX-A7ES TCGA-IE-A4EH TCGA-IW-A3M6 TCGA-JV-A5VE 
       26.56        23.44        14.07        21.37        22.62        16.41 
TCGA-K1-A3PO TCGA-MJ-A68H TCGA-QQ-A5VD TCGA-WP-A9GB 
       36.39        14.99        30.90         9.04 

$subtype6
TCGA-3R-A8YX TCGA-DX-A3LS TCGA-DX-A48K TCGA-DX-AB2P TCGA-DX-AB36 TCGA-FX-A3TO 
        0.56         9.04        19.30        12.07        60.00        20.32 
TCGA-IS-A3K7 TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W TCGA-PC-A5DM TCGA-PC-A5DN 
      143.41         9.04         4.08        11.70         6.35        38.63 
TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-SG-A6Z4 TCGA-SI-AA8B TCGA-WK-A8XO TCGA-X6-A7W8 
       48.59       130.32        18.94         5.06        11.93        26.43 
TCGA-X6-A7WC TCGA-X6-A8C6 
       36.82        35.08 

$subtype7
TCGA-DX-A23T TCGA-DX-A3U6 TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7ET TCGA-DX-A8BQ 
        5.26        17.75         3.06        16.87         7.04        42.44 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-MB-A5Y8 
       49.18         9.21       106.45        13.28        50.40         8.32 
TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SG-A849 
        8.28        20.94         5.03        62.20        11.18         6.58 
TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-A80J 
       19.82         0.72        26.17 

$subtype8
TCGA-DX-A2IZ TCGA-DX-A7EI TCGA-DX-A7EQ TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB3B 
        8.58        34.49        29.49        12.39        40.60        50.89 
TCGA-DX-AB3C TCGA-FX-A8OO TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-MB-A8JL 
       71.31         2.07         5.92         1.05         3.91        19.73 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-PT-A8TR TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z7 
       15.65        10.45        16.96       188.15        10.52         3.88 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XT TCGA-X6-A8C7 
       27.22         9.93        41.49        17.72 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    0.07     0.46     0.07     0.10     9.04     0.56     0.72     1.05 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  124.37   108.13   120.20   101.98    36.39   143.41   106.45   188.15 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  33.070   32.430   29.920   19.990   21.995   19.120   13.280   16.305 
[1] "0.1 - 124.4 (33.1)" "0.5 - 108.1 (32.4)" "0.1 - 120.2 (29.9)"
[4] "0.1 - 102.0 (20.0)" "9.0 - 36.4 (22.0)"  "0.6 - 143.4 (19.1)"
[7] "0.7 - 106.5 (13.3)" "1.1 - 188.2 (16.3)"
D10V2, continuous
D10V3, binary
          cls
clus        0  1
  subtype1 10 11
  subtype2 11 22
  subtype3 27 10
  subtype4 14 10
  subtype5  6  4
  subtype6  7 13
  subtype7 12 10
  subtype8 18  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   11
  subtype2   11   22
  subtype3   27   10
  subtype4   14   10
  subtype5    6    4
  subtype6    7   13
  subtype7   12   10
  subtype8   18    4
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       10       11       27       14        6        7       12
  MALE         11       22       10       10        4       13       10
        clus
vv       subtype8
  FEMALE       18
  MALE          4
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    18
  subtype2     0                         0    24
  subtype3     0                         4    31
  subtype4     1                         2    18
  subtype5     1                         2     7
  subtype6     0                         0    19
  subtype7     1                         1    17
  subtype8     1                         2    18
D10V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        1        1
  BLACK OR AFRICAN AMERICAN        2        0        4        2        2
  WHITE                           18       24       31       18        7
                           clus
vv                          subtype6 subtype7 subtype8
  ASIAN                            0        1        1
  BLACK OR AFRICAN AMERICAN        0        1        2
  WHITE                           19       17       18
[1] 3 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1  0 19
  subtype2  1 22
  subtype3  0 33
  subtype4  0 19
  subtype5  0 10
  subtype6  0 17
  subtype7  2 18
  subtype8  1 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   19
  subtype2    1   22
  subtype3    0   33
  subtype4    0   19
  subtype5    0   10
  subtype6    0   17
  subtype7    2   18
  subtype8    1   14
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        0        0        0
  NOT HISPANIC OR LATINO       19       22       33       19       10       17
                        clus
vv                       subtype7 subtype8
  HISPANIC OR LATINO            2        1
  NOT HISPANIC OR LATINO       18       14
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
