[1] "ofn"        "-oTPRAD-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/PRAD-TP/22506989/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/22553796/PRAD-TP.mergedcluster.txt"

nPatients in clinical file=499, in cluster file=498, common to both=498
[1]  10 498
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
108  91  98 195 
  1   2   3   4 
108  91  98 195 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
161 140 126  71 
  1   2   3   4 
161 140 126  71 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4   5   6 
106  51  45  53  58  39 
  1   2   3   4   5   6 
106  51  45  53  58  39 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 75 114  93  70 
  1   2   3   4 
 75 114  93  70 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
 96 142 151 108 
  1   2   3   4 
 96 142 151 108 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
173 208 116 
  1   2   3 
173 208 116 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
213  71 124  86 
  1   2   3   4 
213  71 124  86 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
148  98  59 133  56 
  1   2   3   4   5 
148  98  59 133  56 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
65 93 78 84 
 1  2  3  4 
65 93 78 84 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
75 88 69 23 65 
 1  2  3  4  5 
75 88 69 23 65 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "GLEASON_SCORE"                       
[17] "PSA_VALUE"                           
[18] "DAYS_TO_PSA"                         
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 498 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=10,	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=432,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'PSA_VALUE':	nDistinctValues=94,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'DAYS_TO_PSA':	nDistinctValues=383,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[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] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 498 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGY_T_STAGE"     "PATHOLOGY_N_STAGE"    
 [4] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
 [7] "NUMBER_OF_LYMPH_NODES" "GLEASON_SCORE"         "PSA_VALUE"            
[10] "RACE"                 
YEARS_TO_BIRTH, nv=36, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T2  T3  T4 
188 293  10 
[1] "table(vv)"
vv
 T2  T3  T4 
188 293  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T2  T3  T4 
188 293  10 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
188 293  10 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=11, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=94, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1 107   1
  subtype2  90   1
  subtype3  96   2
  subtype4 190   5
subtype1 subtype2 subtype3 subtype4 
     108       91       98      195 
subtype1 subtype2 subtype3 subtype4 
       1        1        2        5 
$subtype1
TCGA-CH-5764 TCGA-CH-5790 TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
        1.02        32.02        39.39        44.55        26.04        31.43 
TCGA-J4-A83N TCGA-KK-A7B3 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8W3 
       32.61        29.56        20.42        55.92        45.14        28.37 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5739 TCGA-CH-5744 TCGA-CH-5750 TCGA-EJ-5495 
       41.82        20.22        22.06         1.97        13.02        57.86 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5508 TCGA-EJ-5524 TCGA-EJ-5530 
       56.55        46.52        44.88        64.60        61.87        60.23 
TCGA-EJ-7314 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7783 TCGA-EJ-7785 
       37.81        33.83        27.09        30.35        25.87        38.70 
TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A7NF TCGA-FC-7708 
       32.32        76.41        23.34        12.92         8.22        28.41 
TCGA-FC-A6HD TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6354 TCGA-G9-6362 
       25.94        83.87        55.76        49.81        67.92        47.44 
TCGA-G9-6363 TCGA-G9-6384 TCGA-G9-6496 TCGA-G9-7509 TCGA-G9-7522 TCGA-G9-7523 
       45.30        25.15        56.75        52.93        35.44        28.18 
TCGA-G9-A9S7 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
       23.93        37.35        14.47        40.14        28.60        32.91 
TCGA-HC-7745 TCGA-HC-7752 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-A6HX 
       23.70        25.71        17.85        24.56        19.36         1.25 
TCGA-HC-A6HY TCGA-HC-A8D0 TCGA-HI-7170 TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A83I 
        4.41        25.48        82.92        30.94        30.81        22.52 
TCGA-J9-A8CK TCGA-KC-A4BV TCGA-KC-A7FD TCGA-KK-A59Y TCGA-KK-A6E4 TCGA-KK-A7AU 
       10.55        43.66         8.88        64.70       115.13        58.36 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8I8 
       57.67        49.94        34.95        36.13       101.79        31.79 
TCGA-KK-A8IM TCGA-MG-AAMC TCGA-QU-A6IN TCGA-SU-A7E7 TCGA-V1-A8MJ TCGA-V1-A8MK 
       62.96         5.69       140.19        18.12        58.88        16.70 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9ZG TCGA-V1-A9ZR 
       64.04        30.38        15.58         6.64        49.87        44.75 
TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A88Q TCGA-VP-A876 
       25.51         6.21        25.18        41.42        44.91       109.58 
TCGA-VP-A87C TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XJ-A9DQ TCGA-YL-A8HJ 
       55.56        58.32        42.94        14.76         2.99        52.96 
TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SP TCGA-YL-A9WX TCGA-ZG-A8QZ TCGA-ZG-A9LY 
       51.45        16.83        77.79        49.91        10.13        12.16 

$subtype2
TCGA-CH-5763 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-HC-A6AQ TCGA-2A-A8VV TCGA-CH-5738 
       12.00        36.76        21.60         3.48        22.06         6.97 
TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5789 TCGA-EJ-5494 TCGA-EJ-5497 TCGA-EJ-5502 
       13.97        24.03         9.99        48.56        13.32        38.50 
TCGA-EJ-5503 TCGA-EJ-5506 TCGA-EJ-5515 TCGA-EJ-5532 TCGA-EJ-7125 TCGA-EJ-7792 
       45.73        45.40        60.23        60.10        93.70        45.90 
TCGA-EJ-7793 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65G 
        3.75        20.58        17.23        23.80        21.96        21.90 
TCGA-EJ-A6RA TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A8FP TCGA-EJ-A8FU 
       11.61        14.20         6.48        15.65         9.83         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6336 TCGA-G9-6347 
        4.31         4.77        17.23        20.25        67.99        68.68 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 
       50.70        47.15        44.81        40.18        38.01        40.31 
TCGA-G9-6385 TCGA-G9-7519 TCGA-H9-A6BX TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7740 
       27.29        27.91        30.94        19.76        38.93        23.57 
TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       17.16        30.84        28.27        27.85        30.38        22.55 
TCGA-HC-A76X TCGA-HC-A8D1 TCGA-HI-7169 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
        4.93        18.84        88.24        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 
       25.32        27.58        32.05        29.92         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83K TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52C 
       27.91        16.83        10.78        18.18        27.12         5.85 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KK-A7AV TCGA-KK-A8I7 TCGA-M7-A71Y 
       30.71        59.67        19.96        27.02        65.82        16.21 
TCGA-M7-A720 TCGA-M7-A723 TCGA-QU-A6IP TCGA-V1-A8MF TCGA-V1-A8ML TCGA-V1-A9OY 
       12.62        25.08        86.14        47.64        14.73        35.08 
TCGA-VN-A88I TCGA-VP-A879 TCGA-VP-A87E TCGA-XA-A8JR TCGA-XJ-A9DK TCGA-XK-AAJU 
        8.84        23.93        66.97        12.36         9.04        51.81 
TCGA-ZG-A9L6 
       22.59 

$subtype3
TCGA-EJ-5542 TCGA-EJ-7325 TCGA-EJ-A6RC TCGA-J9-A8CN TCGA-QU-A6IM TCGA-XK-AAK1 
       49.74        35.18        28.70        40.67        41.00        32.19 
TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-AAYF TCGA-CH-5737 TCGA-CH-5740 TCGA-CH-5741 
       45.30         3.68        44.84         2.99         1.02        12.99 
TCGA-CH-5752 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5792 
       31.00        23.01        15.06        24.03         2.04         2.99 
TCGA-CH-5794 TCGA-EJ-5496 TCGA-EJ-5505 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5516 
       29.00        19.56        30.31        62.04        56.98        62.10 
TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-7115 TCGA-EJ-7317 TCGA-EJ-7331 
       62.10        64.50        68.35        88.34        25.35        24.39 
TCGA-EJ-7782 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-A65E 
       38.37        36.03        28.24        77.16        38.10        13.71 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FS TCGA-FC-A5OB TCGA-G9-6332 TCGA-G9-6333 
       10.82         9.27         8.75        22.36        87.35        81.04 
TCGA-G9-6351 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6498 TCGA-G9-7525 TCGA-H9-7775 
       67.33        37.97        58.45        64.18        32.68         6.08 
TCGA-H9-A6BY TCGA-HC-7210 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7744 
        3.68        28.54        36.26        35.84        31.69        17.46 
TCGA-HC-7747 TCGA-HC-7817 TCGA-HC-8257 TCGA-HC-8261 TCGA-HC-8262 TCGA-J4-A67S 
       24.59        30.51        23.87        17.95        22.32        27.39 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J9-A52E TCGA-J9-A8CP TCGA-KC-A4BR TCGA-KC-A7F3 
       23.67        17.85        10.62        12.69        44.35        21.86 
TCGA-KC-A7FE TCGA-KK-A6E3 TCGA-KK-A7B0 TCGA-KK-A8IJ TCGA-M7-A71Z TCGA-M7-A722 
       11.57        67.59        43.69        51.25        21.14        34.85 
TCGA-QU-A6IL TCGA-TP-A8TT TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A9OF TCGA-V1-A9OQ 
        3.19        17.29        39.29        61.68        38.93        12.20 
TCGA-V1-A9OT TCGA-V1-A9Z9 TCGA-VN-A88L TCGA-VN-A88O TCGA-VN-A88R TCGA-VP-A878 
       15.65        17.75        24.53        15.81        25.78       102.90 
TCGA-X4-A8KS TCGA-XJ-A83F TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJR TCGA-XQ-A8TB 
       32.19        37.05        31.96        40.04        36.95        25.32 
TCGA-Y6-A8TL TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A9WJ TCGA-ZG-A8QW 
       32.61        45.14        28.77        53.06        60.99         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY 
       14.53        13.28 

$subtype4
TCGA-CH-5753 TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-A46G 
        1.02        15.98        33.01        84.56        36.13        21.96 
TCGA-EJ-A65J TCGA-HC-A76W TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B4 TCGA-KK-A8IB 
       14.83         7.00        19.66         6.44        32.45         2.73 
TCGA-XK-AAJ3 TCGA-4L-AA1F TCGA-CH-5748 TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5761 
       41.49        11.51         1.02        35.01         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5766 TCGA-CH-5771 TCGA-CH-5788 TCGA-EJ-5504 TCGA-EJ-5507 
       44.02         1.02        13.02        26.99        46.92        47.90 
TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5525 
       48.13        48.53        60.13        69.63        74.93        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7328 
       62.76        58.45        41.85        83.57        33.14        27.68 
TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-7794 TCGA-EJ-8472 
        6.28        35.28        25.68        36.33        42.94        24.85 
TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A65F TCGA-EJ-A65M TCGA-EJ-A7NH TCGA-EJ-A7NM 
       25.18        25.74        18.41         7.56        15.58         4.21 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6329 TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6361 
       15.42        28.83        41.62        66.67        80.55        46.52 
TCGA-G9-6366 TCGA-G9-6369 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6494 TCGA-G9-6499 
       64.01        39.95        26.66        31.50        58.22        50.73 
TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S0 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7080 
       38.96        30.97        26.01        69.53        65.26        36.36 
TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7742 TCGA-HC-7749 TCGA-HC-8216 
       40.08        30.87        38.17        30.84        23.80        22.42 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A8CY TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-A83J 
        9.53        19.30        27.75       109.25        43.69        22.88 
TCGA-J4-AATZ TCGA-J9-A52B TCGA-J9-A8CL TCGA-J9-A8CM TCGA-KC-A7F6 TCGA-KK-A59V 
       13.55        13.87        13.32        15.22         8.65       113.10 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       83.34        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AW 
       68.15       113.33        90.74        58.19        52.93        34.65 
TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       74.27        21.96        32.91        63.48        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IK TCGA-KK-A8IL 
       26.43        82.36        66.18       113.98        67.46        20.65 
TCGA-M7-A721 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IO TCGA-TK-A8OK TCGA-TP-A8TV 
       13.15        29.23        18.84       122.17         0.89        20.05 
TCGA-V1-A8MG TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       28.18        22.55        35.44        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OX TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       20.91        79.00        62.89        37.28        28.73        27.19 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87B 
       53.92        45.47        16.31       119.38        75.91        89.49 
TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XJ-A83H 
       60.92        21.80        44.88        45.47        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJT 
       48.03        31.99        37.25        30.58        41.39        47.15 
TCGA-XQ-A8TA TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO 
        4.80        17.29         4.87        49.02        48.72        75.75 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SJ TCGA-YL-A8SK 
       62.14        60.56        56.52        41.46        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       32.45       114.38        68.48         8.98        14.04        53.36 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       70.22        24.33        36.10         4.27        11.67        42.81 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       37.94        36.43        29.85        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
        3.78        16.96        19.04        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

subtype1 subtype2 subtype3 subtype4 
    1.02     3.48     1.02     0.76 
subtype1 subtype2 subtype3 subtype4 
  140.19    93.70   102.90   165.17 
subtype1 subtype2 subtype3 subtype4 
  32.760   24.030   29.655   33.010 
[1] "1.0 - 140.2 (32.8)" "3.5 - 93.7 (24.0)"  "1.0 - 102.9 (29.7)"
[4] "0.8 - 165.2 (33.0)"
D1V2, continuous
          vv
clus        T2  T3  T4
  subtype1  47  58   3
  subtype2  55  32   1
  subtype3  46  51   0
  subtype4  39 147   6
D1V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T2       47       55       46       39
  T3       58       32       51      147
  T4        3        1        0        6
[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"
D1V4, binary
          cls
clus         0   1
  subtype1  78  13
  subtype2  64   4
  subtype3  73  11
  subtype4 128  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78   13
  subtype2   64    4
  subtype3   73   11
  subtype4  128   49
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       78       64       73      128
  1       13        4       11       49
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus         0   1
  subtype1  91  11
  subtype2  82   4
  subtype3  80  11
  subtype4 137  33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   91   11
  subtype2   82    4
  subtype3   80   11
  subtype4  137   33
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        91       82       80      137
  YES       11        4       11       33
[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"
D1V6, binary
          cls
clus         0   1
  subtype1 103   5
  subtype2  90   1
  subtype3  96   2
  subtype4 189   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  103    5
  subtype2   90    1
  subtype3   96    2
  subtype4  189    6
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA ACINAR TYPE         103       90       96      189
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        5        1        2        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  81  19   3   3
  subtype2  68  16   1   2
  subtype3  64  26   0   4
  subtype4 100  83   1   6
D1V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       81       68       64      100
  R1       19       16       26       83
  R2        3        1        0        1
  RX        3        2        4        6
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
D1V9, continuous
D1V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    36
  subtype2     0                         0    29
  subtype3     0                         3    33
  subtype4     0                         3    48
D1V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        0        0        0
  BLACK OR AFRICAN AMERICAN        1        0        3        3
  WHITE                           36       29       33       48
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1 160   1
  subtype2 136   4
  subtype3 122   4
  subtype4  70   1
subtype1 subtype2 subtype3 subtype4 
     161      140      126       71 
subtype1 subtype2 subtype3 subtype4 
       1        4        4        1 
$subtype1
TCGA-CH-5763 TCGA-EJ-5542 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A6RC TCGA-HC-7233 
       12.00        49.74        36.76        21.60        28.70        44.55 
TCGA-HC-A6AQ TCGA-2A-A8VL TCGA-CH-5738 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5762 
        3.48        20.42         6.97        13.97        24.03        44.02 
TCGA-CH-5766 TCGA-CH-5771 TCGA-CH-5789 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
        1.02        13.02         9.99        19.56        13.32        56.55 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       44.88        38.50        45.73        30.31        45.40        64.60 
TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5522 TCGA-EJ-5531 
       62.04        56.98        60.23        62.10        68.35        41.85 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7785 TCGA-EJ-7792 TCGA-EJ-7793 
       27.68         6.28        35.28        38.70        45.90         3.75 
TCGA-EJ-7797 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       32.32        20.58        17.23        23.80        21.96        23.34 
TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       21.90        11.61        14.20        15.58         6.48        15.65 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.27         9.83         4.54         4.31         4.77        28.41 
TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6347 
       17.23        20.25        41.62        67.99        83.87        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6365 TCGA-G9-6366 
       49.81        67.33        50.70        47.15        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       40.18        38.01        37.97        58.45        25.15        27.29 
TCGA-G9-7519 TCGA-G9-7522 TCGA-H9-A6BX TCGA-HC-7079 TCGA-HC-7209 TCGA-HC-7740 
       27.91        35.44        30.94        38.93        14.47        23.57 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7820 TCGA-HC-8216 
       23.70        24.59        17.16        30.51        24.56        22.42 
TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8266 TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A8D0 
       27.85        22.55        15.55         1.45         1.25        25.48 
TCGA-HC-A8D1 TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O 
       18.84        82.92        40.04        25.32        30.94        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-AATV TCGA-J9-A52C TCGA-J9-A8CK TCGA-KC-A4BL 
       10.78        23.67        18.18         5.85        10.55        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A7FE TCGA-KK-A6E3 TCGA-KK-A7B0 
       59.67        19.96        44.35        11.57        67.59        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8IC TCGA-KK-A8IM 
       34.95        36.13        74.27        65.82        67.43        62.96 
TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A723 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MJ 
       16.21        12.62        25.08        86.14        18.12        58.88 
TCGA-V1-A8MK TCGA-V1-A8WN TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OY TCGA-V1-A9Z8 
       16.70        30.38        82.16        94.36        35.08        27.19 
TCGA-VN-A88I TCGA-VN-A88N TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87E 
        8.84        25.18       102.90        23.93        55.56        66.97 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       45.47        32.19        12.36        48.03         9.04         2.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJU TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8SB 
       31.96        37.25        51.81        52.96        49.02        56.52 
TCGA-YL-A8SK TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QZ TCGA-ZG-A9L2 TCGA-ZG-A9L6 
       46.29        49.91         3.09        10.13        37.94        22.59 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC 
        3.78        16.96        19.04        12.16        14.96 

$subtype2
TCGA-EJ-7123 TCGA-EJ-A65J TCGA-J9-A8CN TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
       84.56        14.83        40.67         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 TCGA-CH-5748 
       32.19        55.92        45.30         3.68         2.99         1.02 
TCGA-CH-5767 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5504 TCGA-EJ-5509 TCGA-EJ-5514 
       15.06         2.99        48.56        46.92        48.13        60.13 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       69.63        64.50        60.10        88.34        93.70        83.57 
TCGA-EJ-7317 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7786 TCGA-EJ-7794 TCGA-EJ-8468 
       25.35        24.39        38.37        36.03        42.94        77.16 
TCGA-EJ-8470 TCGA-EJ-A65E TCGA-EJ-A65M TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-FC-7961 
       38.10        13.71         7.56        10.82         8.75        15.42 
TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6369 
       22.36        25.94        81.04        66.67        80.55        39.95 
TCGA-G9-6371 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 
       40.31        56.75        64.18        50.73        38.96        30.97 
TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7210 
       28.18        26.01        19.76        65.26        36.36        28.54 
TCGA-HC-7211 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7742 TCGA-HC-8256 
       40.14        36.26        35.84        31.69        30.84        28.27 
TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AP 
       17.95         1.58        15.88         2.20        17.42         2.33 
TCGA-HI-7168 TCGA-J4-A83J TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52D TCGA-J9-A8CL 
      109.25        22.88        13.55        27.12         6.97        13.32 
TCGA-J9-A8CP TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KK-A59X TCGA-KK-A5A1 TCGA-KK-A6E0 
       12.69        21.86         2.99        83.34        81.17        48.76 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AV TCGA-KK-A7AW 
       68.15        90.74        58.19        52.93        27.02        34.65 
TCGA-KK-A8I9 TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-M7-A721 
       32.91        26.43        82.36        51.25        67.46        13.15 
TCGA-M7-A722 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IO TCGA-TP-A8TV TCGA-V1-A8MG 
       34.85        29.23         3.19       122.17        20.05        28.18 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A8X3 
       14.73        39.29        61.68        64.04        22.55         6.64 
TCGA-V1-A9OF TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OX TCGA-V1-A9Z9 TCGA-V1-A9ZK 
       38.93        62.89        12.20        37.28        17.75        45.47 
TCGA-VN-A88O TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-AA1N 
       15.81        25.78        16.31        89.49        21.80        44.88 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       48.03        42.08        40.04        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 
       47.15        32.61        17.29        48.72        75.75        60.56 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI 
       28.77        53.06       114.38        68.48         8.98        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9LM TCGA-ZG-A9M4 
       60.99        36.10        14.53        13.28        12.43        17.98 
TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       11.47        13.48 

$subtype3
TCGA-CH-5753 TCGA-CH-5764 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-7325 TCGA-EJ-A46G 
        1.02         1.02        32.02        33.01        35.18        21.96 
TCGA-G9-6364 TCGA-J4-A83N TCGA-KC-A7FA TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-2A-A8VT 
       39.39        32.61        19.66        29.56        32.45        45.14 
TCGA-2A-A8VV TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5739 TCGA-CH-5740 
       22.06        44.84        41.82        20.22        22.06         1.02 
TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5750 TCGA-CH-5754 TCGA-CH-5768 TCGA-CH-5769 
       12.99         1.97        13.02         2.04        24.03         2.04 
TCGA-CH-5788 TCGA-CH-5794 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5517 TCGA-EJ-5521 
       26.99        29.00        47.90        48.53        62.10        74.93 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5530 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       61.87        36.66        60.23        33.83        27.09        30.35 
TCGA-EJ-7784 TCGA-EJ-7788 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A65D 
       25.68        28.24        24.85        25.18        25.74        12.92 
TCGA-EJ-A7NF TCGA-EJ-A7NN TCGA-G9-6332 TCGA-G9-6342 TCGA-G9-6354 TCGA-G9-6362 
        8.22         6.48        87.35        55.76        67.92        47.44 
TCGA-G9-6363 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-7509 TCGA-G9-7525 TCGA-G9-A9S4 
       45.30        26.66        31.50        52.93        32.68        29.79 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BY TCGA-HC-7077 TCGA-HC-7212 TCGA-HC-7213 
       23.93         6.08         3.68        69.53        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7744 TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7818 
       32.91        30.87        17.46        23.80        25.71        30.84 
TCGA-HC-7819 TCGA-HC-8213 TCGA-HC-8259 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6HY 
       17.85        19.36        30.38        22.36         1.78         4.41 
TCGA-HC-A76X TCGA-HC-A9TH TCGA-HI-7169 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67K 
        4.93        27.75        88.24        43.69        20.19        33.01 
TCGA-J4-A67N TCGA-J4-A6M7 TCGA-J4-A83M TCGA-J9-A52B TCGA-J9-A52E TCGA-KC-A7FD 
       30.81        16.83        17.85        13.87        10.62         8.88 
TCGA-KK-A59Y TCGA-KK-A6E1 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AU TCGA-KK-A7AZ 
       64.70        72.26       115.13       113.33        58.36        49.94 
TCGA-KK-A8I5 TCGA-KK-A8I8 TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IL TCGA-M7-A725 
      101.79        31.79        66.18       113.98        20.65        18.84 
TCGA-MG-AAMC TCGA-QU-A6IN TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8WS TCGA-V1-A8WW 
        5.69       140.19        17.29        47.64        15.58        35.44 
TCGA-V1-A9OT TCGA-V1-A9ZI TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88P 
       15.65        53.92        25.51        24.53         6.21        41.42 
TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87D TCGA-VP-A87J 
       44.91       119.38        75.91       109.58        60.92        58.32 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XJ-A83F TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SC 
       42.94        14.76        37.05        51.45        16.83        41.46 
TCGA-YL-A8SJ TCGA-YL-A8SP TCGA-YL-A9WL TCGA-ZG-A9L1 TCGA-ZG-A9L9 TCGA-ZG-A9LZ 
       45.86        77.79        24.33        42.81        20.28        22.75 

$subtype4
TCGA-CH-5772 TCGA-EJ-7312 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A76W TCGA-KK-A7AP 
       15.98        36.13        26.04        31.43         7.00         6.44 
TCGA-2A-A8W3 TCGA-4L-AA1F TCGA-CH-5745 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5761 
       28.37        11.51         2.99        35.01        31.00         0.92 
TCGA-CH-5765 TCGA-EJ-5495 TCGA-EJ-5499 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-7314 
       23.01        57.86        46.52        62.76        58.45        37.81 
TCGA-EJ-7315 TCGA-EJ-7783 TCGA-EJ-7789 TCGA-EJ-8469 TCGA-EJ-A65F TCGA-EJ-A7NM 
       33.14        25.87        36.33        76.41        18.41         4.21 
TCGA-FC-A4JI TCGA-G9-6361 TCGA-G9-6494 TCGA-HC-7081 TCGA-HC-7232 TCGA-HC-8257 
       28.83        46.52        58.22        37.35        38.17        23.87 
TCGA-HC-8262 TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A8CY TCGA-HC-A9TE 
       22.32         0.76         2.01         1.61         9.53        19.30 
TCGA-J4-A83I TCGA-J9-A8CM TCGA-KC-A4BV TCGA-KC-A7F6 TCGA-KK-A59V TCGA-KK-A59Z 
       22.52        15.22        43.66         8.65       113.10        86.40 
TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A7AY TCGA-KK-A8I6 TCGA-KK-A8IA TCGA-KK-A8ID 
      141.21       165.17        57.67        21.96        63.48        69.27 
TCGA-M7-A71Z TCGA-TK-A8OK TCGA-V1-A9O5 TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9Z7 
       21.14         0.89        63.52        20.91        79.00        28.73 
TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-XJ-A9DX TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-YJ-A8SW 
       49.87        44.75        31.99         4.80        25.32         4.87 
TCGA-YL-A8S8 TCGA-YL-A8SF TCGA-YL-A8SL TCGA-YL-A9WH TCGA-YL-A9WK TCGA-ZG-A9KY 
       62.14        45.14        32.45        14.04        70.22         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9NI 
       11.67        36.43        29.85        19.17         4.34 

subtype1 subtype2 subtype3 subtype4 
    1.02     1.02     1.02     0.76 
subtype1 subtype2 subtype3 subtype4 
  102.90   122.17   140.19   165.17 
subtype1 subtype2 subtype3 subtype4 
  27.850   35.935   30.365   28.830 
[1] "1.0 - 102.9 (27.9)" "1.0 - 122.2 (35.9)" "1.0 - 140.2 (30.4)"
[4] "0.8 - 165.2 (28.8)"
D2V2, continuous
          vv
clus       T2 T3 T4
  subtype1 79 77  1
  subtype2 57 81  1
  subtype3 43 81  2
  subtype4  9 54  6
D2V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T2       79       57       43        9
  T3       77       81       81       54
  T4        1        1        2        6
[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"
D2V4, binary
          cls
clus         0   1
  subtype1 115  19
  subtype2 101  19
  subtype3  84  22
  subtype4  46  19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  115   19
  subtype2  101   19
  subtype3   84   22
  subtype4   46   19
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      115      101       84       46
  1       19       19       22       19
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus         0   1
  subtype1 131  21
  subtype2 116  12
  subtype3  97  16
  subtype4  51  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  131   21
  subtype2  116   12
  subtype3   97   16
  subtype4   51   10
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       131      116       97       51
  YES       21       12       16       10
[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"
D2V6, binary
          cls
clus         0   1
  subtype1 157   4
  subtype2 138   2
  subtype3 120   6
  subtype4  68   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  157    4
  subtype2  138    2
  subtype3  120    6
  subtype4   68    3
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA ACINAR TYPE         157      138      120       68
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        4        2        6        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 113  38   1   4
  subtype2  84  46   1   5
  subtype3  84  33   2   4
  subtype4  35  30   1   2
D2V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      113       84       84       35
  R1       38       46       33       30
  R2        1        1        2        1
  RX        4        5        4        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
D2V9, continuous
D2V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    52
  subtype2     0                         2    35
  subtype3     0                         3    42
  subtype4     1                         1    18
D2V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        0        1
  BLACK OR AFRICAN AMERICAN        1        2        3        1
  WHITE                           52       35       42       18
[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"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 105   1
  subtype2  50   1
  subtype3  45   0
  subtype4  49   4
  subtype5  57   1
  subtype6  39   0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     106       51       45       53       58       39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       1        1        0        4        1        0 
$subtype1
TCGA-CH-5753 TCGA-CH-5764 TCGA-CH-5772 TCGA-EJ-5542 TCGA-EJ-A46B TCGA-EJ-A6RC 
        1.02         1.02        15.98        49.74        21.60        28.70 
TCGA-G9-6364 TCGA-HC-7233 TCGA-J4-A83N TCGA-KC-A7FA TCGA-KK-A7B3 TCGA-2A-A8VL 
       39.39        44.55        32.61        19.66        29.56        20.42 
TCGA-2A-A8VV TCGA-CH-5771 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       22.06        13.02        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 
       38.50        64.60        62.04        48.53        56.98        60.23 
TCGA-EJ-5527 TCGA-EJ-7115 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7330 TCGA-EJ-7331 
       58.45        88.34        33.14        25.35         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7785 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       35.28        38.70        45.90         3.75        42.94        32.32 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46F TCGA-EJ-A65M TCGA-EJ-A7NF TCGA-EJ-A7NJ 
       25.18        20.58        25.74         7.56         8.22         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NN TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-FC-A8O0 
       15.65         6.48         8.75         4.54         4.31        20.25 
TCGA-G9-6329 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6367 
       41.62        83.87        55.76        67.33        50.70        40.18 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7522 
       38.01        40.31        25.15        58.22        50.73        35.44 
TCGA-G9-A9S7 TCGA-H9-A6BX TCGA-HC-7232 TCGA-HC-7740 TCGA-HI-7168 TCGA-HI-7169 
       23.93        30.94        38.17        23.57       109.25        88.24 
TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67O 
       82.92        20.19        40.04        33.01        30.94        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A83I TCGA-KC-A4BN TCGA-KC-A4BO 
       32.05        29.92         6.02        22.52        59.67        19.96 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FE TCGA-KK-A6E3 TCGA-KK-A7B0 TCGA-KK-A8I4 
       43.66        21.86        11.57        67.59        43.69        74.27 
TCGA-KK-A8I6 TCGA-M7-A721 TCGA-M7-A723 TCGA-TK-A8OK TCGA-V1-A8MU TCGA-V1-A8WL 
       21.96        13.15        25.08         0.89        61.68        64.04 
TCGA-V1-A8X3 TCGA-V1-A9OT TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88P 
        6.64        15.65        44.75         8.84        24.53        41.42 
TCGA-VP-A878 TCGA-VP-AA1N TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8SH TCGA-YL-A8SI 
      102.90        44.88        32.61        52.96        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SR 
       45.86        46.29        32.45         8.98 

$subtype2
TCGA-EJ-7312 TCGA-2A-A8VO TCGA-2A-AAYO TCGA-4L-AA1F TCGA-CH-5769 TCGA-EJ-5495 
       36.13        55.92        41.82        11.51         2.04        57.86 
TCGA-EJ-7328 TCGA-EJ-8470 TCGA-EJ-A65B TCGA-EJ-A65E TCGA-FC-7708 TCGA-FC-7961 
       27.68        38.10        23.34        13.71        28.41        15.42 
TCGA-FC-A6HD TCGA-G9-6338 TCGA-G9-6379 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7510 
       25.94        66.67        58.45        56.75        64.18        38.96 
TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-HC-7077 TCGA-HC-7079 
       30.97        28.18        32.68         6.08        69.53        38.93 
TCGA-HC-7081 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7817 TCGA-HC-8264 
       37.35        28.54        40.14        28.60        30.51         1.58 
TCGA-HI-7171 TCGA-J9-A8CP TCGA-KC-A4BR TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
       43.69        12.69        44.35        83.34        64.70        86.40 
TCGA-KK-A8I5 TCGA-KK-A8I7 TCGA-KK-A8IH TCGA-TP-A8TT TCGA-V1-A8MJ TCGA-XA-A8JR 
      101.79        65.82        66.18        17.29        58.88        12.36 
TCGA-YL-A8HO TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       75.75        24.33        36.10        10.13        11.67        42.81 
TCGA-ZG-A9L4 TCGA-ZG-A9L9 TCGA-ZG-A9N3 
       36.43        20.28        11.47 

$subtype3
TCGA-CH-5763 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-7791 TCGA-2A-A8VT TCGA-CH-5738 
       12.00        32.02        33.01        36.76        45.14         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5750 
       22.06         1.02        13.97         1.97         2.99        13.02 
TCGA-CH-5762 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5789 TCGA-CH-5794 TCGA-EJ-5496 
       44.02        15.06        24.03         9.99        29.00        19.56 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5509 TCGA-EJ-5524 TCGA-EJ-7218 TCGA-EJ-7314 
       45.73        46.92        48.13        61.87        83.57        37.81 
TCGA-EJ-7783 TCGA-EJ-7786 TCGA-EJ-8468 TCGA-EJ-A46E TCGA-EJ-A7NG TCGA-EJ-A7NM 
       25.87        36.03        77.16        17.23        14.20         4.21 
TCGA-HC-7736 TCGA-J4-A67N TCGA-J4-A83J TCGA-KK-A8IA TCGA-KK-A8IJ TCGA-QU-A6IN 
       36.26        30.81        22.88        63.48        51.25       140.19 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A9Z9 TCGA-VP-A875 TCGA-VP-A87E TCGA-YJ-A8SW 
       86.14        18.12        17.75        75.91        66.97         4.87 
TCGA-YL-A9WX TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       49.91        17.98        14.96 

$subtype4
TCGA-HC-7748 TCGA-2A-A8VX TCGA-CH-5741 TCGA-CH-5761 TCGA-CH-5765 TCGA-CH-5792 
       26.04        45.30        12.99         0.92        23.01         2.99 
TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 
       62.10        64.50        74.93        62.76        60.23        41.85 
TCGA-EJ-7125 TCGA-EJ-7318 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-8469 TCGA-EJ-A65D 
       93.70        33.83        38.37        25.68        76.41        12.92 
TCGA-EJ-A7NH TCGA-EJ-A8FO TCGA-FC-A5OB TCGA-FC-A66V TCGA-G9-6356 TCGA-G9-6365 
       15.58         9.27        22.36        17.23        47.15        44.81 
TCGA-G9-6377 TCGA-G9-A9S0 TCGA-H9-A6BY TCGA-HC-7744 TCGA-HC-A76X TCGA-J4-A6M7 
       31.50        26.01         3.68        17.46         4.93        16.83 
TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KK-A5A1 TCGA-KK-A6E2 TCGA-KK-A6E4 
        2.99         8.65         8.88        81.17       165.17       115.13 
TCGA-KK-A7AZ TCGA-KK-A8II TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 
       49.94       113.98        16.21        21.14        12.62        34.85 
TCGA-M7-A725 TCGA-V1-A9OH TCGA-V1-A9Z8 TCGA-VN-A88K TCGA-VP-A87J TCGA-VP-A87K 
       18.84        79.00        27.19        25.51        58.32        42.94 
TCGA-WW-A8ZI TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SP 
       14.76        49.02        51.45        16.83        77.79 

$subtype5
TCGA-J9-A8CN TCGA-KK-A7AP TCGA-KK-A8IB TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       40.67         6.44         2.73         3.68        28.37        44.84 
TCGA-2A-AAYU TCGA-CH-5737 TCGA-CH-5748 TCGA-CH-5766 TCGA-CH-5788 TCGA-EJ-5494 
       20.22         2.99         1.02         1.02        26.99        48.56 
TCGA-EJ-5505 TCGA-EJ-5518 TCGA-EJ-5522 TCGA-EJ-5532 TCGA-EJ-7321 TCGA-EJ-7789 
       30.31        69.63        68.35        60.10        27.09        36.33 
TCGA-EJ-A6RA TCGA-EJ-A8FN TCGA-EJ-AB27 TCGA-FC-A4JI TCGA-G9-6343 TCGA-G9-6347 
       11.61        10.82         4.77        28.83        80.55        68.68 
TCGA-G9-6366 TCGA-G9-6378 TCGA-J9-A8CM TCGA-KK-A6E0 TCGA-KK-A6E8 TCGA-KK-A7B1 
       64.01        37.97        15.22        48.76        58.19        34.95 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-M7-A724 TCGA-TP-A8TV TCGA-V1-A8MF 
       67.43        69.27        26.43        29.23        20.05        47.64 
TCGA-V1-A9OQ TCGA-V1-A9OX TCGA-V1-A9ZG TCGA-X4-A8KQ TCGA-Y6-A9XI TCGA-YL-A8HM 
       12.20        37.28        49.87        45.47        17.29        48.72 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SQ TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.14        60.56        68.48        53.36        60.99        70.22 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LS 
       14.53        13.28        22.59        19.17        12.43        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9NI 
       19.04        12.16        22.75         4.34 

$subtype6
TCGA-EJ-7325 TCGA-EJ-A46G TCGA-EJ-A65J TCGA-KK-A7B4 TCGA-CH-5751 TCGA-CH-5752 
       35.18        21.96        14.83        32.45        35.01        31.00 
TCGA-CH-5754 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5525 
        2.04        45.40        47.90        60.13        62.10        36.66 
TCGA-EJ-7788 TCGA-EJ-A65F TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6373 
       28.24        18.41        46.52        47.44        45.30        26.66 
TCGA-G9-A9S4 TCGA-HC-7213 TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-KC-A4BL 
       29.79        40.08         5.85        10.62        10.55        30.71 
TCGA-KK-A59V TCGA-KK-A6E1 TCGA-KK-A7AU TCGA-KK-A7B2 TCGA-KK-A8I8 TCGA-V1-A9O5 
      113.10        72.26        58.36        36.13        31.79        63.52 
TCGA-V1-A9OL TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9ZI TCGA-YL-A8SC TCGA-YL-A8SF 
       62.89        35.08        28.73        53.92        41.46        45.14 
TCGA-ZG-A8QW TCGA-ZG-A9KY TCGA-ZG-A9L5 
        3.09         4.27        29.85 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.89     1.58     1.02     0.92     1.02     2.04 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  109.25   101.79   140.19   165.17    80.55   113.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   32.53    36.13    29.00    27.19    29.03    35.08 
[1] "0.9 - 109.2 (32.5)" "1.6 - 101.8 (36.1)" "1.0 - 140.2 (29.0)"
[4] "0.9 - 165.2 (27.2)" "1.0 - 80.5 (29.0)"  "2.0 - 113.1 (35.1)"
D3V2, continuous
          vv
clus       T2 T3 T4
  subtype1 46 56  2
  subtype2 11 40  0
  subtype3 19 23  1
  subtype4 18 34  1
  subtype5 13 43  1
  subtype6  3 31  5
D3V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T2       46       11       19       18       13        3
  T3       56       40       23       34       43       31
  T4        2        0        1        1        1        5
[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"
D3V4, binary
          cls
clus        0  1
  subtype1 80  9
  subtype2 30 13
  subtype3 36  8
  subtype4 40  7
  subtype5 38 12
  subtype6 22 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   80    9
  subtype2   30   13
  subtype3   36    8
  subtype4   40    7
  subtype5   38   12
  subtype6   22   14
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       80       30       36       40       38       22
  1        9       13        8        7       12       14
[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"
D3V5, binary
          cls
clus        0  1
  subtype1 94  7
  subtype2 39  9
  subtype3 37  3
  subtype4 41  7
  subtype5 40 10
  subtype6 32  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94    7
  subtype2   39    9
  subtype3   37    3
  subtype4   41    7
  subtype5   40   10
  subtype6   32    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        94       39       37       41       40       32
  YES        7        9        3        7       10        5
[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"
D3V6, binary
          cls
clus         0   1
  subtype1 105   1
  subtype2  49   2
  subtype3  43   2
  subtype4  49   4
  subtype5  58   0
  subtype6  37   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  105    1
  subtype2   49    2
  subtype3   43    2
  subtype4   49    4
  subtype5   58    0
  subtype6   37    2
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA ACINAR TYPE         105       49       43       49
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        1        2        2        4
                                        clus
vv                                       subtype5 subtype6
  PROSTATE ADENOCARCINOMA ACINAR TYPE          58       37
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        0        2
[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       R0 R1 R2 RX
  subtype1 81 20  0  0
  subtype2 21 21  2  2
  subtype3 35  9  0  1
  subtype4 34 16  1  2
  subtype5 29 26  0  3
  subtype6 21 16  0  2
D3V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       81       21       35       34       29       21
  R1       20       21        9       16       26       16
  R2        0        2        0        1        0        0
  RX        0        2        1        2        3        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
D3V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    41
  subtype2     1                         1    13
  subtype3     0                         0    25
  subtype4     0                         1    17
  subtype5     0                         3    11
  subtype6     0                         0    14
D3V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        0        0        0
  BLACK OR AFRICAN AMERICAN        1        1        0        1        3
  WHITE                           41       13       25       17       11
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        0
  WHITE                           14
[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"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2        0   1
  subtype1  74   1
  subtype2 111   3
  subtype3  92   1
  subtype4  68   2
subtype1 subtype2 subtype3 subtype4 
      75      114       93       70 
subtype1 subtype2 subtype3 subtype4 
       1        3        1        2 
$subtype1
TCGA-CH-5772 TCGA-EJ-5542 TCGA-EJ-A46B TCGA-EJ-A6RC TCGA-KC-A7FA TCGA-2A-A8VL 
       15.98        49.74        21.60        28.70        19.66        20.42 
TCGA-2A-A8VV TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5503 TCGA-EJ-5508 TCGA-EJ-5510 
       22.06        56.55        46.52        45.73        64.60        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5527 TCGA-EJ-7115 TCGA-EJ-7125 
       48.53        56.98        60.23        58.45        88.34        93.70 
TCGA-EJ-7317 TCGA-EJ-7781 TCGA-EJ-7785 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       25.35        35.28        38.70         3.75        42.94        32.32 
TCGA-EJ-A46D TCGA-EJ-A46F TCGA-EJ-A65M TCGA-EJ-A7NF TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       20.58        25.74         7.56         8.22         6.48        15.65 
TCGA-EJ-A7NN TCGA-EJ-A8FO TCGA-EJ-A8FS TCGA-EJ-AB20 TCGA-G9-6329 TCGA-G9-6339 
        6.48         9.27         8.75         4.31        41.62        83.87 
TCGA-G9-6342 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 
       55.76        67.33        50.70        40.18        38.01        40.31 
TCGA-G9-6499 TCGA-H9-A6BX TCGA-HC-7232 TCGA-HI-7168 TCGA-J4-8200 TCGA-J4-A67K 
       50.73        30.94        38.17       109.25        40.04        33.01 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A83I TCGA-KC-A4BN 
       27.58        32.05        29.92         6.02        22.52        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FE TCGA-KK-A6E3 
       19.96        44.35        43.66        21.86        11.57        67.59 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-M7-A721 TCGA-TK-A8OK TCGA-V1-A8X3 TCGA-V1-A9ZR 
       21.96        65.82        13.15         0.89         6.64        44.75 
TCGA-VP-A878 TCGA-VP-AA1N TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8SH 
      102.90        44.88        32.61        52.96        75.75        28.77 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.86        46.29        32.45 

$subtype2
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-7791 
        1.02        12.00         1.02        32.02        33.01        36.76 
TCGA-EJ-A65J TCGA-HC-7748 TCGA-J4-A83N TCGA-KK-A7B4 TCGA-2A-A8VO TCGA-2A-A8VT 
       14.83        26.04        32.61        32.45        55.92        45.14 
TCGA-2A-AAYO TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 
       41.82        11.51         2.99         6.97        22.06         1.02 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5762 
       13.97         1.97         2.99         1.02        13.02        44.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5789 
       23.01         1.02        15.06        24.03        13.02         9.99 
TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5501 TCGA-EJ-5502 
       29.00        57.86        19.56        13.32        44.88        38.50 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5509 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5524 
       46.92        30.31        48.13        62.10        62.10        61.87 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7330 TCGA-EJ-7783 
       41.85        60.10        83.57        37.81         6.28        25.87 
TCGA-EJ-7786 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-A46E TCGA-EJ-A65B TCGA-EJ-A65E 
       36.03        77.16        38.10        17.23        23.34        13.71 
TCGA-EJ-A6RA TCGA-EJ-A7NG TCGA-EJ-A7NM TCGA-EJ-A8FU TCGA-EJ-AB27 TCGA-FC-A4JI 
       11.61        14.20         4.21         4.54         4.77        28.83 
TCGA-FC-A6HD TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6379 TCGA-H9-A6BY TCGA-HC-7077 
       25.94        80.55        68.68        58.45         3.68        69.53 
TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7736 TCGA-HC-7740 
       38.93        37.35        28.54        40.14        36.26        23.57 
TCGA-HC-A76X TCGA-J4-A67N TCGA-J4-A83J TCGA-KK-A59Y TCGA-KK-A6E1 TCGA-KK-A6E4 
        4.93        30.81        22.88        64.70        72.26       115.13 
TCGA-KK-A8IA TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-QU-A6IN TCGA-QU-A6IP 
       63.48        66.18       113.98        51.25       140.19        86.14 
TCGA-SU-A7E7 TCGA-V1-A9Z9 TCGA-VP-A875 TCGA-VP-A87E TCGA-VP-A87J TCGA-YJ-A8SW 
       18.12        17.75        75.91        66.97        58.32         4.87 
TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SI TCGA-YL-A8SQ 
       51.45        62.14        16.83        41.46        53.06        68.48 
TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9L1 
       60.99        49.91         3.09        14.53        10.13        42.81 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LS 
       36.43        22.59        20.28        19.17        12.43        16.96 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       12.16        22.75        17.98        14.96        11.47         4.34 

$subtype3
TCGA-EJ-7312 TCGA-EJ-7325 TCGA-G9-6364 TCGA-HC-7233 TCGA-KK-A7AP TCGA-KK-A7B3 
       36.13        35.18        39.39        44.55         6.44        29.56 
TCGA-2A-A8VX TCGA-EJ-5494 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-7315 
       45.30        48.56        68.35        62.76        60.23        33.14 
TCGA-EJ-7318 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7788 TCGA-EJ-7792 TCGA-EJ-8469 
       33.83        27.68        24.39        28.24        45.90        76.41 
TCGA-EJ-8474 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A8O0 
       25.18        28.41        15.42        22.36        17.23        20.25 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       26.66        37.97        25.15        58.22        56.75        64.18 
TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S4 
       38.96        30.97        35.44        28.18        32.68        29.79 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-HC-7744 TCGA-HC-7817 TCGA-HC-8264 TCGA-HI-7169 
       23.93         6.08        17.46        30.51         1.58        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67M TCGA-J4-A6M7 TCGA-J9-A52C 
       82.92        43.69        20.19        30.94        16.83         5.85 
TCGA-J9-A8CK TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A7F6 TCGA-KC-A7FD 
       10.55        15.22        12.69        30.71         8.65         8.88 
TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A7AU TCGA-KK-A7AZ TCGA-KK-A7B0 
       86.40        48.76       165.17        58.36        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8IF TCGA-M7-A71Y 
       34.95        36.13        74.27       101.79        26.43        16.21 
TCGA-M7-A720 TCGA-M7-A723 TCGA-TP-A8TT TCGA-V1-A8MJ TCGA-V1-A8MU TCGA-V1-A8WL 
       12.62        25.08        17.29        58.88        61.68        64.04 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-VN-A88I TCGA-VN-A88K 
       15.65        37.28        35.08        27.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88P TCGA-X4-A8KQ TCGA-XA-A8JR TCGA-YL-A8SF TCGA-YL-A8SP 
       24.53        41.42        45.47        12.36        45.14        77.79 
TCGA-YL-A8SR TCGA-YL-A9WL TCGA-ZG-A9L0 
        8.98        24.33        11.67 

$subtype4
TCGA-EJ-A46G TCGA-J9-A8CN TCGA-KK-A8IB TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       21.96        40.67         2.73         3.68        28.37        44.84 
TCGA-2A-AAYU TCGA-CH-5741 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 
       20.22        12.99        35.01        31.00         2.04         0.92 
TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5792 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5514 
        2.04        26.99         2.99        45.40        47.90        60.13 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-7321 TCGA-EJ-7782 
       69.63        64.50        74.93        36.66        27.09        38.37 
TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-A65D TCGA-EJ-A65F TCGA-EJ-A7NH TCGA-EJ-A8FN 
       25.68        36.33        12.92        18.41        15.58        10.82 
TCGA-G9-6338 TCGA-G9-6377 TCGA-G9-A9S0 TCGA-HC-7212 TCGA-HC-7213 TCGA-J9-A52E 
       66.67        31.50        26.01        28.60        40.08        10.62 
TCGA-KC-A7F5 TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A5A1 TCGA-KK-A6E8 TCGA-KK-A8I8 
        2.99       113.10        83.34        81.17        58.19        31.79 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-M7-A71Z TCGA-M7-A722 TCGA-M7-A724 TCGA-M7-A725 
       67.43        69.27        21.14        34.85        29.23        18.84 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A9O5 TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       20.05        47.64        63.52        79.00        62.89        12.20 
TCGA-V1-A9Z7 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-VP-A87K TCGA-WW-A8ZI TCGA-Y6-A9XI 
       28.73        49.87        53.92        42.94        14.76        17.29 
TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8S9 TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WY 
       49.02        48.72        60.56        53.36        70.22        36.10 
TCGA-ZG-A8QY TCGA-ZG-A9KY TCGA-ZG-A9L5 TCGA-ZG-A9LU 
       13.28         4.27        29.85        19.04 

subtype1 subtype2 subtype3 subtype4 
    0.89     1.02     1.58     0.92 
subtype1 subtype2 subtype3 subtype4 
  109.25   140.19   165.17   113.10 
subtype1 subtype2 subtype3 subtype4 
  38.010   28.685   33.140   31.645 
[1] "0.9 - 109.2 (38.0)" "1.0 - 140.2 (28.7)" "1.6 - 165.2 (33.1)"
[4] "0.9 - 113.1 (31.6)"
D4V2, continuous
          vv
clus       T2 T3 T4
  subtype1 34 38  1
  subtype2 38 73  1
  subtype3 24 66  3
  subtype4 14 50  5
D4V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T2       34       38       24       14
  T3       38       73       66       50
  T4        1        1        3        5
[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"
D4V4, binary
          cls
clus        0  1
  subtype1 55  6
  subtype2 79 26
  subtype3 62 15
  subtype4 50 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55    6
  subtype2   79   26
  subtype3   62   15
  subtype4   50   16
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       55       79       62       50
  1        6       26       15       16
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1 70  5
  subtype2 85 16
  subtype3 76  9
  subtype4 52 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70    5
  subtype2   85   16
  subtype3   76    9
  subtype4   52   11
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        70       85       76       52
  YES        5       16        9       11
[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"
D4V6, binary
          cls
clus         0   1
  subtype1  73   2
  subtype2 109   5
  subtype3  93   0
  subtype4  66   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    2
  subtype2  109    5
  subtype3   93    0
  subtype4   66    4
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA ACINAR TYPE          73      109       93       66
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        2        5        0        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 56 15  0  0
  subtype2 75 32  2  4
  subtype3 56 29  1  3
  subtype4 34 32  0  3
D4V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       56       75       56       34
  R1       15       32       29       32
  R2        0        2        1        0
  RX        0        4        3        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
D4V9, continuous
D4V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    27
  subtype2     0                         1    47
  subtype3     1                         1    27
  subtype4     0                         3    20
D4V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        1        0
  BLACK OR AFRICAN AMERICAN        1        1        1        3
  WHITE                           27       47       27       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"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  96   0
  subtype2 138   4
  subtype3 147   4
  subtype4 106   2
subtype1 subtype2 subtype3 subtype4 
      96      142      151      108 
subtype1 subtype2 subtype3 subtype4 
       0        4        4        2 
$subtype1
TCGA-CH-5763 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A6RC TCGA-HC-7233 TCGA-2A-A8VL 
       12.00        36.76        21.60        28.70        44.55        20.42 
TCGA-2A-A8VO TCGA-2A-AAYF TCGA-2A-AAYO TCGA-CH-5745 TCGA-CH-5748 TCGA-CH-5767 
       55.92        44.84        41.82         2.99         1.02        15.06 
TCGA-CH-5789 TCGA-EJ-5502 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5511 TCGA-EJ-5512 
        9.99        38.50        46.92        30.31        48.53        56.98 
TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       60.23        62.10        69.63        60.10        88.34        93.70 
TCGA-EJ-7317 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7785 TCGA-EJ-7786 
       25.35         6.28        24.39        35.28        38.70        36.03 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-A46I TCGA-EJ-A65G 
       45.90         3.75        42.94        77.16        21.96        21.90 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FU TCGA-EJ-AB20 
       14.20        15.58        10.82         9.27         4.54         4.31 
TCGA-EJ-AB27 TCGA-G9-6343 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6367 TCGA-G9-6371 
        4.77        80.55        67.33        50.70        40.18        40.31 
TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7519 
       37.97        25.15        27.29        58.22        52.93        27.91 
TCGA-G9-7522 TCGA-G9-7523 TCGA-HC-7075 TCGA-HC-7210 TCGA-HC-7738 TCGA-HC-7740 
       35.44        28.18        19.76        28.54        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8256 TCGA-HC-8259 
       30.84        17.16        30.84        24.56        28.27        30.38 
TCGA-HC-8264 TCGA-HI-7168 TCGA-HI-7169 TCGA-J4-8200 TCGA-J4-A67O TCGA-J4-A67T 
        1.58       109.25        88.24        40.04        27.58         6.02 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-AAU2 TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A7FE 
       10.78        23.67        27.12        59.67        44.35        11.57 
TCGA-KK-A6E3 TCGA-KK-A8IJ TCGA-M7-A723 TCGA-TK-A8OK TCGA-V1-A8MK TCGA-V1-A8WL 
       67.59        51.25        25.08         0.89        16.70        64.04 
TCGA-V1-A8WN TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-VP-A87E TCGA-XA-A8JR TCGA-XK-AAJR 
       30.38         6.64        82.16        66.97        12.36        36.95 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SI TCGA-ZG-A9L6 
       32.61        52.96        75.75        56.52        53.06        22.59 

$subtype2
TCGA-CH-5753 TCGA-CH-5764 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 TCGA-G9-6364 
        1.02         1.02        32.02        33.01        49.74        39.39 
TCGA-HC-7748 TCGA-HC-7821 TCGA-J4-A83N TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-2A-A8VT 
       26.04        31.43        32.61        29.56        32.45        45.14 
TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5739 TCGA-CH-5740 
       22.06        28.37        20.22        11.51        22.06         1.02 
TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5765 TCGA-CH-5768 
       12.99         1.97        31.00         2.04        23.01        24.03 
TCGA-CH-5769 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5501 
        2.04        29.00        57.86        19.56        13.32        44.88 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       47.90        64.60        62.10        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-7314 
       61.87        36.66        62.76        58.45        60.23        37.81 
TCGA-EJ-7315 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-EJ-8469 
       33.14        27.09        30.35        25.68        28.24        76.41 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A65F TCGA-EJ-A7NF TCGA-G9-6332 
       24.85        25.18        25.74        18.41         8.22        87.35 
TCGA-G9-6342 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       55.76        67.92        46.52        47.44        45.30        44.81 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-7525 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 
       26.66        31.50        32.68        29.79        23.93         6.08 
TCGA-H9-A6BY TCGA-HC-7077 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7212 TCGA-HC-7213 
        3.68        69.53        37.35        14.47        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7744 TCGA-HC-7749 TCGA-HC-7819 
       32.91        30.87        38.17        17.46        23.80        17.85 
TCGA-HC-8213 TCGA-HC-8257 TCGA-HC-8262 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6HY 
       19.36        23.87        22.32        22.36         2.01         4.41 
TCGA-HC-A76X TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67N TCGA-J4-A6M7 TCGA-J4-A83I 
        4.93        43.69        20.19        30.81        16.83        22.52 
TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CM TCGA-KC-A4BV TCGA-KK-A59Y TCGA-KK-A6DY 
       13.87        10.55        15.22        43.66        64.70       141.21 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AU TCGA-KK-A7B1 
       72.26       165.17       115.13       113.33        58.36        34.95 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8II TCGA-KK-A8IM 
      101.79        21.96        31.79        63.48       113.98        62.96 
TCGA-M7-A71Z TCGA-MG-AAMC TCGA-TP-A8TT TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A9O9 
       21.14         5.69        17.29        15.58        35.44        94.36 
TCGA-V1-A9ZG TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88Q TCGA-VP-A875 
       49.87        25.51        24.53         6.21        44.91        75.91 
TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87D TCGA-VP-A87J TCGA-VP-A87K TCGA-XJ-A83F 
      109.58        23.93        60.92        58.32        42.94        37.05 
TCGA-XQ-A8TB TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF 
       25.32        49.02        51.45        16.83        41.46        45.14 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WL TCGA-ZG-A8QZ 
       45.86        32.45        77.79        14.04        24.33        10.13 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9LZ 
       42.81        37.94        36.43        22.75 

$subtype3
TCGA-CH-5772 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-A46G TCGA-EJ-A65J 
       15.98        84.56        36.13        35.18        21.96        14.83 
TCGA-HC-A76W TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A8IB TCGA-QU-A6IM 
        7.00        40.67        19.66         6.44         2.73        41.00 
TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 TCGA-CH-5750 
       41.49        32.19        45.30         3.68         2.99        13.02 
TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5788 TCGA-EJ-5494 TCGA-EJ-5509 TCGA-EJ-5514 
       35.01         0.92        26.99        48.56        48.13        60.13 
TCGA-EJ-7218 TCGA-EJ-7782 TCGA-EJ-7789 TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       83.57        38.37        36.33        23.34        12.92        13.71 
TCGA-EJ-A65M TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FS TCGA-FC-7961 TCGA-FC-A4JI 
        7.56         4.21         6.48         8.75        15.42        28.83 
TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6347 TCGA-G9-6366 
       22.36        25.94        81.04        66.67        68.68        64.01 
TCGA-G9-6369 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-A9S0 
       39.95        56.75        64.18        50.73        30.97        26.01 
TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7752 TCGA-HC-8216 TCGA-HC-8261 TCGA-HC-A4ZV 
       65.26        36.36        25.71        22.42        17.95         0.76 
TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A8CY 
        1.78         2.20         1.61        17.42         2.33         9.53 
TCGA-HC-A9TE TCGA-HC-A9TH TCGA-J4-A67Q TCGA-J4-A83J TCGA-J4-AATZ TCGA-J9-A52D 
       19.30        27.75        32.05        22.88        13.55         6.97 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CP TCGA-KC-A7F5 TCGA-KC-A7FD TCGA-KK-A59V 
       10.62        13.32        12.69         2.99         8.88       113.10 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E7 TCGA-KK-A6E8 
       83.34        86.40        81.17        48.76        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A8I9 
       52.93        34.65        57.67        49.94        43.69        32.91 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8IK TCGA-M7-A721 
       69.27        26.43        82.36        66.18        67.46        13.15 
TCGA-M7-A722 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       34.85        29.23        18.84         3.19       140.19       122.17 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A9O5 
       20.05        47.64        28.18        14.73        39.29        63.52 
TCGA-V1-A9OF TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9Z7 TCGA-V1-A9Z9 TCGA-V1-A9ZI 
       38.93        62.89        12.20        28.73        17.75        53.92 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       25.18        15.81        41.42        25.78        16.31       119.38 
TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XJ-A83G TCGA-XJ-A9DX 
       89.49        21.80        44.88        14.76        48.03        31.99 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XQ-A8TA TCGA-Y6-A9XI 
       37.25        40.04        30.58        41.39         4.80        17.29 
TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SH TCGA-YL-A8SO 
        4.87        48.72        62.14        60.56        28.77       114.38 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A8QW 
       68.48         8.98        53.36        70.22        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L9 
       14.53        13.28         4.27        11.67        29.85        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.17        12.43         3.78        17.98        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

$subtype4
TCGA-HC-A6AQ TCGA-CH-5738 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5762 TCGA-CH-5766 
        3.48         6.97        13.97        24.03        44.02         1.02 
TCGA-CH-5771 TCGA-CH-5792 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5503 TCGA-EJ-5506 
       13.02         2.99        56.55        46.52        45.73        45.40 
TCGA-EJ-5510 TCGA-EJ-5531 TCGA-EJ-7318 TCGA-EJ-7328 TCGA-EJ-7783 TCGA-EJ-7797 
       62.04        41.85        33.83        27.68        25.87        32.32 
TCGA-EJ-8470 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A6RA TCGA-EJ-A7NJ 
       38.10        20.58        17.23        23.80        11.61         6.48 
TCGA-EJ-A7NK TCGA-EJ-A8FP TCGA-FC-7708 TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6329 
       15.65         9.83        28.41        17.23        20.25        41.62 
TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6348 TCGA-G9-6356 TCGA-G9-6370 TCGA-G9-6379 
       67.99        83.87        49.81        47.15        38.01        58.45 
TCGA-G9-7510 TCGA-H9-A6BX TCGA-HC-7079 TCGA-HC-7211 TCGA-HC-7736 TCGA-HC-7737 
       38.96        30.94        38.93        40.14        36.26        35.84 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7817 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8265 
       23.70        24.59        30.51        27.85        22.55        15.88 
TCGA-HC-8266 TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7170 
       15.55         1.45         1.25        25.48        18.84        82.92 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A6G1 
       33.01        25.32        30.94        29.92        27.39        25.28 
TCGA-J4-A6G3 TCGA-J4-A83M TCGA-J4-AATV TCGA-J9-A52C TCGA-KC-A4BL TCGA-KC-A7F3 
       27.91        17.85        18.18         5.85        30.71        21.86 
TCGA-KC-A7F6 TCGA-KK-A6E5 TCGA-KK-A7AV TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I7 
        8.65        68.15        27.02        36.13        74.27        65.82 
TCGA-KK-A8IC TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-QU-A6IP TCGA-SU-A7E7 
       67.43        20.65        16.21        12.62        86.14        18.12 
TCGA-V1-A8MJ TCGA-V1-A8MU TCGA-V1-A8WV TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OT 
       58.88        61.68        22.55        20.91        79.00        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       37.28        35.08        27.19        45.47        44.75         8.84 
TCGA-VP-A878 TCGA-VP-A87C TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A83H TCGA-XJ-A9DI 
      102.90        55.56        45.47        32.19        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-YL-A8SK 
        9.04         2.99        31.96        47.15        51.81        46.29 
TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC 
       60.99        49.91        16.96        19.04        12.16        14.96 

subtype1 subtype2 subtype3 subtype4 
    0.89     1.02     0.76     1.02 
subtype1 subtype2 subtype3 subtype4 
  109.25   165.17   140.19   102.90 
subtype1 subtype2 subtype3 subtype4 
  30.840   31.645   28.730   29.165 
[1] "0.9 - 109.2 (30.8)" "1.0 - 165.2 (31.6)" "0.8 - 140.2 (28.7)"
[4] "1.0 - 102.9 (29.2)"
D5V2, continuous
          vv
clus        T2  T3  T4
  subtype1  53  39   2
  subtype2  40  99   3
  subtype3  45 100   4
  subtype4  49  55   1
D5V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T2       53       40       45       49
  T3       39       99      100       55
  T4        2        3        4        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
          cls
clus         0   1
  subtype1  68   5
  subtype2  98  28
  subtype3 106  27
  subtype4  73  19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68    5
  subtype2   98   28
  subtype3  106   27
  subtype4   73   19
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       68       98      106       73
  1        5       28       27       19
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus         0   1
  subtype1  86   5
  subtype2 109  22
  subtype3 117  15
  subtype4  82  17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   86    5
  subtype2  109   22
  subtype3  117   15
  subtype4   82   17
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        86      109      117       82
  YES        5       22       15       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"
D5V6, binary
          cls
clus         0   1
  subtype1  94   2
  subtype2 138   4
  subtype3 143   8
  subtype4 107   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94    2
  subtype2  138    4
  subtype3  143    8
  subtype4  107    1
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA ACINAR TYPE          94      138      143      107
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        2        4        8        1
[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       R0 R1 R2 RX
  subtype1 73 21  1  0
  subtype2 93 36  3  6
  subtype3 81 60  1  4
  subtype4 68 30  0  5
D5V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       73       93       81       68
  R1       21       36       60       30
  R2        1        3        1        0
  RX        0        6        4        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
D5V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    43
  subtype2     0                         2    58
  subtype3     0                         2    20
  subtype4     2                         1    26
D5V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        0        2
  BLACK OR AFRICAN AMERICAN        2        2        2        1
  WHITE                           43       58       20       26
[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"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1 170   3
  subtype2 204   4
  subtype3 113   3
subtype1 subtype2 subtype3 
     173      208      116 
subtype1 subtype2 subtype3 
       3        4        3 
$subtype1
TCGA-CH-5763 TCGA-CH-5764 TCGA-EJ-5542 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-HC-7233 
       12.00         1.02        49.74        36.76        21.60        44.55 
TCGA-HC-7748 TCGA-HC-A6AQ TCGA-J4-A83N TCGA-QU-A6IM TCGA-2A-A8VL TCGA-CH-5738 
       26.04         3.48        32.61        41.00        20.42         6.97 
TCGA-CH-5743 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5762 TCGA-CH-5768 TCGA-CH-5771 
       13.97         2.99        24.03        44.02        24.03        13.02 
TCGA-CH-5789 TCGA-CH-5792 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
        9.99         2.99        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5503 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 
       46.52        44.88        45.73        45.40        64.60        62.04 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 
       56.98        60.23        62.10        68.35        61.87        62.76 
TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7314 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       58.45        41.85        37.81        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7793 TCGA-EJ-7794 
       24.39        35.28        25.87        38.70         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H 
       32.32        38.10        24.85        20.58        17.23        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.96        23.34         7.56        11.61         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.58         6.48        15.65         6.48         9.27         9.83 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A66V TCGA-FC-A8O0 
        4.54         4.31         4.77        28.41        17.23        20.25 
TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       41.62        67.99        83.87        49.81        67.33        50.70 
TCGA-G9-6356 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6377 TCGA-G9-6379 
       47.15        44.81        40.18        38.01        31.50        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-7509 TCGA-G9-7522 TCGA-H9-A6BX TCGA-HC-7079 
       25.15        27.29        52.93        35.44        30.94        38.93 
TCGA-HC-7211 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7740 TCGA-HC-7745 TCGA-HC-7747 
       40.14        38.17        36.26        23.57        23.70        24.59 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8216 TCGA-HC-8258 TCGA-HC-8260 
       30.51        30.84        24.56        22.42        27.85        22.55 
TCGA-HC-8262 TCGA-HC-8266 TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       22.32        15.55         2.33         1.45         1.25         4.41 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67M 
       25.48        18.84        82.92        20.19        33.01        30.94 
TCGA-J4-A67O TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A83K TCGA-J4-AATV 
       27.58        29.92         6.02        25.28        10.78        18.18 
TCGA-J9-A52C TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A7AV 
        5.85        30.71        59.67        67.59        68.15        27.02 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8IC TCGA-KK-A8IL TCGA-KK-A8IM 
       36.13        74.27        65.82        67.43        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A723 TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
       16.21        12.62        25.08       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       47.64        58.88        16.70        61.68        64.04        30.38 
TCGA-V1-A9OA TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9ZG 
       20.91        15.65        37.28        35.08        27.19        49.87 
TCGA-V1-A9ZR TCGA-VP-A879 TCGA-VP-A87C TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A83H 
       44.75        23.93        55.56        45.47        32.19        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAJT TCGA-XK-AAJU 
       48.03         9.04         2.99        31.96        47.15        51.81 
TCGA-YL-A8HK TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SK TCGA-YL-A9WJ TCGA-YL-A9WX 
       49.02        75.75        56.52        46.29        60.99        49.91 
TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC 
       36.43        22.59        19.04        12.16        14.96 

$subtype2
TCGA-CH-5753 TCGA-CH-5772 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-A46G 
        1.02        15.98        84.56        36.13        35.18        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-HC-A76W TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
       14.83        28.70         7.00        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VO TCGA-2A-A8VX 
       29.56         2.73        41.49        32.19        55.92        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-CH-5737 TCGA-CH-5748 
        3.68        28.37        44.84        41.82         2.99         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5767 TCGA-CH-5788 TCGA-EJ-5494 
       13.02        35.01         0.92        15.06        26.99        48.56 
TCGA-EJ-5502 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 
       38.50        46.92        30.31        48.13        48.53        60.13 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       62.10        69.63        64.50        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7782 TCGA-EJ-7786 TCGA-EJ-7788 
       83.57        25.35        33.83        38.37        36.03        28.24 
TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-8468 TCGA-EJ-8474 TCGA-EJ-A65E TCGA-EJ-A65G 
       36.33        45.90        77.16        25.18        13.71        21.90 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.21        10.82         8.75        15.42        28.83        22.36 
TCGA-FC-A6HD TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6366 
       25.94        81.04        66.67        80.55        68.68        64.01 
TCGA-G9-6369 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       39.95        40.31        37.97        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 
       50.73        38.96        27.91        30.97        28.18        26.01 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7737 TCGA-HC-7738 
       19.76        65.26        36.36        28.54        35.84        31.69 
TCGA-HC-7742 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-8256 TCGA-HC-8261 
       30.84        23.80        17.16        25.71        28.27        17.95 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A8CY 
        1.58        15.88         0.76         2.20        17.42         9.53 
TCGA-HC-A9TE TCGA-HI-7168 TCGA-HI-7169 TCGA-J4-8200 TCGA-J4-A67Q TCGA-J4-A6G3 
       19.30       109.25        88.24        40.04        32.05        27.91 
TCGA-J4-A83J TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52D 
       22.88        23.67        17.85        13.55        27.12         6.97 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CP TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F5 
       10.62        13.32        12.69        44.35        21.86         2.99 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A5A1 
        8.88        11.57       113.10        83.34        86.40        81.17 
TCGA-KK-A6E0 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AW TCGA-KK-A7AZ 
       48.76        90.74        58.19        52.93        34.65        49.94 
TCGA-KK-A7B0 TCGA-KK-A8I9 TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ 
       43.69        32.91        69.27        26.43        82.36        51.25 
TCGA-KK-A8IK TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A724 TCGA-QU-A6IL TCGA-TK-A8OK 
       67.46        13.15        34.85        29.23         3.19         0.89 
TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8WV TCGA-V1-A8X3 
       20.05        28.18        14.73        39.29        22.55         6.64 
TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       63.52        82.16        38.93        79.00        62.89        12.20 
TCGA-V1-A9Z7 TCGA-V1-A9Z9 TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-VN-A88I TCGA-VN-A88N 
       28.73        17.75        53.92        45.47         8.84        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A878 TCGA-VP-A87B 
       15.81        41.42        25.78        16.31       102.90        89.49 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XA-A8JR 
       66.97        21.80        58.32        44.88        14.76        12.36 
TCGA-XJ-A83G TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       48.03        31.99        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XQ-A8TA TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
       36.95         4.80        32.61        17.29         4.87        52.96 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI 
       48.72        62.14        60.56        41.46        28.77        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WK 
       45.86       114.38        68.48         8.98        53.36        70.22 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9KY TCGA-ZG-A9L0 
       36.10         3.09        14.53        13.28         4.27        11.67 
TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       29.85        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        11.47        13.48         4.34 

$subtype3
TCGA-CH-5790 TCGA-CH-5791 TCGA-G9-6364 TCGA-HC-7821 TCGA-KK-A7B4 TCGA-2A-A8VT 
       32.02        33.01        39.39        31.43        32.45        45.14 
TCGA-2A-A8VV TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       22.06        20.22        11.51        22.06         1.02        12.99 
TCGA-CH-5744 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5769 
        1.97        31.00         2.04        23.01         1.02         2.04 
TCGA-CH-5794 TCGA-EJ-5507 TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-5530 TCGA-EJ-7315 
       29.00        47.90        74.93        36.66        60.23        33.14 
TCGA-EJ-7321 TCGA-EJ-7784 TCGA-EJ-8469 TCGA-EJ-A46F TCGA-EJ-A65D TCGA-EJ-A65F 
       27.09        25.68        76.41        25.74        12.92        18.41 
TCGA-G9-6332 TCGA-G9-6342 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       87.35        55.76        67.92        46.52        47.44        45.30 
TCGA-G9-6373 TCGA-G9-7525 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BY 
       26.66        32.68        29.79        23.93         6.08         3.68 
TCGA-HC-7077 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       69.53        37.35        14.47        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7744 TCGA-HC-7819 TCGA-HC-8213 TCGA-HC-8257 TCGA-HC-8259 
       30.87        17.46        17.85        19.36        23.87        30.38 
TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A76X TCGA-HC-A9TH 
       22.36         1.78         2.01         1.61         4.93        27.75 
TCGA-HI-7171 TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67S TCGA-J4-A6M7 TCGA-J4-A83I 
       43.69        25.32        30.81        27.39        16.83        22.52 
TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CM TCGA-KC-A4BV TCGA-KC-A7F6 TCGA-KK-A59Y 
       13.87        10.55        15.22        43.66         8.65        64.70 
TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AU 
      141.21        72.26       165.17       115.13       113.33        58.36 
TCGA-KK-A7AY TCGA-KK-A7B1 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8IA 
       57.67        34.95       101.79        21.96        31.79        63.48 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-M7-A71Z TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IN 
       66.18       113.98        21.14        18.84         5.69       140.19 
TCGA-TP-A8TT TCGA-V1-A8WS TCGA-V1-A8WW TCGA-V1-A9O9 TCGA-VN-A88K TCGA-VN-A88L 
       17.29        15.58        35.44        94.36        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87D 
        6.21        44.91       119.38        75.91       109.58        60.92 
TCGA-VP-A87K TCGA-XJ-A83F TCGA-XQ-A8TB TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SF 
       42.94        37.05        25.32        51.45        16.83        45.14 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WL TCGA-ZG-A8QZ TCGA-ZG-A9L1 
       32.45        77.79        14.04        24.33        10.13        42.81 
TCGA-ZG-A9L2 TCGA-ZG-A9LZ 
       37.94        22.75 

subtype1 subtype2 subtype3 
    1.02     0.76     1.02 
subtype1 subtype2 subtype3 
  122.17   114.38   165.17 
subtype1 subtype2 subtype3 
  30.380   30.710   30.595 
[1] "1.0 - 122.2 (30.4)" "0.8 - 114.4 (30.7)" "1.0 - 165.2 (30.6)"
D6V2, continuous
          vv
clus        T2  T3  T4
  subtype1  84  84   2
  subtype2  70 128   6
  subtype3  33  81   2
D6V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2       84       70       33
  T3       84      128       81
  T4        2        6        2
[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"
D6V4, binary
          cls
clus         0   1
  subtype1 127  18
  subtype2 139  37
  subtype3  79  24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  127   18
  subtype2  139   37
  subtype3   79   24
   clus
vv  subtype1 subtype2 subtype3
  0      127      139       79
  1       18       37       24
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus         0   1
  subtype1 144  17
  subtype2 166  21
  subtype3  84  21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  144   17
  subtype2  166   21
  subtype3   84   21
     clus
vv    subtype1 subtype2 subtype3
  NO       144      166       84
  YES       17       21       21
[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"
D6V6, binary
          cls
clus         0   1
  subtype1 170   3
  subtype2 202   6
  subtype3 110   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  170    3
  subtype2  202    6
  subtype3  110    6
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA ACINAR TYPE         170      202      110
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        3        6        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 122  38   0   6
  subtype2 125  72   3   3
  subtype3  68  37   2   6
D6V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      122      125       68
  R1       38       72       37
  R2        0        3        2
  RX        6        3        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
D6V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0    65
  subtype2     0                         5    46
  subtype3     0                         2    36
D6V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        0
  BLACK OR AFRICAN AMERICAN        0        5        2
  WHITE                           65       46       36
[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"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 207   6
  subtype2  70   1
  subtype3 122   2
  subtype4  85   1
subtype1 subtype2 subtype3 subtype4 
     213       71      124       86 
subtype1 subtype2 subtype3 subtype4 
       6        1        2        1 
$subtype1
TCGA-CH-5753 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-A46G TCGA-EJ-A65J TCGA-HC-A76W 
        1.02        36.13        35.18        21.96        14.83         7.00 
TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-QU-A6IM 
       40.67        19.66         6.44        29.56        32.45        41.00 
TCGA-XK-AAJ3 TCGA-2A-A8VL TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       41.49        20.42        45.14        22.06        45.30         3.68 
TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5752 TCGA-CH-5754 
       11.51         2.99         1.02        12.99        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5765 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5788 TCGA-EJ-5494 
        0.92        23.01        24.03         2.04        26.99        48.56 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5519 TCGA-EJ-5525 
       46.92        30.31        47.90        48.13        64.50        36.66 
TCGA-EJ-5526 TCGA-EJ-7318 TCGA-EJ-A46F TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       62.76        33.83        25.74        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65M TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-EJ-A7NM TCGA-EJ-A7NN 
       18.41         7.56         8.22        15.58         4.21         6.48 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6332 TCGA-G9-6354 
       15.42        28.83        22.36        25.94        87.35        67.92 
TCGA-G9-6362 TCGA-G9-6379 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-A9S0 TCGA-G9-A9S4 
       47.44        58.45        56.75        64.18        26.01        29.79 
TCGA-H9-A6BY TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8257 TCGA-HC-A48F TCGA-HC-A4ZV 
        3.68        19.36        22.42        23.87        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AS 
        1.78         2.01         2.20         1.61        17.42         1.45 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A9TH TCGA-J4-A67K TCGA-J4-A67N 
        4.41         4.93         9.53        27.75        33.01        30.81 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-AATZ 
       27.39         6.02        16.83        22.52        22.88        13.55 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.87         5.85         6.97        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BN TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       15.22        12.69        59.67        43.66        21.86         2.99 
TCGA-KC-A7FD TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
        8.88       113.10        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E7 
      141.21        48.76        72.26       165.17        68.15        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AY TCGA-KK-A8I5 
       58.19        52.93        58.36        27.02        57.67       101.79 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH 
       31.79        32.91        63.48        69.27        26.43        66.18 
TCGA-KK-A8II TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Z TCGA-M7-A721 TCGA-M7-A722 
      113.98        67.46        20.65        21.14        13.15        34.85 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-TK-A8OK TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8ML 
       86.14         0.89        20.05        47.64        28.18        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       39.29        61.68        64.04        15.58        22.55        35.44 
TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9Z7 
       63.52        94.36        38.93        79.00        62.89        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-VN-A88K TCGA-VN-A88M 
       27.19        17.75        49.87        53.92        25.51         6.21 
TCGA-VN-A88N TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 
       25.18        44.91        25.78        16.31        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-A87D TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
      102.90        89.49        60.92        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DX 
       14.76        45.47        37.05        48.03        42.08        31.99 
TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XQ-A8TA 
       40.04        30.58        41.39        36.95        47.15         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HL TCGA-YL-A8HM 
       25.32        32.61        17.29         4.87        51.45        48.72 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       62.14        60.56        16.83        41.46        45.14        28.77 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH 
       45.86        32.45       114.38        77.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QY TCGA-ZG-A9KY 
       53.36        70.22        24.33        36.10        13.28         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LY 
       11.67        29.85        19.17        12.43        16.96        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9ND 
       22.75        17.98        13.48 

$subtype2
TCGA-CH-5772 TCGA-EJ-7791 TCGA-EJ-A6RC TCGA-2A-A8VO TCGA-2A-AAYF TCGA-2A-AAYO 
       15.98        36.76        28.70        55.92        44.84        41.82 
TCGA-2A-AAYU TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5530 
       20.22        48.53        60.13        62.10        69.63        60.23 
TCGA-EJ-5532 TCGA-EJ-7218 TCGA-EJ-7792 TCGA-EJ-A65G TCGA-EJ-A8FN TCGA-EJ-AB20 
       60.10        83.57        45.90        21.90        10.82         4.31 
TCGA-EJ-AB27 TCGA-FC-A8O0 TCGA-G9-6338 TCGA-G9-6347 TCGA-G9-6363 TCGA-G9-6365 
        4.77        20.25        66.67        68.68        45.30        44.81 
TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6385 TCGA-G9-7519 TCGA-G9-7523 TCGA-H9-7775 
       40.31        37.97        27.29        27.91        28.18         6.08 
TCGA-H9-A6BX TCGA-HC-7740 TCGA-HC-7750 TCGA-HC-8264 TCGA-HI-7169 TCGA-J4-8200 
       30.94        23.57        17.16         1.58        88.24        40.04 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A83L TCGA-J4-AAU2 TCGA-KC-A4BR TCGA-KC-A7FE 
       27.58        32.05        23.67        27.12        44.35        11.57 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-V1-A8X3 TCGA-V1-A9O7 
       67.59       115.13        82.36        51.25         6.64        82.16 
TCGA-V1-A9OQ TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88O TCGA-VN-A88P TCGA-VP-A87E 
       12.20         8.84        24.53        15.81        41.42        66.97 
TCGA-VP-A87H TCGA-XA-A8JR TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SI 
       21.80        12.36        52.96        75.75        56.52        53.06 
TCGA-YL-A8SK TCGA-YL-A8SQ TCGA-ZG-A8QX TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       46.29        68.48        14.53        42.81        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       22.59        20.28         3.78        11.47         4.34 

$subtype3
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5791 TCGA-EJ-5542 TCGA-EJ-A46B TCGA-G9-6364 
       12.00         1.02        33.01        49.74        21.60        39.39 
TCGA-HC-7748 TCGA-HC-A6AQ TCGA-J4-A83N TCGA-KK-A8IB TCGA-2A-A8W3 TCGA-CH-5738 
       26.04         3.48        32.61         2.73        28.37         6.97 
TCGA-CH-5743 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5762 TCGA-CH-5766 
       13.97         2.99        24.03        13.02        44.02         1.02 
TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 
       13.02         9.99         2.99        29.00        57.86        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       45.40        64.60        62.04        56.98        60.23        62.10 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7783 
       74.93        68.35        61.87        58.45        41.85        25.87 
TCGA-EJ-7797 TCGA-EJ-8472 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I 
       32.32        24.85        20.58        17.23        23.80        21.96 
TCGA-EJ-A6RA TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A8FO TCGA-EJ-A8FP 
       11.61        14.20         6.48        15.65         9.27         9.83 
TCGA-EJ-A8FU TCGA-FC-A66V TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6353 
        4.54        17.23        41.62        67.99        83.87        50.70 
TCGA-G9-6356 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6373 TCGA-G9-6384 TCGA-G9-7509 
       47.15        40.18        38.01        26.66        25.15        52.93 
TCGA-G9-7510 TCGA-G9-7522 TCGA-G9-A9S7 TCGA-HC-7747 TCGA-HC-7817 TCGA-HC-8258 
       38.96        35.44        23.93        24.59        30.51        27.85 
TCGA-HC-8260 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A6AP TCGA-HC-A6HX TCGA-HC-A8D0 
       22.55        15.88        15.55         2.33         1.25        25.48 
TCGA-HC-A8D1 TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A6G1 TCGA-J4-A6G3 
       18.84        25.32        30.94        29.92        25.28        27.91 
TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-AATV TCGA-KC-A4BL TCGA-KC-A4BO TCGA-KC-A7F6 
       10.78        17.85        18.18        30.71        19.96         8.65 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 
       43.69        34.95        36.13        74.27        21.96        65.82 
TCGA-KK-A8IC TCGA-KK-A8IM TCGA-M7-A720 TCGA-M7-A723 TCGA-SU-A7E7 TCGA-V1-A8MJ 
       67.43        62.96        12.62        25.08        18.12        58.88 
TCGA-V1-A8MK TCGA-V1-A8WN TCGA-V1-A9OA TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9ZK 
       16.70        30.38        20.91        37.28        35.08        45.47 
TCGA-V1-A9ZR TCGA-VP-A879 TCGA-VP-A87C TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK 
       44.75        23.93        55.56        32.19        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAJU TCGA-YL-A8HK TCGA-YL-A9WJ TCGA-YL-A9WX 
        2.99        31.96        51.81        49.02        60.99        49.91 
TCGA-ZG-A8QW TCGA-ZG-A8QZ TCGA-ZG-A9LU TCGA-ZG-A9MC 
        3.09        10.13        19.04        14.96 

$subtype4
TCGA-CH-5790 TCGA-EJ-7123 TCGA-HC-7233 TCGA-HC-7821 TCGA-XK-AAK1 TCGA-CH-5739 
       32.02        84.56        44.55        31.43        32.19        22.06 
TCGA-CH-5744 TCGA-CH-5748 TCGA-CH-5767 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7314 
        1.97         1.02        15.06        88.34        93.70        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.14        25.35        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        35.28        38.37        25.68        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-8469 
       28.24        36.33         3.75        42.94        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A8FS TCGA-FC-7708 TCGA-G9-6333 TCGA-G9-6342 
       38.10        25.18         8.75        28.41        81.04        55.76 
TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6361 TCGA-G9-6366 TCGA-G9-6369 
       80.55        49.81        67.33        46.52        64.01        39.95 
TCGA-G9-6377 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-7525 TCGA-HC-7075 
       31.50        58.22        50.73        30.97        32.68        19.76 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7742 TCGA-HC-7744 
       38.17        36.26        35.84        31.69        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       23.70        23.80        25.71        30.84        17.85        24.56 
TCGA-HC-8256 TCGA-HC-8259 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-A9TE TCGA-HI-7168 
       28.27        30.38        17.95        22.32        19.30       109.25 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-KK-A7AW TCGA-TP-A8TT TCGA-V1-A9OT 
       82.92        43.69        20.19        34.65        17.29        15.65 
TCGA-VP-A872 TCGA-XK-AAIV 
      119.38        37.25 

subtype1 subtype2 subtype3 subtype4 
    0.76     1.58     1.02     1.02 
subtype1 subtype2 subtype3 subtype4 
  165.17   115.13    83.87   119.38 
subtype1 subtype2 subtype3 subtype4 
  28.730   36.760   27.255   32.435 
[1] "0.8 - 165.2 (28.7)" "1.6 - 115.1 (36.8)" "1.0 - 83.9 (27.3)" 
[4] "1.0 - 119.4 (32.4)"
D7V2, continuous
          vv
clus        T2  T3  T4
  subtype1  58 148   4
  subtype2  35  32   3
  subtype3  50  70   1
  subtype4  44  41   1
D7V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T2       58       35       50       44
  T3      148       32       70       41
  T4        4        3        1        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
          cls
clus         0   1
  subtype1 137  50
  subtype2  49   8
  subtype3  94  15
  subtype4  64   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  137   50
  subtype2   49    8
  subtype3   94   15
  subtype4   64    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      137       49       94       64
  1       50        8       15        5
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus         0   1
  subtype1 160  29
  subtype2  60   7
  subtype3  98  17
  subtype4  74   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  160   29
  subtype2   60    7
  subtype3   98   17
  subtype4   74    6
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       160       60       98       74
  YES       29        7       17        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus         0   1
  subtype1 202  11
  subtype2  70   1
  subtype3 122   2
  subtype4  85   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  202   11
  subtype2   70    1
  subtype3  122    2
  subtype4   85    1
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA ACINAR TYPE         202       70      122       85
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE       11        1        2        1
[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        R0  R1  R2  RX
  subtype1 114  83   1  10
  subtype2  39  28   2   0
  subtype3  92  25   0   3
  subtype4  68  10   2   2
D7V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      114       39       92       68
  R1       83       28       25       10
  R2        1        2        0        2
  RX       10        0        3        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
D7V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    23
  subtype2     0                         2    17
  subtype3     1                         0    45
  subtype4     1                         5    61
D7V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        1        1
  BLACK OR AFRICAN AMERICAN        0        2        0        5
  WHITE                           23       17       45       61
[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"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 146   2
  subtype2  96   2
  subtype3  57   2
  subtype4 130   3
  subtype5  55   1
subtype1 subtype2 subtype3 subtype4 subtype5 
     148       98       59      133       56 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        2        2        3        1 
$subtype1
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5791 TCGA-EJ-7312 TCGA-EJ-A46B TCGA-G9-6364 
       12.00         1.02        33.01        36.13        21.60        39.39 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-KK-A8IB TCGA-2A-A8VL TCGA-2A-A8W3 TCGA-CH-5738 
        3.48         7.00         2.73        20.42        28.37         6.97 
TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5754 TCGA-CH-5762 
        1.02        13.97         1.97         2.99         2.04        44.02 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 
        2.04        13.02         9.99         2.99        29.00        57.86 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5503 
       19.56        13.32        56.55        46.52        44.88        45.73 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       56.98        60.23        62.10        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7321 TCGA-EJ-8472 
       61.87        62.76        58.45        41.85        27.09        24.85 
TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A6RA 
       17.23        23.80        21.96        23.34        13.71        11.61 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A8FP TCGA-EJ-A8FU 
        8.22        14.20         6.48        15.65         9.83         4.54 
TCGA-FC-7961 TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6336 
       15.42        17.23        20.25        41.62        87.35        67.99 
TCGA-G9-6339 TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 
       83.87        49.81        50.70        67.92        47.15        47.44 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6384 TCGA-G9-6496 TCGA-G9-7509 
       40.18        39.95        38.01        25.15        56.75        52.93 
TCGA-H9-A6BX TCGA-HC-7817 TCGA-HC-8260 TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
       30.94        30.51        22.55         2.33         1.45         1.25 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A67S 
       25.48        18.84        25.32        30.94        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83M 
        6.02        25.28        27.91        22.88        10.78        17.85 
TCGA-J4-AATV TCGA-J9-A52C TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A7F3 
       18.18         5.85        30.71        59.67        19.96        21.86 
TCGA-KC-A7FD TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A7AV 
        8.88       141.21        72.26        67.59        68.15        27.02 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 
       43.69        34.95        36.13        74.27        21.96        65.82 
TCGA-KK-A8I9 TCGA-KK-A8IM TCGA-M7-A720 TCGA-M7-A721 TCGA-QU-A6IP TCGA-SU-A7E7 
       32.91        62.96        12.62        13.15        86.14        18.12 
TCGA-TP-A8TV TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WS 
       20.05        58.88        16.70        14.73        61.68        15.58 
TCGA-V1-A9OL TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z9 TCGA-V1-A9ZK 
       62.89        15.65        37.28        35.08        17.75        45.47 
TCGA-VN-A88Q TCGA-VP-A878 TCGA-VP-A879 TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK 
       44.91       102.90        23.93        32.19        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAJU TCGA-YL-A8HK TCGA-YL-A8SJ TCGA-YL-A8SK 
        2.99        31.96        51.81        49.02        45.86        46.29 
TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QZ TCGA-ZG-A9LU 
       60.99         3.09        10.13        19.04 

$subtype2
TCGA-CH-5772 TCGA-EJ-7791 TCGA-EJ-A6RC TCGA-HC-7233 TCGA-J9-A8CN TCGA-2A-A8VO 
       15.98        36.76        28.70        44.55        40.67        55.92 
TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-EJ-5502 
       45.30         3.68        44.84        41.82        20.22        38.50 
TCGA-EJ-5504 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5530 
       46.92        48.53        60.13        62.10        69.63        60.23 
TCGA-EJ-5532 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7317 TCGA-EJ-7330 TCGA-EJ-7331 
       60.10        93.70        83.57        25.35         6.28        24.39 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-A65G 
       38.70        36.03        28.24        36.33        45.90        21.90 
TCGA-EJ-A8FN TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 
       10.82         4.31         4.77        66.67        55.76        80.55 
TCGA-G9-6347 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6385 
       68.68        45.30        44.81        40.31        37.97        27.29 
TCGA-G9-6494 TCGA-G9-6498 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7523 TCGA-H9-A6BY 
       58.22        64.18        27.91        30.97        28.18         3.68 
TCGA-HC-7075 TCGA-HC-7740 TCGA-HC-7750 TCGA-HC-8258 TCGA-HC-A76X TCGA-HI-7169 
       19.76        23.57        17.16        27.85         4.93        88.24 
TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A6M7 TCGA-J4-A83L 
       82.92        40.04        27.58        32.05        16.83        23.67 
TCGA-J4-AAU2 TCGA-J9-A52E TCGA-KC-A4BR TCGA-KC-A7FE TCGA-KK-A6E4 TCGA-KK-A6E8 
       27.12        10.62        44.35        11.57       115.13        58.19 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-V1-A8WL TCGA-V1-A8X3 
       69.27        26.43        82.36        51.25        64.04         6.64 
TCGA-V1-A9O7 TCGA-V1-A9OQ TCGA-V1-A9Z8 TCGA-VN-A88I TCGA-VN-A88O TCGA-VN-A88P 
       82.16        12.20        27.19         8.84        15.81        41.42 
TCGA-VN-A943 TCGA-VP-A87E TCGA-VP-AA1N TCGA-XA-A8JR TCGA-Y6-A8TL TCGA-YJ-A8SW 
       16.31        66.97        44.88        12.36        32.61         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SB TCGA-YL-A8SH TCGA-YL-A8SI 
       52.96        75.75        62.14        56.52        28.77        53.06 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-ZG-A8QX TCGA-ZG-A9L1 TCGA-ZG-A9L6 TCGA-ZG-A9LN 
       77.79        68.48        14.53        42.81        22.59         3.78 
TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       17.98        14.96 

$subtype3
TCGA-CH-5753 TCGA-CH-5790 TCGA-EJ-5542 TCGA-EJ-A65J TCGA-HC-7748 TCGA-KC-A7FA 
        1.02        32.02        49.74        14.83        26.04        19.66 
TCGA-KK-A7AP TCGA-XK-AAJ3 TCGA-2A-A8VT TCGA-2A-A8VV TCGA-CH-5741 TCGA-CH-5746 
        6.44        41.49        45.14        22.06        12.99        24.03 
TCGA-CH-5750 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 TCGA-EJ-5525 TCGA-EJ-7314 
       13.02        23.01         1.02        24.03        36.66        37.81 
TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-A46D TCGA-EJ-A7NH 
       33.83        30.35        35.28        25.68        20.58        15.58 
TCGA-EJ-A8FO TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6379 TCGA-G9-7525 TCGA-G9-A9S7 
        9.27        26.66        31.50        58.45        32.68        23.93 
TCGA-HC-7745 TCGA-HC-8216 TCGA-HC-A6HY TCGA-HC-A8CY TCGA-J4-8198 TCGA-J4-A67K 
       23.70        22.42         4.41         9.53        20.19        33.01 
TCGA-J4-A67N TCGA-J9-A52B TCGA-KC-A7F6 TCGA-KK-A59Y TCGA-KK-A7AY TCGA-KK-A8II 
       30.81        13.87         8.65        64.70        57.67       113.98 
TCGA-KK-A8IL TCGA-M7-A723 TCGA-M7-A725 TCGA-QU-A6IN TCGA-TP-A8TT TCGA-V1-A8WN 
       20.65        25.08        18.84       140.19        17.29        30.38 
TCGA-V1-A8WV TCGA-V1-A9ZI TCGA-VN-A88L TCGA-VN-A88M TCGA-VP-A876 TCGA-VP-A87K 
       22.55        53.92        24.53         6.21       109.58        42.94 
TCGA-X4-A8KQ TCGA-YL-A8SO TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A9LY 
       45.47       114.38        24.33        49.91        12.16 

$subtype4
TCGA-EJ-7325 TCGA-EJ-A46G TCGA-J4-A83N TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-QU-A6IM 
       35.18        21.96        32.61        29.56        32.45        41.00 
TCGA-XK-AAK1 TCGA-4L-AA1F TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5788 TCGA-EJ-5494 
       32.19        11.51        31.00         0.92        26.99        48.56 
TCGA-EJ-8469 TCGA-EJ-A46F TCGA-EJ-A65D TCGA-EJ-A65F TCGA-EJ-A65M TCGA-EJ-A7NM 
       76.41        25.74        12.92        18.41         7.56         4.21 
TCGA-EJ-A7NN TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6361 TCGA-G9-A9S0 
        6.48        28.83        22.36        25.94        46.52        26.01 
TCGA-G9-A9S4 TCGA-HC-7080 TCGA-HC-7232 TCGA-HC-7742 TCGA-HC-8213 TCGA-HC-8257 
       29.79        36.36        38.17        30.84        19.36        23.87 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
        1.58        15.88        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        2.20         1.61        17.42        19.30        27.75       109.25 
TCGA-J4-A83I TCGA-J4-AATZ TCGA-J9-A52D TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       22.52        13.55         6.97        10.55        13.32        15.22 
TCGA-J9-A8CP TCGA-KC-A4BV TCGA-KC-A7F5 TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z 
       12.69        43.66         2.99       113.10        83.34        86.40 
TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU 
       81.17        48.76       165.17        90.74        52.93        58.36 
TCGA-KK-A8I5 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8IH TCGA-KK-A8IK 
      101.79        31.79        63.48        67.43        66.18        67.46 
TCGA-M7-A71Z TCGA-M7-A722 TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IO 
       21.14        34.85        29.23         5.69         3.19       122.17 
TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MM TCGA-V1-A8WW TCGA-V1-A9O5 
        0.89        47.64        28.18        39.29        35.44        63.52 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9Z7 TCGA-V1-A9ZG 
       94.36        20.91        38.93        79.00        28.73        49.87 
TCGA-V1-A9ZR TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88R TCGA-VP-A875 TCGA-VP-A87B 
       44.75        25.51        25.18        25.78        75.91        89.49 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-A87J TCGA-WW-A8ZI TCGA-XJ-A83G 
       55.56        60.92        21.80        58.32        14.76        48.03 
TCGA-XJ-A83H TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       42.08        31.99        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A9XI TCGA-YL-A8HL 
       36.95        47.15         4.80        25.32        17.29        51.45 
TCGA-YL-A8HM TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SL 
       48.72        60.56        16.83        41.46        45.14        32.45 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A8QY 
        8.98        14.04        53.36        70.22        36.10        13.28 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L9 
        4.27        11.67        37.94        36.43        29.85        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LZ TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.17        12.43        16.96        22.75        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

$subtype5
TCGA-EJ-7123 TCGA-HC-7821 TCGA-CH-5737 TCGA-CH-5739 TCGA-CH-5748 TCGA-CH-5767 
       84.56        31.43         2.99        22.06         1.02        15.06 
TCGA-EJ-7115 TCGA-EJ-7315 TCGA-EJ-7328 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7793 
       88.34        33.14        27.68        38.37        25.87         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A8FS 
       42.94        32.32        77.16        38.10        25.18         8.75 
TCGA-FC-7708 TCGA-G9-6333 TCGA-G9-6351 TCGA-G9-6366 TCGA-G9-6499 TCGA-G9-7510 
       28.41        81.04        67.33        64.01        50.73        38.96 
TCGA-G9-7522 TCGA-H9-7775 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 
       35.44         6.08        69.53        65.26        38.93        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7744 TCGA-HC-7747 
       30.87        36.26        35.84        31.69        17.46        24.59 
TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8256 
       23.80        25.71        30.84        17.85        24.56        28.27 
TCGA-HC-8259 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8266 TCGA-HI-7171 TCGA-KK-A7AW 
       30.38        17.95        22.32        15.55        43.69        34.65 
TCGA-VP-A872 TCGA-XJ-A83F 
      119.38        37.05 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.02     3.68     1.02     0.76     1.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
  141.21   115.13   140.19   165.17   119.38 
subtype1 subtype2 subtype3 subtype4 subtype5 
  28.685   38.235   24.530   29.790   31.560 
[1] "1.0 - 141.2 (28.7)" "3.7 - 115.1 (38.2)" "1.0 - 140.2 (24.5)"
[4] "0.8 - 165.2 (29.8)" "1.0 - 119.4 (31.6)"
D8V2, continuous
          vv
clus       T2 T3 T4
  subtype1 64 81  0
  subtype2 45 48  4
  subtype3 21 37  1
  subtype4 27 99  4
  subtype5 30 26  0
D8V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T2       64       45       21       27       30
  T3       81       48       37       99       26
  T4        0        4        1        4        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
          cls
clus         0   1
  subtype1 111  18
  subtype2  70   9
  subtype3  40  12
  subtype4  82  36
  subtype5  41   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  111   18
  subtype2   70    9
  subtype3   40   12
  subtype4   82   36
  subtype5   41    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      111       70       40       82       41
  1       18        9       12       36        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus         0   1
  subtype1 119  14
  subtype2  83   7
  subtype3  43  10
  subtype4 101  23
  subtype5  46   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  119   14
  subtype2   83    7
  subtype3   43   10
  subtype4  101   23
  subtype5   46    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO       119       83       43      101       46
  YES       14        7       10       23        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus         0   1
  subtype1 144   4
  subtype2  96   2
  subtype3  56   3
  subtype4 128   5
  subtype5  55   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  144    4
  subtype2   96    2
  subtype3   56    3
  subtype4  128    5
  subtype5   55    1
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA ACINAR TYPE         144       96       56      128
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        4        2        3        5
                                        clus
vv                                       subtype5
  PROSTATE ADENOCARCINOMA ACINAR TYPE          55
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 109  31   0   6
  subtype2  57  36   1   2
  subtype3  41  14   0   2
  subtype4  65  59   2   3
  subtype5  41   6   2   2
D8V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0      109       57       41       65       41
  R1       31       36       14       59        6
  R2        0        1        0        2        2
  RX        6        2        2        3        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
D8V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    51
  subtype2     0                         3    30
  subtype3     0                         0    18
  subtype4     0                         0     9
  subtype5     1                         3    38
D8V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        0        0        1
  BLACK OR AFRICAN AMERICAN        1        3        0        0        3
  WHITE                           51       30       18        9       38
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 64  1
  subtype2 89  4
  subtype3 78  0
  subtype4 82  2
subtype1 subtype2 subtype3 subtype4 
      65       93       78       84 
subtype1 subtype2 subtype3 subtype4 
       1        4        0        2 
$subtype1
TCGA-CH-5763 TCGA-CH-5764 TCGA-EJ-5542 TCGA-EJ-A46B TCGA-2A-A8VL TCGA-2A-A8VV 
       12.00         1.02        49.74        21.60        20.42        22.06 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5746 
       28.37         2.99         6.97        22.06        12.99        24.03 
TCGA-CH-5750 TCGA-CH-5762 TCGA-CH-5766 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
       13.02        44.02         1.02         9.99         2.99        29.00 
TCGA-EJ-5497 TCGA-EJ-5506 TCGA-EJ-5512 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5522 
       13.32        45.40        56.98        62.10        62.10        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-A46I TCGA-EJ-A6RA TCGA-EJ-A7NJ 
       61.87        62.76        58.45        21.96        11.61         6.48 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-AB27 TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 
        9.27         9.83         4.77        20.25        41.62        67.99 
TCGA-G9-6353 TCGA-G9-7509 TCGA-G9-7522 TCGA-HC-7747 TCGA-HC-A6AP TCGA-HC-A8D0 
       50.70        52.93        35.44        24.59         2.33        25.48 
TCGA-HC-A8D1 TCGA-J4-A67R TCGA-J4-A6G1 TCGA-J4-A83K TCGA-J4-AATV TCGA-KC-A4BO 
       18.84        29.92        25.28        10.78        18.18        19.96 
TCGA-KC-A7F3 TCGA-KK-A8IJ TCGA-KK-A8IM TCGA-M7-A720 TCGA-V1-A8MJ TCGA-V1-A8MK 
       21.86        51.25        62.96        12.62        58.88        16.70 
TCGA-V1-A8WL TCGA-VN-A88L TCGA-VP-A878 TCGA-VP-A879 TCGA-X4-A8KS TCGA-XJ-A9DI 
       64.04        24.53       102.90        23.93        32.19        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8SR 
        9.04         2.99        51.81        32.61         8.98 

$subtype2
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-HC-A76W TCGA-KC-A7FA TCGA-KK-A7B3 TCGA-KK-A8IB 
       21.96        14.83         7.00        19.66        29.56         2.73 
TCGA-QU-A6IM TCGA-XK-AAK1 TCGA-2A-AAYF TCGA-2A-AAYU TCGA-CH-5752 TCGA-EJ-5525 
       41.00        32.19        44.84        20.22        31.00        36.66 
TCGA-EJ-A65F TCGA-EJ-A7NH TCGA-EJ-A7NM TCGA-FC-7961 TCGA-G9-6339 TCGA-G9-6354 
       18.41        15.58         4.21        15.42        83.87        67.92 
TCGA-G9-6379 TCGA-G9-6498 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-HC-A4ZV TCGA-HC-A631 
       58.45        64.18        29.79        23.93         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A9TE 
        2.01         2.20         1.61         1.25         4.41        19.30 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67T TCGA-J4-A6G3 TCGA-J4-A83I TCGA-J4-A83J 
       25.32        30.94         6.02        27.91        22.52        22.88 
TCGA-J4-A83M TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CM 
       17.85        27.12        13.87         5.85        10.62        15.22 
TCGA-KC-A4BV TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
       43.66       113.10        64.70        86.40        81.17       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 
       48.76        72.26       165.17       115.13        68.15        90.74 
TCGA-KK-A7AQ TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IL 
       52.93        65.82        31.79        32.91        63.48        20.65 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IO TCGA-QU-A6IP TCGA-V1-A8MG TCGA-V1-A8MM 
       18.84         5.69       122.17        86.14        28.18        39.29 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OQ TCGA-V1-A9OT 
       22.55        35.44        20.91        79.00        12.20        15.65 
TCGA-V1-A9ZI TCGA-VP-A872 TCGA-VP-A87K TCGA-XJ-A83H TCGA-XK-AAIW TCGA-XK-AAJT 
       53.92       119.38        42.94        42.08        40.04        47.15 
TCGA-Y6-A9XI TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SO 
       17.29        75.75        62.14        45.14        28.77       114.38 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LU 
        4.27        11.67        29.85        19.17        12.43        19.04 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9ND 
       22.75        17.98        13.48 

$subtype3
TCGA-CH-5772 TCGA-EJ-7791 TCGA-EJ-A6RC TCGA-2A-AAYO TCGA-4L-AA1F TCGA-CH-5769 
       15.98        36.76        28.70        41.82        11.51         2.04 
TCGA-EJ-5514 TCGA-EJ-7314 TCGA-EJ-7792 TCGA-EJ-A46H TCGA-EJ-A7NK TCGA-EJ-A8FN 
       60.13        37.81        45.90        23.80        15.65        10.82 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-G9-6347 TCGA-G9-6361 TCGA-G9-6365 TCGA-G9-7519 
        4.54         4.31        68.68        46.52        44.81        27.91 
TCGA-G9-7523 TCGA-H9-A6BX TCGA-HC-7081 TCGA-HC-7740 TCGA-HC-7749 TCGA-HC-7817 
       28.18        30.94        37.35        23.57        23.80        30.51 
TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8264 TCGA-HI-7168 TCGA-HI-7169 TCGA-J4-8200 
       27.85        22.55         1.58       109.25        88.24        40.04 
TCGA-J4-A67Q TCGA-J4-A83L TCGA-J9-A8CK TCGA-J9-A8CL TCGA-KC-A4BL TCGA-KC-A4BR 
       32.05        23.67        10.55        13.32        30.71        44.35 
TCGA-KC-A7FE TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I5 TCGA-KK-A8IC 
       11.57        43.69        34.95        36.13       101.79        67.43 
TCGA-KK-A8IG TCGA-TK-A8OK TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       82.36         0.89         6.64        82.16        28.73        27.19 
TCGA-V1-A9ZG TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88P TCGA-VP-A87C TCGA-VP-A87E 
       49.87         8.84        25.51        41.42        55.56        66.97 
TCGA-X4-A8KQ TCGA-XA-A8JR TCGA-XQ-A8TB TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8SI 
       45.47        12.36        25.32        52.96        49.02        53.06 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A9WH TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       45.86        46.29        14.04        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
       13.28        10.13        42.81        37.94        36.43        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       20.28         3.78        16.96        14.96        11.47         4.34 

$subtype4
TCGA-EJ-7123 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-KK-A7B4 TCGA-XK-AAJ3 
       84.56        44.55        26.04        31.43        32.45        41.49 
TCGA-EJ-5494 TCGA-EJ-5504 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7315 TCGA-EJ-7317 
       48.56        46.92        88.34        93.70        33.14        25.35 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       27.09        30.35        27.68         6.28        24.39        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7793 
       25.87        25.68        38.70        36.03        28.24         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-FC-7708 TCGA-G9-6333 TCGA-G9-6338 
       25.18        20.58        17.23        28.41        81.04        66.67 
TCGA-G9-6342 TCGA-G9-6351 TCGA-G9-6369 TCGA-G9-6377 TCGA-G9-6499 TCGA-G9-7510 
       55.76        67.33        39.95        31.50        50.73        38.96 
TCGA-G9-7521 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
       30.97        26.01         6.08        19.76        65.26        38.93 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7737 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7750 
       38.17        35.84        30.84        17.46        23.70        17.16 
TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-8266 
       30.84        24.56        17.95        22.32        15.88        15.55 
TCGA-HC-A9TH TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-KK-A8I6 TCGA-KK-A8IH 
       27.75        82.92        43.69        20.19        21.96        66.18 
TCGA-M7-A723 TCGA-TP-A8TT TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OL TCGA-V1-A9OX 
       25.08        17.29        63.52        94.36        62.89        37.28 
TCGA-V1-A9Z9 TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VP-AA1N TCGA-XK-AAIV TCGA-XK-AAJA 
       17.75        45.47        44.75        44.88        37.25        30.58 

subtype1 subtype2 subtype3 subtype4 
    1.02     0.76     0.89     3.75 
subtype1 subtype2 subtype3 subtype4 
  102.90   165.17   109.25    94.36 
subtype1 subtype2 subtype3 subtype4 
  23.930   28.180   28.715   31.465 
[1] "1.0 - 102.9 (23.9)" "0.8 - 165.2 (28.2)" "0.9 - 109.2 (28.7)"
[4] "3.8 - 94.4 (31.5)" 
D9V2, continuous
          vv
clus       T2 T3 T4
  subtype1 35 28  0
  subtype2 23 67  2
  subtype3 26 49  1
  subtype4 34 47  2
D9V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T2       35       23       26       34
  T3       28       67       49       47
  T4        0        2        1        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
          cls
clus        0  1
  subtype1 47  8
  subtype2 65 16
  subtype3 51 16
  subtype4 64  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47    8
  subtype2   65   16
  subtype3   51   16
  subtype4   64    9
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       47       65       51       64
  1        8       16       16        9
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
          cls
clus        0  1
  subtype1 52  6
  subtype2 70 13
  subtype3 58 15
  subtype4 72 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    6
  subtype2   70   13
  subtype3   58   15
  subtype4   72   10
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        52       70       58       72
  YES        6       13       15       10
[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"
D9V6, binary
          cls
clus        0  1
  subtype1 63  2
  subtype2 88  5
  subtype3 77  1
  subtype4 84  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    2
  subtype2   88    5
  subtype3   77    1
  subtype4   84    0
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA ACINAR TYPE          63       88       77       84
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        2        5        1        0
[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       R0 R1 R2 RX
  subtype1 52  9  0  3
  subtype2 47 41  0  4
  subtype3 38 32  2  2
  subtype4 59 17  0  2
D9V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       52       47       38       59
  R1        9       41       32       17
  R2        0        0        2        0
  RX        3        4        2        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
D9V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    27
  subtype2     0                         0     3
  subtype3     0                         0    13
  subtype4     1                         3    48
D9V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        0        3
  WHITE                           27        3       13       48
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 74  1
  subtype2 85  3
  subtype3 67  2
  subtype4 23  0
  subtype5 64  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      75       88       69       23       65 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        3        2        0        1 
$subtype1
TCGA-EJ-A46B TCGA-HC-A76W TCGA-KC-A7FA TCGA-2A-A8VL TCGA-2A-A8W3 TCGA-CH-5792 
       21.60         7.00        19.66        20.42        28.37         2.99 
TCGA-EJ-7793 TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65F TCGA-EJ-A6RA 
        3.75        17.23        23.80        21.96        18.41        11.61 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-G9-6329 TCGA-G9-6333 
        6.48        15.65         9.83         4.54        41.62        81.04 
TCGA-G9-6339 TCGA-G9-6353 TCGA-G9-6499 TCGA-G9-7509 TCGA-H9-A6BX TCGA-HC-7817 
       83.87        50.70        50.73        52.93        30.94        30.51 
TCGA-HC-8260 TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AP TCGA-HC-A6HX 
       22.55         0.76         2.01         2.20         2.33         1.25 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A6G1 
       25.48        18.84        25.32        30.94        29.92        25.28 
TCGA-J4-A6G3 TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-AATV TCGA-J9-A52C TCGA-J9-A52E 
       27.91        10.78        17.85        18.18         5.85        10.62 
TCGA-KC-A4BL TCGA-KC-A4BO TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KK-A6DY TCGA-KK-A6E2 
       30.71        19.96        43.66        21.86       141.21       165.17 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8IJ 
       43.69        34.95        36.13        21.96        65.82        51.25 
TCGA-KK-A8IM TCGA-M7-A720 TCGA-M7-A723 TCGA-QU-A6IP TCGA-V1-A8MJ TCGA-V1-A8MK 
       62.96        12.62        25.08        86.14        58.88        16.70 
TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VP-A878 TCGA-VP-A879 
       20.91        79.00        45.47        44.75       102.90        23.93 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       45.47        32.19        42.08        48.03         9.04         2.99 
TCGA-XK-AAJU TCGA-YL-A8HK TCGA-ZG-A8QZ 
       51.81        49.02        10.13 

$subtype2
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM 
       21.96        14.83        29.56        32.45         2.73        41.00 
TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VV TCGA-CH-5737 TCGA-CH-5752 TCGA-EJ-5494 
       41.49        32.19        22.06         2.99        31.00        48.56 
TCGA-EJ-5525 TCGA-EJ-A46D TCGA-EJ-A7NH TCGA-EJ-A7NM TCGA-EJ-A8FO TCGA-FC-7961 
       36.66        20.58        15.58         4.21         9.27        15.42 
TCGA-G9-6354 TCGA-G9-6379 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-HC-7231 
       67.92        58.45        26.01        29.79        23.93        30.87 
TCGA-HC-A631 TCGA-HC-A6HY TCGA-HC-A9TE TCGA-HC-A9TH TCGA-J4-A67T TCGA-J4-A83I 
        1.78         4.41        19.30        27.75         6.02        22.52 
TCGA-J4-A83J TCGA-J9-A52B TCGA-J9-A8CL TCGA-J9-A8CM TCGA-KK-A59V TCGA-KK-A59Y 
       22.88        13.87        13.32        15.22       113.10        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E5 TCGA-KK-A6E7 
       86.40        81.17        48.76        72.26        68.15        90.74 
TCGA-KK-A7AQ TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IH TCGA-KK-A8IL 
       52.93        31.79        32.91        63.48        66.18        20.65 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IO TCGA-TP-A8TT TCGA-V1-A8MG TCGA-V1-A8MM 
       18.84         5.69       122.17        17.29        28.18        39.29 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OL TCGA-V1-A9OT 
       22.55        35.44        63.52        94.36        62.89        15.65 
TCGA-V1-A9OX TCGA-V1-A9Z9 TCGA-V1-A9ZI TCGA-VN-A88L TCGA-VP-A872 TCGA-VP-A87K 
       37.28        17.75        53.92        24.53       119.38        42.94 
TCGA-VP-AA1N TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJT TCGA-Y6-A9XI 
       44.88        37.25        40.04        30.58        47.15        17.29 
TCGA-YL-A8S8 TCGA-YL-A8SF TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WY 
       62.14        45.14       114.38         8.98        14.04        36.10 
TCGA-ZG-A8QW TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LM 
        3.09         4.27        11.67        29.85        19.17        12.43 
TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9ND TCGA-ZG-A9NI 
       19.04        22.75        13.48         4.34 

$subtype3
TCGA-CH-5772 TCGA-EJ-A6RC TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
       15.98        28.70        44.84        41.82        20.22        11.51 
TCGA-CH-5769 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-7125 TCGA-EJ-7317 TCGA-EJ-A8FN 
        2.04        60.13        62.10        93.70        25.35        10.82 
TCGA-EJ-AB20 TCGA-FC-A8O0 TCGA-G9-6338 TCGA-G9-6347 TCGA-G9-6361 TCGA-G9-6369 
        4.31        20.25        66.67        68.68        46.52        39.95 
TCGA-G9-6498 TCGA-G9-7519 TCGA-G9-7523 TCGA-HC-7075 TCGA-HC-7081 TCGA-HC-A6AN 
       64.18        27.91        28.18        19.76        37.35         1.61 
TCGA-HI-7168 TCGA-J4-8200 TCGA-J4-A67Q TCGA-J4-A83L TCGA-J4-AAU2 TCGA-J9-A8CK 
      109.25        40.04        32.05        23.67        27.12        10.55 
TCGA-KC-A4BR TCGA-KC-A7FE TCGA-KK-A6E4 TCGA-KK-A8I5 TCGA-KK-A8IC TCGA-KK-A8IG 
       44.35        11.57       115.13       101.79        67.43        82.36 
TCGA-TK-A8OK TCGA-V1-A8WL TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9OQ TCGA-V1-A9Z7 
        0.89        64.04         6.64        82.16        12.20        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9ZG TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88P TCGA-VP-A87E 
       27.19        49.87         8.84        25.51        41.42        66.97 
TCGA-XA-A8JR TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8SH 
       12.36        25.32        32.61        52.96        75.75        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9L1 
       53.06        45.86        46.29        14.53        13.28        42.81 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9LS 
       37.94        36.43        22.59        20.28         3.78        16.96 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       17.98        14.96        11.47 

$subtype4
TCGA-CH-5763 TCGA-CH-5764 TCGA-EJ-5542 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 
       12.00         1.02        49.74         6.97        22.06        12.99 
TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5762 TCGA-CH-5766 TCGA-CH-5789 TCGA-CH-5794 
       24.03        13.02        44.02         1.02         9.99        29.00 
TCGA-EJ-5497 TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5512 TCGA-EJ-5516 TCGA-EJ-5522 
       13.32        46.92        45.40        56.98        62.10        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-G9-6336 TCGA-G9-6365 
       61.87        62.76        58.45        67.99        44.81 

$subtype5
TCGA-EJ-7123 TCGA-EJ-7791 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-EJ-7115 
       84.56        36.76        44.55        26.04        31.43        88.34 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       37.81        33.14        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       24.39        38.37        25.87        25.68        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       28.24        45.90        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-G9-6342 
       38.10        24.85        25.18         4.77        28.41        55.76 
TCGA-G9-6351 TCGA-G9-6377 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7522 TCGA-H9-7775 
       67.33        31.50        38.96        30.97        35.44         6.08 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 
       65.26        38.93        14.47        28.54        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       32.91        38.17        35.84        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 
       23.70        24.59        23.80        17.16        30.84        24.56 
TCGA-HC-8258 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       27.85        17.95        22.32         1.58        15.88        15.55 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-VP-A87C 
       88.24        82.92        43.69        20.19        55.56 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.76     1.78     0.89     1.02     1.58 
subtype1 subtype2 subtype3 subtype4 subtype5 
  165.17   122.17   115.13    68.35    88.34 
subtype1 subtype2 subtype3 subtype4 subtype5 
  25.080   29.675   28.730   44.020   30.840 
[1] "0.8 - 165.2 (25.1)" "1.8 - 122.2 (29.7)" "0.9 - 115.1 (28.7)"
[4] "1.0 - 68.3 (44.0)"  "1.6 - 88.3 (30.8)" 
D10V2, continuous
          vv
clus       T2 T3 T4
  subtype1 36 37  1
  subtype2 20 64  3
  subtype3 24 43  0
  subtype4  6 14  1
  subtype5 32 33  0
D10V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T2       36       20       24        6       32
  T3       37       64       43       14       33
  T4        1        3        0        1        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
          cls
clus        0  1
  subtype1 52  8
  subtype2 59 21
  subtype3 46 11
  subtype4 17  5
  subtype5 53  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    8
  subtype2   59   21
  subtype3   46   11
  subtype4   17    5
  subtype5   53    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       52       59       46       17       53
  1        8       21       11        5        4
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1 55 11
  subtype2 67 15
  subtype3 55 10
  subtype4 18  3
  subtype5 57  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55   11
  subtype2   67   15
  subtype3   55   10
  subtype4   18    3
  subtype5   57    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        55       67       55       18       57
  YES       11       15       10        3        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus        0  1
  subtype1 73  2
  subtype2 83  5
  subtype3 68  1
  subtype4 23  0
  subtype5 65  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73    2
  subtype2   83    5
  subtype3   68    1
  subtype4   23    0
  subtype5   65    0
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA ACINAR TYPE          73       83       68       23
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        2        5        1        0
                                        clus
vv                                       subtype5
  PROSTATE ADENOCARCINOMA ACINAR TYPE          65
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 55 16  0  3
  subtype2 43 39  0  4
  subtype3 35 29  2  1
  subtype4 16  6  0  1
  subtype5 47  9  0  2
D10V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       55       43       35       16       47
  R1       16       39       29        6        9
  R2        0        0        2        0        0
  RX        3        4        1        1        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
D10V9, continuous
D10V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0     6
  subtype2     0                         0     6
  subtype3     0                         0    12
  subtype4     0                         0    23
  subtype5     1                         3    44
D10V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        0        0        3
  WHITE                            6        6       12       23       44
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
