[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/15087329/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/15115159/PRAD-TP.mergedcluster.txt"

nPatients in clinical file=489, in cluster file=498, common to both=488
[1]   8 488
[1] "CN_CNMF"
[1] 3
  1   2   3 
269 128  85 
  1   2   3 
269 128  85 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
160 164 164 
  1   2   3 
160 164 164 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
145 173 169 
  1   2   3 
145 173 169 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
173 203 111 
  1   2   3 
173 203 111 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
157 145 182 
  1   2   3 
157 145 182 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
147  97  59 125  56 
  1   2   3   4   5 
147  97  59 125  56 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
 62 103  58  88 
  1   2   3   4 
 62 103  58  88 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
68 40 35 83 25 60 
 1  2  3  4  5  6 
68 40 35 83 25 60 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "COMPLETENESS_OF_RESECTION"             
[17] "NUMBER_OF_LYMPH_NODES"                 
[18] "GLEASON_SCORE_COMBINED"                
[19] "GLEASON_SCORE_PRIMARY"                 
[20] "GLEASON_SCORE_SECONDARY"               
[21] "HIGHEST_GLEASON_SCORE"                 
[22] "GLEASON_SCORE"                         
[23] "PSA_RESULT_PREOP"                      
[24] "DAYS_TO_PREOP_PSA"                     
[25] "PSA_VALUE"                             
[26] "DAYS_TO_PSA"                           
[27] "RACE"                                  
[28] "ETHNICITY"                             
[29] "BATCH_NUMBER"                          

Input Data has 29 rows and 488 columns.

[1] "Batch" "29"   
[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=8,	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=428,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE 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:'DCC_UPLOAD_DATE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'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 12:'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 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE_COMBINED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'GLEASON_SCORE_PRIMARY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE_SECONDARY':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'HIGHEST_GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HIGHEST_GLEASON_SCORE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 22:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'PSA_RESULT_PREOP':	nDistinctValues=209,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'DAYS_TO_PREOP_PSA':	nDistinctValues=206,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 25:'PSA_VALUE':	nDistinctValues=111,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'DAYS_TO_PSA':	nDistinctValues=379,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 27:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 28:'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)"
Variable 29:'BATCH_NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "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 488 columns, 1 survival variables, and 13 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"        
 [3] "PATHOLOGY_N_STAGE"         "HISTOLOGICAL_TYPE"        
 [5] "COMPLETENESS_OF_RESECTION" "NUMBER_OF_LYMPH_NODES"    
 [7] "GLEASON_SCORE_COMBINED"    "GLEASON_SCORE_PRIMARY"    
 [9] "GLEASON_SCORE_SECONDARY"   "GLEASON_SCORE"            
[11] "PSA_RESULT_PREOP"          "PSA_VALUE"                
[13] "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 
189 286  10 
[1] "table(vv)"
vv
 T2  T3  T4 
189 286  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T2  T3  T4 
189 286  10 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
189 286  10 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=12, binary=FALSE, numeric=TRUE
GLEASON_SCORE_COMBINED, nv=6, binary=FALSE, numeric=TRUE
GLEASON_SCORE_PRIMARY, nv=5, binary=FALSE, numeric=TRUE
GLEASON_SCORE_SECONDARY, nv=4, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_RESULT_PREOP, nv=209, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=111, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1 264   4
  subtype2 125   3
  subtype3  84   1
subtype1 subtype2 subtype3 
     268      128       85 
subtype1 subtype2 subtype3 
       4        3        1 
$subtype1
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 
       31.96        30.31        20.22         6.97        22.06         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5752 
       12.99        13.97         1.97        24.03        13.02        31.00 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5794 TCGA-EJ-5496 
        2.04        13.02         9.99        32.02        29.00        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5506 
       13.32        29.79        46.52        44.88        26.30        27.19 
TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5516 TCGA-EJ-5517 
       38.93        36.69        48.53        38.53        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 
       64.50        68.35        39.75        60.23        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7314 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       88.34        37.81        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7791 
       27.68        23.90        25.87        20.55        14.14        19.59 
TCGA-EJ-7793 TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
        3.75        19.92        76.41        38.10        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       20.58        17.23        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       13.71         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB27 
        4.21         9.27         9.83         8.75         4.54         4.77 
TCGA-FC-7708 TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       28.41        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       81.04        67.99        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       49.81        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 
       45.30        39.39        40.18        38.01        40.31        31.50 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7522 
       58.45        25.15        27.29        58.22        52.93        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       28.18        32.68        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 
       19.76         2.93        37.35        14.47         0.79        28.60 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7740 
        1.68         2.37        38.17        44.55         0.72        23.57 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        26.04         1.97        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8259 
       30.84        17.85        24.56        19.36        28.27         2.27 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ 
       22.32         1.58         2.20         1.61        17.42         3.48 
TCGA-HC-A6AS TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7169 
        1.45         4.41         4.93        25.48        18.84        88.24 
TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       82.92        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       27.91        16.83        22.52        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A8CN TCGA-KC-A4BL TCGA-KC-A4BN 
       20.28        11.77        27.12        40.67        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       19.96        44.35        43.66         8.65         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A7AU 
      113.10        44.68       165.17        67.59       115.13        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       27.02        34.65        51.68        49.94        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A8I5 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IC TCGA-KK-A8IJ 
       29.56       101.79        65.82        31.79        67.43        51.25 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-MG-AAMC 
       20.65        47.28         5.19        21.14        12.62         5.69 
TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TP-A8TT 
        3.19       140.19       122.17        86.14        18.12        11.90 
TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL 
       41.23        40.44        16.70        14.73        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8X3 TCGA-V1-A9O9 TCGA-V1-A9OH TCGA-V1-A9OY 
       30.38        15.58         6.64         6.71        41.19         5.59 
TCGA-V1-A9Z8 TCGA-V1-A9ZG TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
        6.15        49.87         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VP-A876 TCGA-VP-A879 
       15.52        15.81        41.42        44.91       109.58        23.93 
TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XJ-A83F 
       55.56        66.97        53.36        42.94        14.76        37.05 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJR TCGA-XK-AAJU 
        9.04         2.99        31.96        40.04        36.95        51.81 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SP 
       52.96        49.02        51.45        41.46        45.14        71.34 
TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QZ TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       60.99        49.91         3.09        10.13        37.94        36.43 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC 
       16.96        19.04        12.16        14.96 

$subtype2
TCGA-2A-A8VT TCGA-4L-AA1F TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
       32.71        11.51        35.01         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5507 TCGA-EJ-5514 
       44.02        26.99        33.01        33.11        23.90        36.23 
TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-7123 
       52.27        51.88        43.07        36.66        38.76        74.10 
TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-8472 TCGA-EJ-A46F 
       36.13        33.14        25.68        18.15        24.85        25.74 
TCGA-EJ-A46G TCGA-EJ-A65F TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6366 TCGA-G9-6373 
       21.96        18.41        15.42        13.45         3.32        26.66 
TCGA-G9-6496 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-A9S0 TCGA-HC-7078 TCGA-HC-7213 
       56.75        50.73        30.97        26.01        65.26        40.08 
TCGA-HC-7742 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
        1.48        31.43        22.42        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A8CY TCGA-HI-7168 TCGA-HI-7171 
        0.76         1.78         2.01         9.53        78.61        43.69 
TCGA-J4-A83J TCGA-J4-AATZ TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       22.88        13.55        13.87        10.62        13.32        15.22 
TCGA-KC-A7FA TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E6 
       19.66        56.28        86.40       115.86        54.54       113.33 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I6 
       58.19         6.44        52.93        20.94        67.99        21.96 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
       63.48         2.73        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IK TCGA-M7-A724 TCGA-M7-A725 TCGA-TP-A8TV TCGA-V1-A8MG 
      113.98        51.39        29.23        18.84        13.32        28.18 
TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9OL TCGA-V1-A9Z7 
       22.55        58.39        79.73        20.91        19.36         4.27 
TCGA-V1-A9ZI TCGA-V1-A9ZR TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87D TCGA-VP-A87H 
        4.70         5.82       111.39        75.91        60.92        21.80 
TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83H TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAJ3 
       44.88        45.47        42.08        31.99        37.25        41.49 
TCGA-XK-AAJP TCGA-XK-AAJT TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       41.39        47.15         4.87        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       60.56        16.83        56.52        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK 
      114.38        62.79         8.98        14.04        53.36        62.37 
TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L9 
       24.33        28.34         4.27        11.67        29.85        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       19.17        12.43         3.78        22.75        17.98        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

$subtype3
TCGA-CH-5737 TCGA-CH-5748 TCGA-CH-5772 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5503 
        2.99         1.02        15.98         2.99        27.16        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5509 TCGA-EJ-5515 TCGA-EJ-5531 TCGA-EJ-7125 
       28.93        30.31        48.13        60.23        41.85        93.70 
TCGA-EJ-7218 TCGA-EJ-7317 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7786 
       83.57        25.35         6.28        24.39        38.37        14.53 
TCGA-EJ-7792 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       17.29        23.05        77.16        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A8FN TCGA-EJ-AB20 TCGA-FC-A5OB TCGA-G9-6338 
       11.61        28.70        10.82         4.31        22.36        66.67 
TCGA-G9-6351 TCGA-G9-6365 TCGA-G9-6369 TCGA-G9-6378 TCGA-G9-6498 TCGA-G9-7510 
       46.16        44.81        39.95        37.97        64.18        38.96 
TCGA-G9-7519 TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7744 
       27.91        36.36        28.54         2.10        31.69         1.68 
TCGA-HC-7750 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-A6AP 
       17.16        23.87         2.17        22.55        17.95         2.33 
TCGA-HC-A6HX TCGA-HC-A76W TCGA-J4-8198 TCGA-J9-A52C TCGA-J9-A8CP TCGA-KC-A7F3 
        1.25         7.00        20.19         5.85        12.69        21.86 
TCGA-KK-A6E0 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A7B0 TCGA-KK-A8I9 TCGA-M7-A721 
       30.02        49.25        67.07        32.84        32.91        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-QU-A6IM TCGA-V1-A8MM TCGA-V1-A9OF TCGA-V1-A9OQ 
       34.85        25.08        41.00        39.29        38.93        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9Z9 TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A878 
       15.65         8.42        17.75        25.78        16.31        97.41 
TCGA-VP-A87B TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XK-AAJA 
       85.18        32.19         3.91        38.04        48.03        30.58 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8SH TCGA-YL-A8SI TCGA-ZG-A8QX TCGA-ZG-A8QY 
       32.19        25.48        28.77        53.06        14.53        13.28 
TCGA-ZG-A9L6 
       22.59 

subtype1 subtype2 subtype3 
    0.72     0.76     1.02 
subtype1 subtype2 subtype3 
  165.17   115.86    97.41 
subtype1 subtype2 subtype3 
   26.17    28.26    25.48 
[1] "0.7 - 165.2 (26.2)" "0.8 - 115.9 (28.3)" "1.0 - 97.4 (25.5)" 
D1V2, continuous
          vv
clus        T2  T3  T4
  subtype1 129 136   2
  subtype2  15 106   7
  subtype3  44  39   1
D1V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2      129       15       44
  T3      136      106       39
  T4        2        7        1
[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"
D1V4, binary
          cls
clus         0   1
  subtype1 197  26
  subtype2  80  41
  subtype3  61   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  197   26
  subtype2   80   41
  subtype3   61    8
   clus
vv  subtype1 subtype2 subtype3
  0      197       80       61
  1       26       41        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus         0   1
  subtype1   9 260
  subtype2   5 123
  subtype3   0  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  260
  subtype2    5  123
  subtype3    0   85
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        9        5        0
  PROSTATE ADENOCARCINOMA ACINAR TYPE         260      123       85
[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 198  53   3   7
  subtype2  60  61   1   4
  subtype3  52  24   1   4
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      198       60       52
  R1       53       61       24
  R2        3        1        1
  RX        7        4        4
[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"
D1V7, continuous
D1V8, continuous
D1V9, continuous
D1V10, continuous
D1V11, continuous
D1V12, continuous
D1V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         3    90
  subtype2     0                         1    29
  subtype3     0                         3    27
D1V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        0
  BLACK OR AFRICAN AMERICAN        3        1        3
  WHITE                           90       29       27
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1 159   1
  subtype2 161   3
  subtype3 159   4
subtype1 subtype2 subtype3 
     160      164      163 
subtype1 subtype2 subtype3 
       1        3        4 
$subtype1
TCGA-2A-A8VL TCGA-CH-5738 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5762 TCGA-CH-5763 
       20.42         6.97        13.97        24.03        44.02        12.00 
TCGA-CH-5766 TCGA-CH-5771 TCGA-CH-5789 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5501 
        1.02        13.02         9.99        13.32        29.79        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 
       26.30        45.73        30.31        27.19        38.93        36.69 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5522 TCGA-EJ-5527 
       38.53        60.23        46.55        47.80        68.35        39.75 
TCGA-EJ-5531 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7785 TCGA-EJ-7786 
       41.85        27.68         6.28        23.90        20.55        14.53 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-A46B 
       19.59        17.29         3.75        23.05        19.92        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65G 
       20.58        17.23        23.80        21.96        23.34        21.90 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61        28.70        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-G9-6347 TCGA-G9-6348 
       17.23         1.78        41.62        67.99        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 
       46.16        50.70        47.15         3.32        40.18        38.01 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-7519 TCGA-G9-7522 
       37.97        58.45        25.15        27.29        27.91        35.34 
TCGA-H9-A6BX TCGA-HC-7079 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 
       30.94         2.93        44.55         2.10        23.57         1.48 
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-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        2.17        22.55         1.15         3.48         1.45         1.25 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67L TCGA-J4-A67M 
       25.48        18.84        82.92        12.30        25.32        30.94 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A83L TCGA-J4-AATV TCGA-J4-AAU2 TCGA-J9-A52C TCGA-KC-A4BL 
       27.91        23.67        11.77        27.12         5.85        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        32.84 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8IC TCGA-KK-A8IL TCGA-KK-A8IM 
       36.13        67.99        65.82        67.43        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A723 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
        5.19        12.62        25.08        86.14        18.12        41.23 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8WN TCGA-V1-A9O7 TCGA-V1-A9OA TCGA-V1-A9Z8 
       40.44        16.70        30.38        79.73        20.91         6.15 
TCGA-VN-A88I TCGA-VN-A88N TCGA-VP-A878 TCGA-VP-A87C TCGA-VP-A87E TCGA-X4-A8KQ 
        8.84        15.52        97.41        55.56        66.97        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR 
       32.19         3.91        48.03         9.04         2.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAJU TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8SB TCGA-YL-A8SK 
       37.25        51.81        52.96        49.02        56.52        46.29 
TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QZ TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9LN 
       49.91         3.09        10.13        37.94        36.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9MC 
       16.96        19.04        12.16        14.96 

$subtype2
TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5748 
       43.79        33.96         3.68        25.35         2.99         1.02 
TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5767 TCGA-CH-5772 TCGA-CH-5792 TCGA-EJ-5494 
       35.01         0.92        15.06        15.98         2.99        27.16 
TCGA-EJ-5504 TCGA-EJ-5509 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5532 
       28.93        48.13        36.23        52.27        64.50        47.87 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 
       88.34        74.10        93.70        83.57        36.13        33.14 
TCGA-EJ-7317 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7789 TCGA-EJ-8468 TCGA-EJ-8470 
       25.35        24.39        38.37        18.15        77.16        38.10 
TCGA-EJ-A65E TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS 
       13.71        14.83         7.56         4.21        10.82         8.75 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6333 TCGA-G9-6338 
       15.42        13.45        22.36        16.24        81.04        66.67 
TCGA-G9-6343 TCGA-G9-6369 TCGA-G9-6371 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       18.21        39.95        40.31        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7075 
       50.73        38.96        30.97        28.18        26.01        19.76 
TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7736 TCGA-HC-7738 
       65.26        36.36        28.54         0.79         0.72        31.69 
TCGA-HC-8256 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A6AL 
       28.27        17.95         1.58        15.88         0.76         2.20 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A76W TCGA-HI-7168 TCGA-J4-A83J TCGA-J4-AATZ 
       17.42         2.33         7.00        78.61        22.88        13.55 
TCGA-J9-A52D TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A7F3 TCGA-KC-A7F5 
        6.97        13.32        40.67        12.69        21.86         2.99 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E5 
      113.10        56.28        86.40        77.72        30.02        49.25 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AV TCGA-KK-A7AW 
       67.07        58.19         6.44        52.93        27.02        34.65 
TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ 
       32.91         2.73        69.27        26.43        82.36        51.25 
TCGA-KK-A8IK TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM 
       51.39        13.15        34.85        29.23         3.19        41.00 
TCGA-QU-A6IO TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
      122.17        13.32        28.18        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9OF TCGA-V1-A9OH 
       52.08        22.55         6.64        58.39        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OX TCGA-V1-A9Z7 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       19.36        12.20         8.42         4.27        17.75        49.87 
TCGA-V1-A9ZR TCGA-VN-A88O TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A87B TCGA-VP-A87H 
        5.82        15.81        25.78        16.31        85.18        21.80 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XK-AAIW TCGA-XK-AAJ3 
       44.88        14.76        38.04        42.08        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAK1 TCGA-Y6-A8TL 
       30.58        41.39        36.95        47.15        32.19        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SH 
        4.87        48.72        71.77        62.14        60.56        28.77 
TCGA-YL-A8SI TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ 
       53.06       114.38        62.79         8.98        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9KY TCGA-ZG-A9L0 
       62.37        28.34        14.53        13.28         4.27        11.67 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9M4 TCGA-ZG-A9N3 
       29.85        22.59        19.17        12.43        17.98        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

$subtype3
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
       32.71        22.06        31.96        30.31        20.22        11.51 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5750 
       22.06         1.02        12.99         1.97         2.99        13.02 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5768 
       31.00         1.02         2.04         1.02        23.01        24.03 
TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5495 
        2.04        26.99        32.02        33.01        29.00        33.11 
TCGA-EJ-5496 TCGA-EJ-5499 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5521 TCGA-EJ-5524 
       19.56        46.52        23.90        48.53        51.88        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5542 TCGA-EJ-7314 TCGA-EJ-7318 
       36.66        38.76        60.23        29.06        37.81        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7788 
       27.09        35.18        30.35        25.87        25.68        14.14 
TCGA-EJ-8469 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65D 
       76.41        24.85        25.18        25.74        21.96        12.92 
TCGA-EJ-A65F TCGA-EJ-A7NF TCGA-EJ-A7NN TCGA-G9-6332 TCGA-G9-6339 TCGA-G9-6342 
       18.41         8.22         6.48        87.35        83.87        55.76 
TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       49.35        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-7509 TCGA-G9-7525 TCGA-G9-A9S4 TCGA-G9-A9S7 
       26.66        31.50        52.93        32.68        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BY TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7212 TCGA-HC-7213 
        6.08         3.68        37.35        14.47        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7744 TCGA-HC-7748 TCGA-HC-7749 
        1.68         2.37        38.17         1.68        26.04         1.97 
TCGA-HC-7752 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8257 
       25.71        30.84        17.85        31.43        19.36        23.87 
TCGA-HC-8259 TCGA-HC-8262 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN 
        2.27        22.32        22.36         1.78         2.01         1.61 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HI-7169 TCGA-HI-7171 TCGA-J4-8198 
        4.41         4.93         9.53        88.24        43.69        20.19 
TCGA-J4-A67K TCGA-J4-A67N TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M 
       33.01        16.54        16.83        22.52        10.78        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CM TCGA-KC-A4BV TCGA-KC-A7F6 
       20.28        13.87        10.62        15.22        43.66         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 
       19.66         8.88        44.68       115.86        54.54       165.17 
TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AU TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B1 
      115.13       113.33        58.36        51.68        49.94        34.95 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8IA 
       29.56        20.94       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-A9O9 TCGA-V1-A9OT TCGA-V1-A9OY TCGA-V1-A9ZI 
       11.90        15.58         6.71        15.65         5.59         4.70 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88P TCGA-VN-A88Q TCGA-VP-A872 
       25.51        24.53         6.21        41.42        44.91       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87D TCGA-VP-A87J TCGA-VP-A87K 
       75.91       109.58        23.93        60.92        53.36        42.94 
TCGA-XJ-A83F TCGA-XJ-A9DX TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF 
       37.05        31.99        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-A9L9 
       45.86        32.45        71.34        14.04        24.33        20.28 
TCGA-ZG-A9LZ 
       22.75 

subtype1 subtype2 subtype3 
    1.02     0.72     1.02 
subtype1 subtype2 subtype3 
   97.41   122.17   165.17 
subtype1 subtype2 subtype3 
  24.835   28.655   25.870 
[1] "1.0 - 97.4 (24.8)"  "0.7 - 122.2 (28.7)" "1.0 - 165.2 (25.9)"
D2V2, continuous
          vv
clus        T2  T3  T4
  subtype1  81  76   0
  subtype2  57 100   7
  subtype3  51 110   3
D2V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2       81       57       51
  T3       76      100      110
  T4        0        7        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
          cls
clus         0   1
  subtype1 114  21
  subtype2 116  26
  subtype3 111  30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  114   21
  subtype2  116   26
  subtype3  111   30
   clus
vv  subtype1 subtype2 subtype3
  0      114      116      111
  1       21       26       30
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus         0   1
  subtype1   4 156
  subtype2   4 160
  subtype3   7 157
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  156
  subtype2    4  160
  subtype3    7  157
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        4        4        7
  PROSTATE ADENOCARCINOMA ACINAR TYPE         156      160      157
[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 113  37   1   4
  subtype2  90  63   1   5
  subtype3 110  41   3   6
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      113       90      110
  R1       37       63       41
  R2        1        1        3
  RX        4        5        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"
D2V7, continuous
D2V8, continuous
D2V9, continuous
D2V10, continuous
D2V11, continuous
D2V12, continuous
D2V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    53
  subtype2     0                         2    37
  subtype3     1                         3    57
D2V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        0        1
  BLACK OR AFRICAN AMERICAN        2        2        3
  WHITE                           53       37       57
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 142   3
  subtype2 171   2
  subtype3 165   3
subtype1 subtype2 subtype3 
     145      173      168 
subtype1 subtype2 subtype3 
       3        2        3 
$subtype1
TCGA-2A-A8VL TCGA-CH-5738 TCGA-CH-5743 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5762 
       20.42         6.97        13.97         2.99        24.03        44.02 
TCGA-CH-5763 TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 TCGA-EJ-5497 TCGA-EJ-5498 
       12.00        13.02         9.99         2.99        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5506 TCGA-EJ-5508 
       46.52        44.88        26.30        45.73        27.19        38.93 
TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-5531 
       36.69        38.53        60.23        68.35        38.76        41.85 
TCGA-EJ-7115 TCGA-EJ-7318 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7783 
       88.34        33.83        27.68         6.28        23.90        25.87 
TCGA-EJ-7785 TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8470 
       20.55        19.59         3.75        23.05        19.92        38.10 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A6RA 
       21.60        20.58        17.23        23.80        21.96        11.61 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A8FO TCGA-EJ-A8FP 
       14.20        15.58         6.48        15.65         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         1.78 
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        46.16        50.70 
TCGA-G9-6356 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6379 TCGA-G9-6384 
       47.15        44.81        40.18        38.01        58.45        25.15 
TCGA-G9-6385 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7522 TCGA-H9-A6BX TCGA-HC-7079 
       27.29        52.93        38.96        35.34        30.94         2.93 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7745 
       28.54         0.79         0.72         2.10        23.57        23.70 
TCGA-HC-7747 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8262 
       24.59        30.51        30.84         2.17        22.55        22.32 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A76W 
       15.88         1.15         3.48         1.45         1.25         7.00 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7170 TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A67T 
       25.48        18.84        82.92        30.94        29.92         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A83K TCGA-J4-AATV TCGA-J9-A52C TCGA-KC-A4BL 
       25.28        27.91        10.78        11.77         5.85        30.71 
TCGA-KC-A4BN TCGA-KC-A7F3 TCGA-KC-A7FE TCGA-KK-A6E5 TCGA-KK-A7AV TCGA-KK-A7B2 
       59.67        21.86        11.57        49.25        27.02        36.13 
TCGA-KK-A8I7 TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-QU-A6IP TCGA-SU-A7E7 
       65.82        20.65         5.19        12.62        86.14        18.12 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A9OA TCGA-V1-A9OH 
       40.44        16.70        53.16        30.38        20.91        41.19 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-VN-A88I TCGA-VP-A878 TCGA-VP-A879 
        8.42         5.59         6.15         8.84        97.41        23.93 
TCGA-VP-A87C TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       55.56        45.47        32.19        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-YL-A8HJ 
        2.99        31.96        36.95        47.15        51.81        52.96 
TCGA-YL-A8SK TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       46.29        60.99        49.91        16.96        19.04        12.16 
TCGA-ZG-A9MC 
       14.96 

$subtype2
TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-CH-5737 
       43.79        33.96         3.68        31.96        30.31         2.99 
TCGA-CH-5748 TCGA-CH-5751 TCGA-CH-5767 TCGA-CH-5772 TCGA-CH-5788 TCGA-EJ-5494 
        1.02        35.01        15.06        15.98        26.99        27.16 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5509 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 
       28.93        30.31        48.13        36.23        47.80        52.27 
TCGA-EJ-5532 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7317 
       47.87        74.10        93.70        83.57        36.13        25.35 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-8468 
       24.39        38.37        14.53        18.15        17.29        77.16 
TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RC 
       23.34        13.71        21.90        14.83         7.56        28.70 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        6.48        10.82         8.75        15.42        13.45        22.36 
TCGA-FC-A6HD TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6366 
       16.24        81.04        66.67        18.21        68.68         3.32 
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-G9-7519 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7075 
       50.73        27.91        30.97        28.18        26.01        19.76 
TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7233 TCGA-HC-7738 TCGA-HC-7742 TCGA-HC-7750 
       65.26        36.36        44.55        31.69         1.48        17.16 
TCGA-HC-7752 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8259 TCGA-HC-8261 TCGA-HC-8264 
       25.71        22.42        28.27         2.27        17.95         1.58 
TCGA-HC-A4ZV TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HI-7168 TCGA-HI-7169 
        0.76         2.20        17.42         2.33        78.61        88.24 
TCGA-J4-8200 TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A83J TCGA-J4-A83L TCGA-J4-AAU2 
       12.30        27.58        32.05        22.88        23.67        27.12 
TCGA-J9-A52D TCGA-J9-A8CL TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BR TCGA-KC-A7F5 
        6.97        13.32        40.67        12.69        44.35         2.99 
TCGA-KC-A7FA TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E3 
       19.66        56.28        86.40        77.72        30.02        67.59 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7B0 TCGA-KK-A8I9 TCGA-KK-A8IB 
       67.07        58.19        52.93        32.84        32.91         2.73 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-M7-A721 
       69.27        26.43        82.36        51.25        51.39        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO 
       34.85        25.08        29.23         3.19        41.00       122.17 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8WL 
       13.32        41.23        28.18        14.73        39.29        52.08 
TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9OF TCGA-V1-A9OQ TCGA-V1-A9Z7 TCGA-V1-A9Z9 
        6.64        79.73        38.93        12.20         4.27        17.75 
TCGA-V1-A9ZI TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 
        4.70        15.52        15.81        41.42        25.78        16.31 
TCGA-VP-A87B TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XA-A8JR 
       85.18        66.97        21.80        44.88        14.76         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       38.04        31.99        37.25        41.49        30.58        41.39 
TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       32.19        25.48         4.87        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SO TCGA-YL-A8SQ 
       60.56        56.52        28.77        53.06       114.38        62.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
        8.98        53.36        62.37         3.09        14.53        13.28 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
        4.27        11.67        37.94        22.59        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       12.43         3.78        11.47        13.48         4.34 

$subtype3
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5739 
       32.71        22.06        25.35        20.22        11.51        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.02        12.99         1.97        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 
        2.04         0.92         1.02        23.01         1.02        24.03 
TCGA-CH-5769 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 
        2.04        32.02        33.01        29.00        33.11        19.56 
TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5524 
       23.90        48.53        46.55        64.50        51.88        43.07 
TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5542 TCGA-EJ-7314 TCGA-EJ-7315 
       36.66        39.75        60.23        29.06        37.81        33.14 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-EJ-8469 
       27.09        35.18        30.35        25.68        14.14        76.41 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65D TCGA-EJ-A65F 
       24.85        25.18        25.74        21.96        12.92        18.41 
TCGA-EJ-A7NF TCGA-EJ-A7NM TCGA-G9-6332 TCGA-G9-6342 TCGA-G9-6354 TCGA-G9-6361 
        8.22         4.21        87.35        55.76        49.35        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-7525 
       47.44        45.30        39.39        26.66        31.50        32.68 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BY TCGA-HC-7081 TCGA-HC-7209 
       29.79        23.93         6.08         3.68        37.35        14.47 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7744 
       28.60        40.08         1.68         2.37        38.17         1.68 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       26.04         1.97        17.85        24.56        31.43        19.36 
TCGA-HC-8257 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6HY 
       23.87        22.36         1.78         2.01         1.61         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67L 
        4.93         9.53        43.69        20.19        33.01        25.32 
TCGA-J4-A67N TCGA-J4-A67S TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83M TCGA-J4-A83N 
       16.54        27.39        16.83        22.52        14.37        20.28 
TCGA-J4-AATZ TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CM TCGA-KC-A4BV TCGA-KC-A7F6 
       13.55        13.87        10.62        15.22        43.66         8.65 
TCGA-KC-A7FD TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 
        8.88       113.10        44.68       115.86        54.54       165.17 
TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AW TCGA-KK-A7AY 
      115.13       113.33         6.44        58.36        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        34.95        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8IH TCGA-KK-A8II 
       21.96        31.79        63.48        67.43        66.18       113.98 
TCGA-KK-A8IM TCGA-M7-A71Z TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IN TCGA-TP-A8TT 
       47.28        21.14        18.84         5.69       140.19        11.90 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OL TCGA-V1-A9OT 
       15.58        22.55        58.39         6.71        19.36        15.65 
TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88Q 
       49.87         5.82        25.51        24.53         6.21        44.91 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87D TCGA-VP-A87J TCGA-VP-A87K 
      111.39        75.91       109.58        60.92        53.36        42.94 
TCGA-XJ-A83F TCGA-XK-AAIW TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SC 
       37.05        40.04        49.02        51.45        16.83        41.46 
TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WL 
       45.14        45.86        32.45        71.34        14.04        24.33 
TCGA-YL-A9WY TCGA-ZG-A8QZ TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9LZ TCGA-ZG-A9M4 
       28.34        10.13        36.43        29.85        22.75        17.98 

subtype1 subtype2 subtype3 
    0.72     0.76     0.92 
subtype1 subtype2 subtype3 
   97.41   122.17   165.17 
subtype1 subtype2 subtype3 
   24.03    28.18    26.35 
[1] "0.7 - 97.4 (24.0)"  "0.8 - 122.2 (28.2)" "0.9 - 165.2 (26.4)"
D3V2, continuous
          vv
clus        T2  T3  T4
  subtype1  73  69   1
  subtype2  70  98   4
  subtype3  45 119   5
D3V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2       73       70       45
  T3       69       98      119
  T4        1        4        5
[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"
D3V4, binary
          cls
clus         0   1
  subtype1 105  17
  subtype2 120  24
  subtype3 115  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  105   17
  subtype2  120   24
  subtype3  115   36
   clus
vv  subtype1 subtype2 subtype3
  0      105      120      115
  1       17       24       36
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus         0   1
  subtype1   3 142
  subtype2   4 169
  subtype3   8 161
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  142
  subtype2    4  169
  subtype3    8  161
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        3        4        8
  PROSTATE ADENOCARCINOMA ACINAR TYPE         142      169      161
[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 102  32   0   5
  subtype2 101  62   2   4
  subtype3 109  47   3   6
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      102      101      109
  R1       32       62       47
  R2        0        2        3
  RX        5        4        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"
D3V7, continuous
D3V8, continuous
D3V9, continuous
D3V10, continuous
D3V11, continuous
D3V12, continuous
D3V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    51
  subtype2     0                         3    40
  subtype3     0                         3    56
D3V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        0
  BLACK OR AFRICAN AMERICAN        1        3        3
  WHITE                           51       40       56
[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(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2        0   1
  subtype1 170   3
  subtype2 201   2
  subtype3 107   3
subtype1 subtype2 subtype3 
     173      203      110 
subtype1 subtype2 subtype3 
       3        2        3 
$subtype1
TCGA-2A-A8VL TCGA-CH-5738 TCGA-CH-5743 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5762 
       20.42         6.97        13.97         2.99        24.03        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 
       12.00         1.02        24.03        13.02         9.99         2.99 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5503 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 
       45.73        27.19        38.93        36.69        38.53        60.23 
TCGA-EJ-5516 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 
       46.55        68.35        43.07        38.76        39.75        41.85 
TCGA-EJ-5542 TCGA-EJ-7314 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       29.06        37.81        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7794 
       23.90        25.87        20.55        19.59         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       19.92        38.10        24.85        21.60        20.58        17.23 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       23.80        21.96        23.34         7.56        11.61         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NN TCGA-EJ-A8FO 
       14.20        15.58         6.48        15.65         6.48         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A66V 
        9.83         4.54         4.31         4.77        28.41        17.23 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6348 TCGA-G9-6351 
        1.78        41.62        67.99        83.87        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6377 
       50.70        47.15        44.81        40.18        38.01        31.50 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-7509 TCGA-G9-7522 TCGA-H9-A6BX 
       58.45        25.15        27.29        52.93        35.34        30.94 
TCGA-HC-7079 TCGA-HC-7211 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7740 
        2.93         0.79        38.17        44.55         0.72        23.57 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 
       23.70        24.59        26.04        30.51        30.84        24.56 
TCGA-HC-8216 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8262 TCGA-HC-8266 TCGA-HC-A6AP 
       22.42         2.17        22.55        22.32         1.15         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A8D0 TCGA-HC-A8D1 
        3.48         1.45         1.25         4.41        25.48        18.84 
TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67R 
       82.92        20.19        33.01        30.94        27.58        29.92 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A83K TCGA-J4-A83N TCGA-J4-AATV TCGA-J9-A52C 
        6.02        25.28        10.78        20.28        11.77         5.85 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A7AV TCGA-KK-A7B2 
       30.71        59.67        67.59        49.25        27.02        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I7 TCGA-KK-A8IC TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       67.99        65.82        67.43        20.65        47.28         5.19 
TCGA-M7-A720 TCGA-M7-A723 TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
       12.62        25.08        41.00       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       41.23        40.44        16.70        53.16        52.08        30.38 
TCGA-V1-A9OA TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z8 TCGA-V1-A9ZG 
       20.91        15.65         8.42         5.59         6.15        49.87 
TCGA-V1-A9ZR TCGA-VP-A879 TCGA-VP-A87C TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A83H 
        5.82        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        71.77        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-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO 
       43.79        33.96         3.68        25.35        31.96        30.31 
TCGA-CH-5737 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5761 
        2.99         1.02        13.02        35.01         1.02         0.92 
TCGA-CH-5767 TCGA-CH-5772 TCGA-CH-5788 TCGA-EJ-5494 TCGA-EJ-5502 TCGA-EJ-5504 
       15.06        15.98        26.99        27.16        26.30        28.93 
TCGA-EJ-5505 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 
       30.31        48.13        48.53        36.23        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       64.50        47.87        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7325 TCGA-EJ-7782 TCGA-EJ-7786 
       36.13        25.35        33.83        35.18        38.37        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-8468 TCGA-EJ-8474 TCGA-EJ-A46G 
       14.14        18.15        17.29        77.16        25.18        21.96 
TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-EJ-A7NM TCGA-EJ-A8FN 
       13.71        21.90        14.83        28.70         4.21        10.82 
TCGA-EJ-A8FS TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6333 
        8.75        15.42        13.45        22.36        16.24        81.04 
TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6366 TCGA-G9-6369 TCGA-G9-6371 
       66.67        18.21        68.68         3.32        39.95        40.31 
TCGA-G9-6378 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       37.97        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7075 TCGA-HC-7078 
       27.91        30.97        28.18        26.01        19.76        65.26 
TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7742 TCGA-HC-7749 
       36.36        28.54         2.10        31.69         1.48         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-8256 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 
       17.16        25.71        28.27        17.95         1.58        15.88 
TCGA-HC-A4ZV TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A76W TCGA-HC-A8CY TCGA-HI-7168 
        0.76         2.20        17.42         7.00         9.53        78.61 
TCGA-HI-7169 TCGA-J4-8200 TCGA-J4-A67Q TCGA-J4-A6G3 TCGA-J4-A83J TCGA-J4-A83L 
       88.24        12.30        32.05        27.91        22.88        23.67 
TCGA-J4-A83M TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       14.37        13.55        27.12         6.97        10.62        13.32 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7FA 
       40.67        12.69        44.35        21.86         2.99        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A5A1 
        8.88        11.57       113.10        56.28        86.40        77.72 
TCGA-KK-A6E0 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AW 
       30.02        67.07        58.19         6.44        52.93        34.65 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B3 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8ID 
       49.94        32.84        29.56        32.91         2.73        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-M7-A721 TCGA-M7-A722 
       26.43        82.36        51.25        51.39        13.15        34.85 
TCGA-M7-A724 TCGA-QU-A6IL TCGA-TP-A8TV TCGA-V1-A8MG TCGA-V1-A8ML TCGA-V1-A8MM 
       29.23         3.19        13.32        28.18        14.73        39.29 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9OF TCGA-V1-A9OH 
       22.55         6.64        58.39        79.73        38.93        41.19 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9Z7 TCGA-V1-A9Z9 TCGA-V1-A9ZI TCGA-VN-A88I 
       19.36        12.20         4.27        17.75         4.70         8.84 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A878 
       15.52        15.81        41.42        25.78        16.31        97.41 
TCGA-VP-A87B TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-AA1N TCGA-WW-A8ZI 
       85.18        66.97        21.80        53.36        44.88        14.76 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        3.91        38.04        31.99        37.25        40.04        41.49 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YJ-A8SW 
       30.58        41.39        36.95        32.19        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SC TCGA-YL-A8SH 
       52.96        48.72        62.14        60.56        41.46        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI 
       53.06        45.86       114.38        62.79         8.98        53.36 
TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9KY 
       62.37        28.34         3.09        14.53        13.28         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       11.67        29.85        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       16.96        17.98        11.47        13.48         4.34 

$subtype3
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5739 TCGA-CH-5740 
       32.71        22.06        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-5766 
       12.99         1.97        31.00         2.04        23.01         1.02 
TCGA-CH-5769 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5507 TCGA-EJ-5521 
        2.04        32.02        33.01        29.00        23.90        51.88 
TCGA-EJ-5525 TCGA-EJ-5530 TCGA-EJ-7315 TCGA-EJ-7321 TCGA-EJ-7784 TCGA-EJ-8469 
       36.66        60.23        33.14        27.09        25.68        76.41 
TCGA-EJ-A46F TCGA-EJ-A65D TCGA-EJ-A65F TCGA-G9-6332 TCGA-G9-6342 TCGA-G9-6354 
       25.74        12.92        18.41        87.35        55.76        49.35 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6373 TCGA-G9-7525 
       46.52        47.44        45.30        39.39        26.66        32.68 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BY TCGA-HC-7081 TCGA-HC-7209 
       29.79        23.93         6.08         3.68        37.35        14.47 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7744 TCGA-HC-7819 
       28.60        40.08         1.68         2.37         1.68        17.85 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8257 TCGA-HC-8259 TCGA-HC-A48F TCGA-HC-A631 
       31.43        19.36        23.87         2.27        22.36         1.78 
TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A76X TCGA-HI-7171 TCGA-J4-A67L TCGA-J4-A67N 
        2.01         1.61         4.93        43.69        25.32        16.54 
TCGA-J4-A67S TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J9-A52B TCGA-J9-A8CM TCGA-KC-A4BV 
       27.39        16.83        22.52        13.87        15.22        43.66 
TCGA-KC-A7F6 TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 
        8.65        44.68       115.86        54.54       165.17       115.13 
TCGA-KK-A6E6 TCGA-KK-A7AU TCGA-KK-A7AY TCGA-KK-A7B1 TCGA-KK-A7B4 TCGA-KK-A8I5 
      113.33        58.36        51.68        34.95        20.94       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IH TCGA-KK-A8II TCGA-M7-A71Z 
       21.96        31.79        63.48        66.18       113.98        21.14 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IN TCGA-TP-A8TT TCGA-V1-A8WS TCGA-V1-A9O9 
       18.84         5.69       140.19        11.90        15.58         6.71 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 
       25.51        24.53         6.21        44.91       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A87D TCGA-VP-A87K TCGA-XJ-A83F TCGA-YL-A8HL TCGA-YL-A8SA 
      109.58        60.92        42.94        37.05        51.45        16.83 
TCGA-YL-A8SF TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WL TCGA-ZG-A8QZ 
       45.14        32.45        71.34        14.04        24.33        10.13 
TCGA-ZG-A9L2 TCGA-ZG-A9LZ 
       37.94        22.75 

subtype1 subtype2 subtype3 
    0.72     0.76     1.02 
subtype1 subtype2 subtype3 
  122.17   114.38   165.17 
subtype1 subtype2 subtype3 
   25.15    27.91    26.20 
[1] "0.7 - 122.2 (25.1)" "0.8 - 114.4 (27.9)" "1.0 - 165.2 (26.2)"
D4V2, continuous
          vv
clus        T2  T3  T4
  subtype1  85  84   2
  subtype2  70 126   6
  subtype3  33  76   2
D4V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2       85       70       33
  T3       84      126       76
  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"
D4V4, binary
          cls
clus         0   1
  subtype1 127  18
  subtype2 136  37
  subtype3  77  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  127   18
  subtype2  136   37
  subtype3   77   22
   clus
vv  subtype1 subtype2 subtype3
  0      127      136       77
  1       18       37       22
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus         0   1
  subtype1   3 170
  subtype2   6 197
  subtype3   6 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  170
  subtype2    6  197
  subtype3    6  105
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        3        6        6
  PROSTATE ADENOCARCINOMA ACINAR TYPE         170      197      105
[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 121  38   0   6
  subtype2 124  70   3   3
  subtype3  67  33   2   6
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      121      124       67
  R1       38       70       33
  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"
D4V7, continuous
D4V8, continuous
D4V9, continuous
D4V10, continuous
D4V11, continuous
D4V12, continuous
D4V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0    65
  subtype2     0                         5    46
  subtype3     0                         2    36
D4V14, 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(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 154   3
  subtype2 144   1
  subtype3 177   4
subtype1 subtype2 subtype3 
     157      145      181 
subtype1 subtype2 subtype3 
       3        1        4 
$subtype1
TCGA-2A-A8VL TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-CH-5740 TCGA-CH-5743 
       20.42        32.71        22.06        25.35         1.02        13.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5754 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5766 
        2.99        24.03         2.04        12.00         1.02         1.02 
TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 
       13.02         9.99        33.01         2.99        29.00        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5503 
       19.56        13.32        29.79        46.52        44.88        45.73 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5515 
       30.31        27.19        38.93        48.13        36.69        60.23 
TCGA-EJ-5516 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 
       46.55        51.88        68.35        43.07        38.76        39.75 
TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7312 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       41.85        29.06        36.13        21.60        20.58        17.23 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65M 
       23.80        21.96        23.34        13.71        18.41         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
       11.61        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-FC-7961 TCGA-FC-A66V TCGA-FC-A8O0 
        9.27         9.83         4.54        15.42        17.23         1.78 
TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       41.62        67.99        83.87        50.70        49.35        47.15 
TCGA-G9-6379 TCGA-G9-7509 TCGA-G9-A9S7 TCGA-H9-A6BX TCGA-HC-7747 TCGA-HC-7817 
       58.45        52.93        23.93        30.94        24.59        30.51 
TCGA-HC-8216 TCGA-HC-8260 TCGA-HC-8265 TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AQ 
       22.42        22.55        15.88         1.61         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.45         1.25         4.41         7.00        25.48        18.84 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67R TCGA-J4-A67S 
       25.32        30.94        16.54        27.58        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N 
        6.02        25.28        27.91        10.78        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BO 
       13.87         5.85        15.22        12.69        30.71        19.96 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KK-A6DY TCGA-KK-A7AV TCGA-KK-A7B2 TCGA-KK-A8I4 
       21.86         8.65       115.86        27.02        36.13        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IC 
      101.79        21.96        65.82        32.91         2.73        67.43 
TCGA-KK-A8IJ TCGA-KK-A8IM TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A723 TCGA-QU-A6IP 
       51.25        47.28        12.62        13.15        25.08        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU 
       18.12        11.90        40.44        16.70        14.73        53.16 
TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A9OA TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9ZR 
       30.38        22.55        20.91         8.42         5.59         5.82 
TCGA-VN-A88Q TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-X4-A8KQ TCGA-X4-A8KS 
       44.91        97.41        23.93        55.56        45.47        32.19 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAJU TCGA-Y6-A8TL 
       48.03         9.04         2.99        31.96        51.81        25.48 
TCGA-YL-A8HK TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A9WJ 
       49.02        28.77        45.86        46.29       114.38        60.99 
TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QZ TCGA-ZG-A9LU TCGA-ZG-A9LY 
       62.37        49.91        28.34        10.13        19.04        12.16 
TCGA-ZG-A9M4 
       17.98 

$subtype2
TCGA-2A-A8VO TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5738 TCGA-CH-5762 
       43.79        31.96        30.31        20.22         6.97        44.02 
TCGA-CH-5767 TCGA-CH-5772 TCGA-EJ-5502 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       15.06        15.98        26.30        48.53        38.53        36.23 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       47.80        52.27        60.23        47.87        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       83.57        37.81        25.35        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       24.39        23.90        25.87        20.55        14.53        14.14 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 
       19.59        17.29        23.05        19.92        77.16        38.10 
TCGA-EJ-8472 TCGA-EJ-A65G TCGA-EJ-A6RC TCGA-EJ-A8FN TCGA-EJ-AB20 TCGA-EJ-AB27 
       24.85        21.90        28.70        10.82         4.31         4.77 
TCGA-FC-7708 TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       28.41        81.04        66.67        55.76        18.21        68.68 
TCGA-G9-6351 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.16        46.52        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6378 
       40.18        39.95        38.01        40.31        26.66        37.97 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7079 
       30.97        35.34        28.18         6.08        19.76         2.93 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 
       37.35        14.47        28.54         1.68        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 
       23.70        26.04         1.97        17.16        30.84        24.56 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 
        2.17         2.27        17.95        22.32         1.58         1.15 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67Q 
       78.61        88.24        82.92        20.19        12.30        32.05 
TCGA-J4-A6M7 TCGA-J4-A83L TCGA-J4-AATV TCGA-J4-AAU2 TCGA-KC-A4BR TCGA-KC-A7FE 
       16.83        23.67        11.77        27.12        44.35        11.57 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A8IG TCGA-V1-A8WL 
       67.59       115.13        32.84        34.95        82.36        52.08 
TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9Z7 TCGA-V1-A9Z8 
        6.64        79.73        12.20        15.65         4.27         6.15 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88O TCGA-VN-A88P TCGA-VP-A87E TCGA-VP-A87H 
        8.84        24.53        15.81        41.42        66.97        21.80 
TCGA-VP-AA1N TCGA-XA-A8JR TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SI 
       44.88         3.91        52.96        71.77        56.52        53.06 
TCGA-YL-A8SQ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       62.79         3.09        14.53        13.28        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9MC TCGA-ZG-A9N3 
       22.59        20.28         3.78        16.96        14.96        11.47 
TCGA-ZG-A9NI 
        4.34 

$subtype3
TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5739 TCGA-CH-5741 
       33.96         3.68        11.51         2.99        22.06        12.99 
TCGA-CH-5744 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5761 
        1.97         1.02        13.02        31.00         1.02         0.92 
TCGA-CH-5765 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5790 TCGA-EJ-5494 
       23.01        24.03         2.04        26.99        32.02        27.16 
TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5519 TCGA-EJ-5525 TCGA-EJ-7123 TCGA-EJ-7315 
       28.93        23.90        64.50        36.66        74.10        33.14 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7789 
       33.83        27.09        35.18        38.37        25.68        18.15 
TCGA-EJ-7793 TCGA-EJ-8469 TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65D 
        3.75        76.41        25.18        25.74        21.96        12.92 
TCGA-EJ-A65J TCGA-EJ-A7NF TCGA-EJ-A7NN TCGA-EJ-A8FS TCGA-FC-A4JI TCGA-FC-A5OB 
       14.83         8.22         6.48         8.75        13.45        22.36 
TCGA-FC-A6HD TCGA-G9-6332 TCGA-G9-6348 TCGA-G9-6362 TCGA-G9-6377 TCGA-G9-6496 
       16.24        87.35        49.81        47.44        31.50        56.75 
TCGA-G9-6498 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-H9-A6BY TCGA-HC-7078 
       64.18        32.68        26.01        29.79         3.68        65.26 
TCGA-HC-7080 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7752 
       36.36         0.79        28.60        40.08         2.37        25.71 
TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-A48F 
       17.85        31.43        19.36        28.27        23.87        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A76X 
        0.76         1.78         2.01         2.20        17.42         4.93 
TCGA-HC-A8CY TCGA-HI-7171 TCGA-J4-A67K TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-AATZ 
        9.53        43.69        33.01        22.52        22.88        13.55 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN TCGA-KC-A4BN TCGA-KC-A4BV 
        6.97        10.62        13.32        40.67        59.67        43.66 
TCGA-KC-A7F5 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        2.99        19.66         8.88       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 
       86.40        77.72        30.02        54.54       165.17        49.25 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AW 
       67.07        58.19         6.44        52.93        58.36        34.65 
TCGA-KK-A7AY TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8ID 
       51.68        29.56        20.94        31.79        63.48        69.27 
TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Z 
       26.43        66.18       113.98        51.39        20.65        21.14 
TCGA-M7-A722 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IM 
       34.85        29.23        18.84         5.69         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MM 
      140.19       122.17        13.32        41.23        28.18        39.29 
TCGA-V1-A8WS TCGA-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       15.58        58.39         6.71        38.93        41.19        19.36 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N 
       17.75        49.87         4.70        25.51         6.21        15.52 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87B 
       25.78        16.31       111.39        75.91       109.58        85.18 
TCGA-VP-A87D TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XJ-A83F TCGA-XJ-A83G 
       60.92        53.36        42.94        14.76        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       42.08        31.99        37.25        40.04        41.49        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAK1 TCGA-YJ-A8SW TCGA-YL-A8HL 
       41.39        36.95        47.15        32.19         4.87        51.45 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF 
       48.72        62.14        60.56        16.83        41.46        45.14 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WL 
       32.45        71.34         8.98        14.04        53.36        24.33 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LZ 
        4.27        11.67        29.85        19.17        12.43        22.75 
TCGA-ZG-A9ND 
       13.48 

subtype1 subtype2 subtype3 
    1.02     0.72     0.76 
subtype1 subtype2 subtype3 
  115.86   115.13   165.17 
subtype1 subtype2 subtype3 
   23.93    26.66    28.93 
[1] "1.0 - 115.9 (23.9)" "0.7 - 115.1 (26.7)" "0.8 - 165.2 (28.9)"
D5V2, continuous
          vv
clus        T2  T3  T4
  subtype1  64  89   2
  subtype2  69  71   4
  subtype3  55 124   3
D5V3, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T2       64       69       55
  T3       89       71      124
  T4        2        4        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
          cls
clus         0   1
  subtype1 110  26
  subtype2 105  11
  subtype3 124  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  110   26
  subtype2  105   11
  subtype3  124   39
   clus
vv  subtype1 subtype2 subtype3
  0      110      105      124
  1       26       11       39
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus         0   1
  subtype1   7 150
  subtype2   1 144
  subtype3   7 175
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  150
  subtype2    1  144
  subtype3    7  175
                                        clus
vv                                       subtype1 subtype2 subtype3
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        7        1        7
  PROSTATE ADENOCARCINOMA ACINAR TYPE         150      144      175
[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 108  38   0   6
  subtype2  93  41   3   2
  subtype3 109  61   2   7
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      108       93      109
  R1       38       41       61
  R2        0        3        2
  RX        6        2        7
[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"
D5V7, continuous
D5V8, continuous
D5V9, continuous
D5V10, continuous
D5V11, continuous
D5V12, continuous
D5V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    39
  subtype2     1                         3    69
  subtype3     0                         4    38
D5V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        0        3        4
  WHITE                           39       69       38
[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(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1 145   2
  subtype2  95   2
  subtype3  57   2
  subtype4 124   1
  subtype5  54   1
subtype1 subtype2 subtype3 subtype4 subtype5 
     147       97       59      125       55 
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        2        2        1        1 
$subtype1
TCGA-2A-A8VL TCGA-2A-A8W3 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 
       20.42        25.35         6.97         1.02        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5769 
        2.99         2.04        44.02        12.00         1.02         2.04 
TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 
       13.02         9.99        33.01         2.99        29.00        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5503 
       19.56        13.32        29.79        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        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       38.53        60.23        46.55        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7312 TCGA-EJ-7321 
       43.07        38.76        39.75        41.85        36.13        27.09 
TCGA-EJ-8472 TCGA-EJ-A46B TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       24.85        21.60        17.23        23.80        21.96        23.34 
TCGA-EJ-A65E TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       13.71        11.61         8.22        14.20         6.48        15.65 
TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-FC-7961 TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6329 
        9.83         4.54        15.42        17.23         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6354 
       87.35        67.99        83.87        49.81        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6364 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       47.15        47.44        39.39        40.18        39.95        38.01 
TCGA-G9-6384 TCGA-G9-6496 TCGA-G9-7509 TCGA-H9-A6BX TCGA-HC-7817 TCGA-HC-8260 
       25.15        56.75        52.93        30.94        30.51        22.55 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A76W TCGA-HC-A8D0 
        2.33         3.48         1.45         1.25         7.00        25.48 
TCGA-HC-A8D1 TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       18.84        25.32        30.94        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-AATV 
       25.28        27.91        22.88        10.78        14.37        11.77 
TCGA-J9-A52C TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A7F3 TCGA-KC-A7FD 
        5.85        30.71        59.67        19.96        21.86         8.88 
TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A7AV TCGA-KK-A7B0 
      115.86        54.54        67.59        49.25        27.02        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I9 
       34.95        36.13        67.99        21.96        65.82        32.91 
TCGA-KK-A8IB TCGA-KK-A8IM TCGA-M7-A720 TCGA-M7-A721 TCGA-QU-A6IP TCGA-SU-A7E7 
        2.73        47.28        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 
       13.32        40.44        16.70        14.73        53.16        15.58 
TCGA-V1-A9OL TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z9 TCGA-VN-A88Q 
       19.36        15.65         8.42         5.59        17.75        44.91 
TCGA-VP-A878 TCGA-VP-A879 TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       97.41        23.93        32.19        48.03         9.04         2.99 
TCGA-XK-AAIR TCGA-XK-AAJU TCGA-YL-A8HK TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A9WJ 
       31.96        51.81        49.02        45.86        46.29        60.99 
TCGA-ZG-A8QW TCGA-ZG-A8QZ TCGA-ZG-A9LU 
        3.09        10.13        19.04 

$subtype2
TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU 
       43.79        33.96         3.68        31.96        30.31        20.22 
TCGA-CH-5772 TCGA-EJ-5502 TCGA-EJ-5504 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 
       15.98        26.30        28.93        48.53        36.23        47.80 
TCGA-EJ-5518 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7317 
       52.27        60.23        47.87        93.70        83.57        25.35 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
        6.28        24.39        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-A65G TCGA-EJ-A6RC TCGA-EJ-A8FN TCGA-EJ-AB20 
       19.59        17.29        21.90        28.70        10.82         4.31 
TCGA-EJ-AB27 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6363 
        4.77        66.67        55.76        18.21        68.68        45.30 
TCGA-G9-6365 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6498 
       44.81        40.31        37.97        27.29        58.22        64.18 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7523 TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7233 
       27.91        30.97        28.18         3.68        19.76        44.55 
TCGA-HC-7740 TCGA-HC-7750 TCGA-HC-8258 TCGA-HC-A76X TCGA-HI-7169 TCGA-HI-7170 
       23.57        17.16         2.17         4.93        88.24        82.92 
TCGA-J4-8200 TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A6M7 TCGA-J4-A83L TCGA-J4-AAU2 
       12.30        27.58        32.05        16.83        23.67        27.12 
TCGA-J9-A52E TCGA-J9-A8CN TCGA-KC-A4BR TCGA-KC-A7FE TCGA-KK-A6E4 TCGA-KK-A6E8 
       10.62        40.67        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        52.08         6.64 
TCGA-V1-A9O7 TCGA-V1-A9OQ TCGA-V1-A9Z8 TCGA-VN-A88I TCGA-VN-A88O TCGA-VN-A88P 
       79.73        12.20         6.15         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         3.91        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SB TCGA-YL-A8SH TCGA-YL-A8SI 
       52.96        71.77        62.14        56.52        28.77        53.06 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-ZG-A8QX TCGA-ZG-A9L6 TCGA-ZG-A9LN TCGA-ZG-A9M4 
       71.34        62.79        14.53        22.59         3.78        17.98 
TCGA-ZG-A9MC 
       14.96 

$subtype3
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5753 
       32.71        22.06        12.99        24.03        13.02         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5790 TCGA-EJ-5525 TCGA-EJ-5542 
       23.01         1.02        24.03        32.02        36.66        29.06 
TCGA-EJ-7314 TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-A46D 
       37.81        33.83        30.35        23.90        25.68        20.58 
TCGA-EJ-A65J TCGA-EJ-A7NH TCGA-EJ-A8FO TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6379 
       14.83        15.58         9.27        26.66        31.50        58.45 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-8216 TCGA-HC-A6HY 
       32.68        23.93        23.70        26.04        22.42         4.41 
TCGA-HC-A8CY TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67N TCGA-J9-A52B TCGA-KC-A7F6 
        9.53        20.19        33.01        16.54        13.87         8.65 
TCGA-KC-A7FA TCGA-KK-A59Y TCGA-KK-A7AP TCGA-KK-A7AY TCGA-KK-A8II TCGA-KK-A8IL 
       19.66        44.68         6.44        51.68       113.98        20.65 
TCGA-M7-A723 TCGA-M7-A725 TCGA-QU-A6IN TCGA-TP-A8TT TCGA-V1-A8WN TCGA-V1-A8WV 
       25.08        18.84       140.19        11.90        30.38        22.55 
TCGA-V1-A9ZI TCGA-VN-A88L TCGA-VN-A88M TCGA-VP-A876 TCGA-VP-A87K TCGA-X4-A8KQ 
        4.70        24.53         6.21       109.58        42.94        45.47 
TCGA-XK-AAJ3 TCGA-YL-A8SO TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A9LY 
       41.49       114.38        24.33        49.91        12.16 

$subtype4
TCGA-4L-AA1F TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5788 TCGA-EJ-5494 TCGA-EJ-7325 
       11.51        31.00         0.92        26.99        27.16        35.18 
TCGA-EJ-8469 TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65D TCGA-EJ-A65F TCGA-EJ-A65M 
       76.41        25.74        21.96        12.92        18.41         7.56 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6361 
        4.21         6.48        13.45        22.36        16.24        46.52 
TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-HC-7080 TCGA-HC-7232 TCGA-HC-7742 TCGA-HC-8213 
       26.01        29.79        36.36        38.17         1.48        19.36 
TCGA-HC-8257 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
       23.87         1.58        15.88        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HI-7168 TCGA-J4-A83I 
        2.01         2.20         1.61        17.42        78.61        22.52 
TCGA-J4-A83N TCGA-J4-AATZ TCGA-J9-A52D TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
       20.28        13.55         6.97        13.32        15.22        12.69 
TCGA-KC-A4BV TCGA-KC-A7F5 TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A5A1 
       43.66         2.99       113.10        56.28        86.40        77.72 
TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7B3 
       30.02       165.17        67.07        52.93        58.36        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8IH 
       20.94       101.79        31.79        63.48        67.43        66.18 
TCGA-KK-A8IK TCGA-M7-A71Z TCGA-M7-A722 TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL 
       51.39        21.14        34.85        29.23         5.69         3.19 
TCGA-QU-A6IM TCGA-QU-A6IO TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MM TCGA-V1-A9O5 
       41.00       122.17        41.23        28.18        39.29        58.39 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9Z7 TCGA-V1-A9ZG 
        6.71        20.91        38.93        41.19         4.27        49.87 
TCGA-V1-A9ZR TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88R TCGA-VP-A875 TCGA-VP-A87B 
        5.82        25.51        15.52        25.78        75.91        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-A87J TCGA-WW-A8ZI TCGA-XJ-A83G 
       55.56        60.92        21.80        53.36        14.76        38.04 
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-XK-AAK1 TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S9 
       36.95        47.15        32.19        51.45        48.72        60.56 
TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SL TCGA-YL-A8SR TCGA-YL-A9WH 
       16.83        41.46        45.14        32.45         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A8QY TCGA-ZG-A9KY TCGA-ZG-A9L0 
       53.36        62.37        28.34        13.28         4.27        11.67 
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-A9LS TCGA-ZG-A9LZ TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       16.96        22.75        11.47        13.48         4.34 

$subtype5
TCGA-CH-5737 TCGA-CH-5739 TCGA-CH-5748 TCGA-CH-5767 TCGA-EJ-7115 TCGA-EJ-7123 
        2.99        22.06         1.02        15.06        88.34        74.10 
TCGA-EJ-7315 TCGA-EJ-7328 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7793 TCGA-EJ-7794 
       33.14        27.68        38.37        25.87         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A8FS TCGA-FC-7708 
       19.92        77.16        38.10        25.18         8.75        28.41 
TCGA-G9-6333 TCGA-G9-6351 TCGA-G9-6366 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7522 
       81.04        46.16         3.32        50.73        38.96        35.34 
TCGA-H9-7775 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        6.08        65.26         2.93        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7736 
        0.79        28.60        40.08         1.68         2.37         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7752 
        2.10        31.69         1.68        24.59         1.97        25.71 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8256 TCGA-HC-8259 
       30.84        17.85        24.56        31.43        28.27         2.27 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8266 TCGA-HI-7171 TCGA-KK-A7AW TCGA-VP-A872 
       17.95        22.32         1.15        43.69        34.65       111.39 
TCGA-XJ-A83F 
       37.05 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.02     2.17     1.02     0.76     0.72 
subtype1 subtype2 subtype3 subtype4 subtype5 
  115.86   115.13   140.19   165.17   111.39 
subtype1 subtype2 subtype3 subtype4 subtype5 
   25.48    28.18    24.03    28.18    25.71 
[1] "1.0 - 115.9 (25.5)" "2.2 - 115.1 (28.2)" "1.0 - 140.2 (24.0)"
[4] "0.8 - 165.2 (28.2)" "0.7 - 111.4 (25.7)"
D6V2, continuous
          vv
clus       T2 T3 T4
  subtype1 65 80  0
  subtype2 45 47  4
  subtype3 21 37  1
  subtype4 27 94  4
  subtype5 30 26  0
D6V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T2       65       45       21       27       30
  T3       80       47       37       94       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"
D6V4, binary
          cls
clus         0   1
  subtype1 110  18
  subtype2  70   8
  subtype3  40  12
  subtype4  78  35
  subtype5  41   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  110   18
  subtype2   70    8
  subtype3   40   12
  subtype4   78   35
  subtype5   41    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      110       70       40       78       41
  1       18        8       12       35        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"
D6V5, binary
          cls
clus         0   1
  subtype1   4 143
  subtype2   2  95
  subtype3   3  56
  subtype4   5 120
  subtype5   1  55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  143
  subtype2    2   95
  subtype3    3   56
  subtype4    5  120
  subtype5    1   55
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        4        2        3        5
  PROSTATE ADENOCARCINOMA ACINAR TYPE         143       95       56      120
                                        clus
vv                                       subtype5
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        1
  PROSTATE ADENOCARCINOMA ACINAR TYPE          55
[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 108  31   0   6
  subtype2  57  35   1   2
  subtype3  41  14   0   2
  subtype4  64  54   2   3
  subtype5  40   6   2   2
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0      108       57       41       64       40
  R1       31       35       14       54        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"
D6V7, continuous
D6V8, continuous
D6V9, continuous
D6V10, continuous
D6V11, continuous
D6V12, continuous
D6V13, 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
D6V14, 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(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  61   1
  subtype2 100   3
  subtype3  58   0
  subtype4  86   2
subtype1 subtype2 subtype3 subtype4 
      62      103       58       88 
subtype1 subtype2 subtype3 subtype4 
       1        3        0        2 
$subtype1
TCGA-2A-A8VL TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       20.42        22.06        25.35         2.99         6.97        22.06 
TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
       12.99        24.03        13.02        44.02        12.00         1.02 
TCGA-CH-5766 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5497 
        1.02        15.98         9.99         2.99        29.00        13.32 
TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5512 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5522 
       28.93        27.19        38.53        46.55        47.80        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5542 TCGA-EJ-A46B TCGA-EJ-A46D 
       43.07        38.76        39.75        29.06        21.60        20.58 
TCGA-EJ-A46I TCGA-EJ-A6RA TCGA-EJ-A7NJ TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-AB27 
       21.96        11.61         6.48         9.27         9.83         4.77 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-7509 TCGA-HC-A6AP TCGA-HC-A8D0 
        1.78        41.62        67.99        52.93         2.33        25.48 
TCGA-HC-A8D1 TCGA-J4-A6G1 TCGA-J4-A83K TCGA-KC-A4BO TCGA-KK-A8IJ TCGA-KK-A8IM 
       18.84        25.28        10.78        19.96        51.25        47.28 
TCGA-M7-A720 TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-VN-A88L TCGA-VP-A878 TCGA-VP-A879 
       12.62        40.44        16.70        24.53        97.41        23.93 
TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAJU TCGA-Y6-A8TL 
       32.19        48.03         9.04         2.99        51.81        25.48 
TCGA-YL-A8SR TCGA-ZG-A8QZ 
        8.98        10.13 

$subtype2
TCGA-2A-AAYF TCGA-2A-AAYU TCGA-CH-5752 TCGA-EJ-5525 TCGA-EJ-A46G TCGA-EJ-A65F 
       31.96        20.22        31.00        36.66        21.96        18.41 
TCGA-EJ-A65J TCGA-EJ-A7NH TCGA-EJ-A7NM TCGA-FC-7961 TCGA-G9-6339 TCGA-G9-6354 
       14.83        15.58         4.21        15.42        83.87        49.35 
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-A76W 
        2.01         2.20         1.61         1.25         4.41         7.00 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G3 TCGA-J4-A83J 
       25.32        30.94        29.92         6.02        27.91        22.88 
TCGA-J4-A83M TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL 
       14.37        27.12        13.87         5.85        10.62        13.32 
TCGA-J9-A8CM TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FA TCGA-KK-A59V TCGA-KK-A59Y 
       15.22        43.66        21.86        19.66       113.10        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7B3 TCGA-KK-A8I7 
      115.13        49.25        67.07        52.93        29.56        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A725 
       31.79        32.91        63.48         2.73        20.65        18.84 
TCGA-MG-AAMC TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP TCGA-V1-A8MG TCGA-V1-A8MM 
        5.69        41.00       122.17        86.14        28.18        39.29 
TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OL 
       52.08        22.55        58.39        20.91        41.19        19.36 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9Z9 TCGA-V1-A9ZI TCGA-VP-A872 TCGA-VP-A87K 
       12.20        15.65        17.75         4.70       111.39        42.94 
TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83H TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       44.88        45.47        42.08        40.04        41.49        30.58 
TCGA-XK-AAJT TCGA-XK-AAK1 TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SF TCGA-YL-A8SH 
       47.15        32.19        71.77        62.14        45.14        28.77 
TCGA-YL-A8SO TCGA-YL-A9WH TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9LB 
      114.38        14.04         4.27        11.67        29.85        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9ND 
       12.43        16.96        19.04        22.75        17.98        13.48 
TCGA-ZG-A9NI 
        4.34 

$subtype3
TCGA-2A-AAYO TCGA-4L-AA1F TCGA-CH-5769 TCGA-EJ-5514 TCGA-EJ-7791 TCGA-EJ-7792 
       30.31        11.51         2.04        36.23        19.59        17.29 
TCGA-EJ-A46H TCGA-EJ-A6RC TCGA-EJ-A7NK TCGA-EJ-A8FN TCGA-EJ-A8FU TCGA-EJ-AB20 
       23.80        28.70        15.65        10.82         4.54         4.31 
TCGA-G9-6347 TCGA-G9-6361 TCGA-G9-6365 TCGA-G9-7519 TCGA-G9-7523 TCGA-H9-A6BX 
       68.68        46.52        44.81        27.91        28.18        30.94 
TCGA-HC-7817 TCGA-HC-8264 TCGA-HI-7169 TCGA-J4-8200 TCGA-J4-A67Q TCGA-J4-A83L 
       30.51         1.58        88.24        12.30        32.05        23.67 
TCGA-KC-A4BL TCGA-KC-A4BR TCGA-KC-A7FE TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       30.71        44.35        11.57        32.84        34.95        36.13 
TCGA-KK-A8IC TCGA-KK-A8IG TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       67.43        82.36         6.64        79.73         4.27         6.15 
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-XA-A8JR TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
        3.91        52.96        49.02        53.06        45.86        46.29 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L6 
        3.09        14.53        13.28        37.94        36.43        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LN TCGA-ZG-A9MC TCGA-ZG-A9N3 
       20.28         3.78        14.96        11.47 

$subtype4
TCGA-EJ-5494 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 
       27.16        88.34        74.10        93.70        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       25.35        27.09        30.35        27.68         6.28        24.39 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46E TCGA-FC-7708 TCGA-G9-6333 TCGA-G9-6338 
       24.85        25.18        17.23        28.41        81.04        66.67 
TCGA-G9-6342 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6369 TCGA-G9-6377 TCGA-G9-6499 
       55.76        46.16        50.70        39.95        31.50        50.73 
TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-HC-7075 
       38.96        30.97        35.34        26.01         6.08        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 
       65.26         2.93        37.35        14.47        28.54        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 
       40.08         1.68         2.37        38.17        44.55         2.10 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8258 
        1.97        17.16        30.84        24.56        31.43         2.17 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-8266 TCGA-HI-7168 
       22.55        17.95        22.32        15.88         1.15        78.61 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A83I TCGA-J4-AATV TCGA-KK-A7B4 
       82.92        43.69        20.19        22.52        11.77        20.94 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8IH TCGA-M7-A723 TCGA-TP-A8TT TCGA-V1-A9O9 
      101.79        21.96        66.18        25.08        11.90         6.71 
TCGA-V1-A9OX TCGA-V1-A9ZR TCGA-XK-AAIV TCGA-YL-A9WY 
        8.42         5.82        37.25        28.34 

subtype1 subtype2 subtype3 subtype4 
    1.02     0.76     1.58     1.15 
subtype1 subtype2 subtype3 subtype4 
   97.41   165.17    88.24   101.79 
subtype1 subtype2 subtype3 subtype4 
  22.010   28.180   28.440   25.775 
[1] "1.0 - 97.4 (22.0)"  "0.8 - 165.2 (28.2)" "1.6 - 88.2 (28.4)" 
[4] "1.1 - 101.8 (25.8)"
D7V2, continuous
          vv
clus       T2 T3 T4
  subtype1 32 29  0
  subtype2 26 74  3
  subtype3 22 34  1
  subtype4 39 47  1
D7V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T2       32       26       22       39
  T3       29       74       34       47
  T4        0        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 43 10
  subtype2 72 18
  subtype3 40 11
  subtype4 67  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   10
  subtype2   72   18
  subtype3   40   11
  subtype4   67    8
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       43       72       40       67
  1       10       18       11        8
[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  2 60
  subtype2  5 98
  subtype3  1 57
  subtype4  0 88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   60
  subtype2    5   98
  subtype3    1   57
  subtype4    0   88
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        2        5        1        0
  PROSTATE ADENOCARCINOMA ACINAR TYPE          60       98       57       88
[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 48 10  0  3
  subtype2 52 45  0  5
  subtype3 33 21  1  1
  subtype4 61 17  1  2
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       48       52       33       61
  R1       10       45       21       17
  R2        0        0        1        1
  RX        3        5        1        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"
D7V7, continuous
D7V8, continuous
D7V9, continuous
D7V10, continuous
D7V11, continuous
D7V12, continuous
D7V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    27
  subtype2     0                         0     3
  subtype3     0                         0     7
  subtype4     1                         3    54
D7V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        0        3
  WHITE                           27        3        7       54
[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_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 67  1
  subtype2 39  1
  subtype3 34  1
  subtype4 81  2
  subtype5 25  0
  subtype6 59  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      68       40       35       83       25       60 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       1        1        1        2        0        1 
$subtype1
TCGA-2A-A8VL TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-EJ-7793 TCGA-EJ-A46B TCGA-EJ-A46D 
       20.42        22.06        25.35         3.75        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65F TCGA-EJ-A6RA TCGA-EJ-A7NJ 
       17.23        23.80        21.96        18.41        11.61         6.48 
TCGA-EJ-A7NK TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-G9-6329 TCGA-G9-6333 
       15.65         9.27         9.83         4.54        41.62        81.04 
TCGA-G9-6339 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6499 TCGA-G9-7509 TCGA-H9-A6BX 
       83.87        50.70        49.35        50.73        52.93        30.94 
TCGA-HC-7817 TCGA-HC-8260 TCGA-HC-A6AP TCGA-HC-A6HX TCGA-HC-A8D0 TCGA-HC-A8D1 
       30.51        22.55         2.33         1.25        25.48        18.84 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67R TCGA-J4-A6G1 TCGA-J4-A83K TCGA-J4-AATV 
       25.32        30.94        29.92        25.28        10.78        11.77 
TCGA-J9-A52C TCGA-KC-A4BL TCGA-KC-A4BO TCGA-KC-A7F3 TCGA-KK-A7B0 TCGA-KK-A7B1 
        5.85        30.71        19.96        21.86        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I9 TCGA-KK-A8IB TCGA-KK-A8IJ 
       36.13        21.96        65.82        32.91         2.73        51.25 
TCGA-KK-A8IM TCGA-M7-A720 TCGA-M7-A723 TCGA-QU-A6IP TCGA-V1-A8MJ TCGA-V1-A8MK 
       47.28        12.62        25.08        86.14        40.44        16.70 
TCGA-V1-A9OH TCGA-V1-A9ZR TCGA-VN-A88L TCGA-VP-A878 TCGA-VP-A879 TCGA-X4-A8KQ 
       41.19         5.82        24.53        97.41        23.93        45.47 
TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAJU TCGA-YL-A8HK 
       32.19        48.03         9.04         2.99        51.81        49.02 
TCGA-YL-A8SK TCGA-ZG-A8QZ 
       46.29        10.13 

$subtype2
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-EJ-7125 TCGA-EJ-7317 TCGA-EJ-7331 
       31.96        30.31        20.22        93.70        25.35        24.39 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7792 TCGA-EJ-A6RC TCGA-EJ-A8FN TCGA-EJ-AB20 
       14.53        14.14        17.29        28.70        10.82         4.31 
TCGA-EJ-AB27 TCGA-G9-6338 TCGA-G9-6347 TCGA-G9-6369 TCGA-G9-7519 TCGA-G9-7523 
        4.77        66.67        68.68        39.95        27.91        28.18 
TCGA-HC-7075 TCGA-HC-7750 TCGA-HI-7169 TCGA-J4-8200 TCGA-J4-A67Q TCGA-J4-A83L 
       19.76        17.16        88.24        12.30        32.05        23.67 
TCGA-J4-AAU2 TCGA-KC-A7FE TCGA-KK-A8IG TCGA-V1-A9O7 TCGA-V1-A9OQ TCGA-V1-A9Z8 
       27.12        11.57        82.36        79.73        12.20         6.15 
TCGA-VN-A88I TCGA-VN-A88P TCGA-VP-A87E TCGA-XA-A8JR TCGA-YL-A8HJ TCGA-YL-A8S8 
        8.84        41.42        66.97         3.91        52.96        62.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-ZG-A8QX TCGA-ZG-A9L6 
       28.77        53.06        14.53        22.59 

$subtype3
TCGA-4L-AA1F TCGA-CH-5769 TCGA-EJ-5514 TCGA-G9-7521 TCGA-G9-A9S0 TCGA-G9-A9S7 
       11.51         2.04        36.23        30.97        26.01        23.93 
TCGA-HC-7231 TCGA-J4-A83I TCGA-KK-A7B4 TCGA-KK-A8I5 TCGA-KK-A8IA TCGA-KK-A8IC 
        2.37        22.52        20.94       101.79        63.48        67.43 
TCGA-KK-A8IH TCGA-TP-A8TT TCGA-V1-A8X3 TCGA-V1-A9O9 TCGA-V1-A9ZG TCGA-VN-A88K 
       66.18        11.90         6.64         6.71        49.87        25.51 
TCGA-VP-A872 TCGA-VP-A87C TCGA-XK-AAIV TCGA-YL-A8SF TCGA-YL-A9WH TCGA-YL-A9WY 
      111.39        55.56        37.25        45.14        14.04        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L9 TCGA-ZG-A9LM 
        3.09        13.28        37.94        36.43        20.28        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
        3.78        22.75        17.98        14.96        11.47 

$subtype4
TCGA-CH-5737 TCGA-CH-5752 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5525 TCGA-EJ-7123 
        2.99        31.00         2.99        27.16        36.66        74.10 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A7NH TCGA-EJ-A7NM TCGA-FC-7961 TCGA-FC-A8O0 
       21.96        14.83        15.58         4.21        15.42         1.78 
TCGA-G9-6379 TCGA-G9-6498 TCGA-G9-A9S4 TCGA-HC-7078 TCGA-HC-A4ZV TCGA-HC-A631 
       58.45        64.18        29.79        65.26         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6HY TCGA-HC-A76W TCGA-J4-A67T 
        2.01         2.20         1.61         4.41         7.00         6.02 
TCGA-J4-A6G3 TCGA-J4-A83J TCGA-J9-A52B TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.91        22.88        13.87        10.62        13.32        15.22 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7FA TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z 
       44.35        43.66        19.66       113.10        44.68        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 
       77.72       115.86        30.02        54.54       165.17       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A7AQ TCGA-KK-A7B3 TCGA-KK-A8I8 TCGA-KK-A8IL 
       49.25        67.07        52.93        29.56        31.79        20.65 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IM TCGA-QU-A6IO TCGA-V1-A8MG TCGA-V1-A8MM 
       18.84         5.69        41.00       122.17        28.18        39.29 
TCGA-V1-A8WL TCGA-V1-A8WV TCGA-V1-A9O5 TCGA-V1-A9OA TCGA-V1-A9OL TCGA-V1-A9OT 
       52.08        22.55        58.39        20.91        19.36        15.65 
TCGA-V1-A9Z7 TCGA-V1-A9Z9 TCGA-V1-A9ZI TCGA-VP-A87K TCGA-VP-AA1N TCGA-XK-AAIW 
        4.27        17.75         4.70        42.94        44.88        40.04 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJT TCGA-XK-AAK1 TCGA-Y6-A8TL TCGA-YL-A8HO 
       41.49        30.58        47.15        32.19        25.48        71.77 
TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SR TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L5 
       45.86       114.38         8.98         4.27        11.67        29.85 
TCGA-ZG-A9LB TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9ND TCGA-ZG-A9NI 
       19.17        16.96        19.04        13.48         4.34 

$subtype5
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5762 
        6.97        22.06        12.99        24.03        13.02        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5794 
       12.00         1.02         1.02        15.98         9.99        29.00 
TCGA-EJ-5497 TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5512 TCGA-EJ-5516 TCGA-EJ-5517 
       13.32        28.93        27.19        38.53        46.55        47.80 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5542 TCGA-G9-6336 
       68.35        43.07        38.76        39.75        29.06        67.99 
TCGA-G9-6365 
       44.81 

$subtype6
TCGA-EJ-7115 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       88.34        37.81        33.14        27.09        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7791 
        6.28        38.37        25.87        25.68        20.55        19.59 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-FC-7708 TCGA-G9-6342 TCGA-G9-6351 TCGA-G9-6361 TCGA-G9-6377 
       25.18        28.41        55.76        46.16        46.52        31.50 
TCGA-G9-7510 TCGA-G9-7522 TCGA-H9-7775 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 
       38.96        35.34         6.08         2.93        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 
       28.54        28.60        40.08         1.68        38.17        44.55 
TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.10        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8258 
       26.04         1.97        30.84        24.56        31.43         2.17 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HI-7168 
       17.95        22.32         1.58        15.88         1.15        78.61 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A83M TCGA-V1-A9OX TCGA-XJ-A83H 
       82.92        43.69        20.19        14.37         8.42        42.08 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    1.25     3.91     2.04     0.76     1.02     1.15 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   97.41    93.70   111.39   165.17    68.35    88.34 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  24.805   26.235   22.750   27.160   28.930   25.955 
[1] "1.2 - 97.4 (24.8)"  "3.9 - 93.7 (26.2)"  "2.0 - 111.4 (22.8)"
[4] "0.8 - 165.2 (27.2)" "1.0 - 68.3 (28.9)"  "1.1 - 88.3 (26.0)" 
D8V2, continuous
          vv
clus       T2 T3 T4
  subtype1 35 31  1
  subtype2 23 16  0
  subtype3  6 29  0
  subtype4 19 61  3
  subtype5  8 15  1
  subtype6 28 32  0
D8V3, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T2       35       23        6       19        8       28
  T3       31       16       29       61       15       32
  T4        1        0        0        3        1        0
[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"
D8V4, binary
          cls
clus        0  1
  subtype1 45  8
  subtype2 31  0
  subtype3 18 16
  subtype4 61 15
  subtype5 19  5
  subtype6 48  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    8
  subtype2   31    0
  subtype3   18   16
  subtype4   61   15
  subtype5   19    5
  subtype6   48    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       45       31       18       61       19       48
  1        8        0       16       15        5        3
[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"
D8V5, binary
          cls
clus        0  1
  subtype1  3 65
  subtype2  1 39
  subtype3  1 34
  subtype4  3 80
  subtype5  0 25
  subtype6  0 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   65
  subtype2    1   39
  subtype3    1   34
  subtype4    3   80
  subtype5    0   25
  subtype6    0   60
                                        clus
vv                                       subtype1 subtype2 subtype3 subtype4
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        3        1        1        3
  PROSTATE ADENOCARCINOMA ACINAR TYPE          65       39       34       80
                                        clus
vv                                       subtype5 subtype6
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE        0        0
  PROSTATE ADENOCARCINOMA ACINAR TYPE          25       60
[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 52 10  0  4
  subtype2 27 11  1  0
  subtype3 16 17  0  2
  subtype4 42 38  0  2
  subtype5 17  7  0  1
  subtype6 40 10  1  2
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       52       27       16       42       17       40
  R1       10       11       17       38        7       10
  R2        0        1        0        0        0        1
  RX        4        0        2        2        1        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"
D8V7, continuous
D8V8, continuous
D8V9, continuous
D8V10, continuous
D8V11, continuous
D8V12, continuous
D8V13, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0     5
  subtype2     0                         0    11
  subtype3     0                         0     3
  subtype4     0                         0     8
  subtype5     0                         0    25
  subtype6     1                         3    39
D8V14, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        0        0
  BLACK OR AFRICAN AMERICAN        0        0        0        0        0
  WHITE                            5       11        3        8       25
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN        3
  WHITE                           39
[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"
