[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTSKCM-TM"
[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/SKCM-TM/11541723/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/11591333/SKCM-TM.mergedcluster.txt"

nPatients in clinical file=349, in cluster file=367, common to both=349
[1]  10 349
[1] "CN_CNMF"
[1] 3
  1   2   3 
 94 133 121 
  1   2   3 
 94 133 121 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
118 139  89 
  1   2   3 
118 139  89 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
47 58 26 38 
 1  2  3  4 
47 58 26 38 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
27 58 35 49 
 1  2  3  4 
27 58 35 49 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
132 100 116 
  1   2   3 
132 100 116 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
101 159  88 
  1   2   3 
101 159  88 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4   5 
 44  99  73 109   8 
  1   2   3   4   5 
 44  99  73 109   8 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 88 138  70  37 
  1   2   3   4 
 88 138  70  37 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
 90 102 127 
  1   2   3 
 90 102 127 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
157 133  29 
  1   2   3 
157 133  29 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DAYSTOSUBMITTEDSPECIMENDX"             
 [6] "PRIMARYSITEOFDISEASE"                  
 [7] "NEOPLASM.DISEASESTAGE"                 
 [8] "PATHOLOGY.T.STAGE"                     
 [9] "PATHOLOGY.N.STAGE"                     
[10] "PATHOLOGY.M.STAGE"                     
[11] "MELANOMA.ULCERATION"                   
[12] "MELANOMA.PRIMARY.KNOWN"                
[13] "BRESLOW.THICKNESS"                     
[14] "DCCUPLOADDATE"                         
[15] "GENDER"                                
[16] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[17] "RADIATIONTHERAPY"                      
[18] "RADIATIONS.RADIATION.REGIMENINDICATION"
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 349 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
          NA         1856           NA           NA           NA         3408 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
          NA           NA         4053           NA           NA         2765 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
        2912           NA           NA           NA           NA         3514 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
          NA         2639           NA         1888           NA         1280 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
          NA         5219         1709         2010         1812         3976 
TCGA-D3-A3C1 TCGA-D3-A3C3 TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
          NA           NA           NA         1429         1409         5065 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
        2644           NA           NA           NA           NA         3151 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51G TCGA-D3-A51H 
        1209         1378         5318         1695           NA         1714 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
        4414         1002          688         1941          818         3826 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
        4129         4195         5424          553         3808           NA 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
          NA          353          462           NA         6965         5177 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GO TCGA-D3-A8GP TCGA-D3-A8GQ 
          NA         2897         4897           NA         4191           NA 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
          NA           NA         4609         1663          111          195 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
         551          345          678          338          301          766 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2015           NA         1487           NA         3565           NA 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        5926           NA           NA         3265         1861           NA 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
          NA          713           NA          870           NA         6553 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
         477          422          309          543         2076         1643 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
         526         1582          193          371           NA           NA 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
          NA         4070           NA         2785           NA           NA 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
          NA         2452         1455           NA         1940           NA 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        1966           NA         1729           NA         1716         1136 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
         440         1701        11252           NA         5932           NA 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
          NA         3130         1120           NA         2620         1803 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
        2051         9568         4898         6328         1482         2717 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
        1665         2423         2296         2767         3857           NA 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
         435         1691         1365         2884           NA         3932 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
          NA           NA           NA           NA         4825         6176 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
          NA           NA         7563           NA         4088         4942 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
        2166         1620         3781         3733         1570          112 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        1658           NA          714           NA           NA           NA 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
          NA         1949           NA           NA         6138           NA 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        1562         3333         4504           NA           NA           NA 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
          NA           NA         2365           NA           NA           NA 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
          NA           NA         8180           NA           NA           NA 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
          NA         1340           NA           NA           NA         1133 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
          NA           NA         2433           NA           NA           NA 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
         498          951          975           NA         2443         1429 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FR-A69P 
        1010          206         2828           NA         5299          478 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
        6390          461          213         1164           NA          896 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        2871           NA           NA           NA           NA           NA 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        1225           NA           NA           NA           NA           NA 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
        3080           NA           NA           NA         4526         1617 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
          NA         1505           NA           NA         2367           NA 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
          NA           NA           NA          378           NA         1504 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2369            6          697         1446            5          587 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
         301          220           62          357         4255           NA 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
        2577           NA           NA           NA           NA         1204 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
        1410          384           NA           NA           NA           NA 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
          NA        10860         8966          203           NA           10 
TCGA-RP-A694 TCGA-RP-A695 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
          21           NA         6455           NA           NA           NA 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
          NA         6666           NA          731         1173         1654 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZR 
         262         2746         1733         1807         1592          133 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
         114          690         1330           67          918          315 
TCGA-WE-AAA4 TCGA-YD-A9TB TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
         461           NA         1096          439          719         2831 
TCGA-Z2-AA3V 
         357 
Variable 1:'AGE':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=165,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=190,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=275,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'NEOPLASM.DISEASESTAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.T.STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.N.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA.ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MELANOMA.PRIMARY.KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BRESLOW.THICKNESS':	nDistinctValues=125,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=21,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
 [3] "NEOPLASM.DISEASESTAGE"   "PATHOLOGY.T.STAGE"      
 [5] "PATHOLOGY.N.STAGE"       "PATHOLOGY.M.STAGE"      
 [7] "MELANOMA.ULCERATION"     "MELANOMA.PRIMARY.KNOWN" 
 [9] "BRESLOW.THICKNESS"       "GENDER"                 
[11] "RACE"                    "ETHNICITY"              
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 349 columns, 2 survival variables, and 12 non-survival variables.
AGE, nv=68, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
NEOPLASM.DISEASESTAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
23 40 71 74 68 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   63    71    74    68 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 40 71 74 68 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   63    71    74    68 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
168  62  38  47 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
168  62  38  47 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
168  62  38  47 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
168  62  38  47 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
MELANOMA.ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA.PRIMARY.KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW.THICKNESS, nv=125, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 39 51
  subtype2 72 54
  subtype3 57 60
subtype1 subtype2 subtype3 
      90      126      117 
subtype1 subtype2 subtype3 
      51       54       60 
$subtype1
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A2JD TCGA-D3-A3C7 TCGA-D3-A3ML 
        3.02         6.97        16.47        11.41        46.98         6.31 
TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GQ 
       93.21        32.61        52.01        38.93        87.62        11.44 
TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA 
        5.56        21.93        48.79        39.19        36.69         4.93 
TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 
        6.64         7.00         0.20        19.00        13.35         8.12 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        1.35         5.13         4.31         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S 
        9.90        11.15         1.08        39.62         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GS TCGA-EE-A2GU 
        2.43        36.30        30.08        19.43        13.02        36.33 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       25.08        21.60        53.16        52.67       122.73        51.62 
TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       15.95        21.60        22.22         3.52        11.11       114.15 
TCGA-ER-A19Q TCGA-ER-A2NF TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P 
        9.57        13.08        22.49         1.71        18.41        15.72 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZG 
        2.20         4.70        64.47        23.80         7.30         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ 
       30.87        12.92        12.89        40.64         8.68         5.23 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U9 
        2.27         0.20        16.24        15.42        14.70        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1O 
       14.50        14.50         0.43         5.79        18.05         2.99 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YG-AA3O 
       71.01        11.84        13.12         5.36         1.94         6.18 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        6.97         8.52        70.16       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH 
       81.24        85.32         8.38        21.14        68.22        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
        6.31        92.42        64.44       114.67        46.32        82.29 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A5GL TCGA-D3-A8GB 
       24.00       103.59        54.74        31.30       110.24        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
       22.06        10.22        15.19       142.45       108.79        75.65 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1I0 TCGA-DA-A1IB 
      124.47        24.07         4.01         9.90        10.03        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       19.36        14.83        23.15        13.22         0.20        11.57 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29N 
       12.20         4.34        15.85        37.97         8.55         9.50 
TCGA-EE-A29Q TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        8.09        11.31        49.22        34.29        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 
       47.21        16.01        35.54         1.15        34.98         8.84 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
        6.18        47.51         9.53        29.46        44.25        14.56 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
       63.42       111.91        56.02        60.49         5.56       124.31 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
       21.60        16.14        27.35        18.41        21.73        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19N TCGA-ER-A19P 
       12.95        38.40         5.72        76.41        42.84        34.68 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       36.07        17.72        78.44        12.62        11.74         9.04 
TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z4 
       85.74         5.36        13.28         3.29        11.01        15.52 
TCGA-FS-A1ZB TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F8 
        3.39        52.08        49.15        27.39        53.85        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       10.78         6.41         0.99         0.16        17.33         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 
        0.85        11.61        44.28        84.72        10.13        11.84 
TCGA-GN-A9SD TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 
       14.50       164.19        60.03        10.98       185.16         5.49 
TCGA-WE-A8ZN TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3V 
       21.07         1.08        19.96        12.07         8.22         5.98 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC 
      111.09        32.42        22.55        10.29        88.50        86.76 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC 
       44.19         7.50        56.19        59.57        15.25        61.38 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K 
       13.32         9.34        26.37        29.23        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       21.44        25.78        47.87        13.68        17.72        23.11 
TCGA-D3-A8GI TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
        4.18         5.72        11.31        13.22        14.60        35.80 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
       51.12        13.68         9.99        44.52        25.15        17.56 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B 
       13.15         0.13        10.55         6.31         1.12        60.23 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       62.79        36.85        12.03        30.44        32.15         8.09 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
        9.67        36.33        51.12        28.31        33.83        55.69 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK 
        5.42        98.27         2.70         2.73         7.96       125.65 
TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       26.99         3.68        30.15        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19C 
       22.92         0.95        33.60        31.40        25.18         3.78 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19T 
       11.90        34.88         4.21        13.45        28.60         6.58 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A729 
       11.80         1.87         1.51         6.58         5.62         6.71 
TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        3.58         3.45        14.24         7.33        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY 
       19.53        11.08        47.38         8.65         8.81         0.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A4EO 
        3.22         7.36        28.73         5.98         0.13         7.23 
TCGA-GN-A264 TCGA-GN-A26A TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 
       31.33        12.16        15.81        11.05         0.33         0.69 
TCGA-W3-A825 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.98         6.48         7.10        18.67         3.72         3.42 
TCGA-WE-A8ZX TCGA-YG-AA3P TCGA-Z2-AA3S 
       21.83         4.70         6.67 

subtype1 subtype2 subtype3 
    0.20     0.16     0.13 
subtype1 subtype2 subtype3 
  122.73   185.16   125.65 
subtype1 subtype2 subtype3 
  12.970   20.515   13.320 
[1] "0.2 - 122.7 (13.0)" "0.2 - 185.2 (20.5)" "0.1 - 125.7 (13.3)"
D1V2, survival
          sevent
clus2       0  1
  subtype1 40 52
  subtype2 76 54
  subtype3 57 60
subtype1 subtype2 subtype3 
      92      130      117 
subtype1 subtype2 subtype3 
      52       54       60 
$subtype1
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A2JD TCGA-D3-A3C7 TCGA-D3-A3ML 
       17.03        61.02        16.57        11.87        46.98        13.87 
TCGA-D3-A51E TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GQ 
      174.84        63.81       135.75        89.13       137.79        29.06 
TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I1 
      129.63         3.65         6.41        22.29        48.89       194.83 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SH 
       61.18        65.92        68.09        10.49        10.16        54.02 
TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20H 
       17.29        94.98        14.70        68.15         4.96       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
       13.55        63.35        80.61        13.97         2.60        56.84 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2GJ 
       14.47        55.92        25.87        36.82        48.72        89.33 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       55.59        94.82        47.54        43.23       162.48        71.21 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A19D 
      122.73        51.62        23.47        64.08        53.19        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19Q TCGA-ER-A2NF TCGA-ER-A3EV TCGA-ER-A3PL 
       26.37       268.93        50.89        16.37        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 
       92.98        15.72        34.82        29.46       216.92       202.65 
TCGA-FS-A1ZA TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZT 
       27.72         9.70        32.75        47.38        23.93        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A268 
       26.56        27.02        77.88         0.20        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS 
       39.58        12.62        50.10        21.37       357.04         6.67 
TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZO TCGA-WE-A8ZY 
       18.05         4.01       105.04        24.03        59.41        43.73 
TCGA-WE-AAA3 TCGA-YG-AA3O 
       10.36        36.03 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       12.99        16.67        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JH 
       95.74       103.10        65.49        23.77       168.00        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
       12.10       171.58        66.08       130.72        46.32       166.52 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A5GL TCGA-D3-A8GB 
       24.53       103.59        55.73        56.35       125.79        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
       79.59        11.61        15.19       228.99       170.20        95.24 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z1 
      161.00       117.17       151.53        54.67        18.12        11.34 
TCGA-D9-A6E9 TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG 
        9.90        20.38        23.44        28.60        15.68        68.25 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C 
       52.01         6.35        12.20        29.82        26.89       151.27 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A2A0 
       91.56        47.84        72.07        18.61        37.35        46.82 
TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
      102.90        67.43       314.56       161.03       208.04        54.74 
TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       79.66        14.30        44.88        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
       47.28       103.27       103.20       204.66        96.23       203.05 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-EE-A3J8 
      167.90       134.40        53.26       124.31        36.95        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35        51.35       109.58        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W 
        9.17        77.75        44.05       162.08        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A44A TCGA-FR-A7U9 
       79.99        31.27        32.05       247.04       174.21         7.00 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZP 
       38.27        94.39       228.59        28.08        48.85        74.73 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC 
      148.80        49.48        77.82       174.84        12.43        49.45 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       22.92         0.16        19.30         9.90         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-W3-A824 
      139.89        84.72        10.13        46.36        59.41       212.22 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-AA9Y 
      121.08        42.08       219.16        38.56        56.98         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3V 
       30.18        15.16        23.64        11.74 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JC 
      112.04       112.57        31.59        43.43       115.53        86.76 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC 
       62.07       113.52        56.19        59.57        58.06        86.93 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K 
       60.23         9.34        39.75        45.30       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       22.62        26.89       137.92       178.32        18.18       125.19 
TCGA-D3-A8GI TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       58.52        11.11        25.18        66.25        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
      117.21       176.55        35.93       107.34        53.92       215.44 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B 
       13.87        17.85        27.22         8.65        33.73       133.81 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       63.78        64.64        56.42       369.93       195.02        17.92 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       39.29        86.14        59.28        75.48        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK 
       13.91       129.27        28.83       268.73        16.96       158.63 
TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
      248.65         3.68        54.51        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19C 
      127.20       201.80       148.08        31.40        98.40        48.89 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19T 
       13.02       152.35         6.44       131.51        61.05         8.88 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A729 
       43.82        23.34        20.15        80.32         6.77       210.08 
TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.16        48.59        20.91         7.79       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY 
       40.27        15.45       101.26       133.55        11.41        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A4EO 
       50.14        66.67        28.73        26.73        47.54         7.23 
TCGA-GN-A264 TCGA-GN-A26A TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 
      117.93        32.48        65.88       294.77         0.33         0.69 
TCGA-W3-A825 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       63.02        54.38         8.61        90.28        52.34         3.75 
TCGA-WE-A8ZX TCGA-YG-AA3P TCGA-Z2-AA3S 
       22.68        14.43        93.07 

subtype1 subtype2 subtype3 
    0.20     0.16     0.33 
subtype1 subtype2 subtype3 
  357.04   314.56   369.93 
subtype1 subtype2 subtype3 
   46.98    51.68    54.38 
[1] "0.2 - 357.0 (47.0)" "0.2 - 314.6 (51.7)" "0.3 - 369.9 (54.4)"
D1V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 26             1
  subtype2                 14             1
  subtype3                 21             3
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        13                  54
  subtype2                                        29                  88
  subtype3                                        30                  67
D1V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              26       14       21
  PRIMARY TUMOR                                    1        1        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       13       29       30
  REGIONAL LYMPH NODE                             54       88       67
[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"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       2       6        5        9        3         4
  subtype2           5       3      15        6        9       10         6
  subtype3           6       2       7        6        9        9         4
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         4         4        11          4         11         18
  subtype2        10         2        11          4          9         23
  subtype3         5         6        13          7         12         17
          vv
clus       STAGE IV
  subtype1        4
  subtype2        5
  subtype3       10
D1V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        1        5        6
  STAGE 0            2        3        2
  STAGE I            6       15        7
  STAGE IA           5        6        6
  STAGE IB           9        9        9
  STAGE II           3       10        9
  STAGE IIA          4        6        4
  STAGE IIB          4       10        5
  STAGE IIC          4        2        6
  STAGE III         11       11       13
  STAGE IIIA         4        4        7
  STAGE IIIB        11        9       12
  STAGE IIIC        18       23       17
  STAGE IV           4        5       10
[1] 14  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       T0+T1 T2 T3 T4
  subtype1    19 20 19 21
  subtype2    19 25 32 25
  subtype3    25 26 23 21
D1V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       19       19       25
  T2          20       25       26
  T3          19       32       23
  T4          21       25       21
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 42 16 17 10
  subtype2 67 17 11 22
  subtype3 59 28 10 15
D1V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       42       67       59
  N1       16       17       28
  N2       17       11       10
  N3       10       22       15
[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"
          vv
clus        M0  M1 M1A M1B M1C
  subtype1  84   1   1   0   2
  subtype2 115   1   1   3   1
  subtype3 107   2   1   1   6
D1V8, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        84      115      107
  M1         1        1        2
  M1A        1        1        1
  M1B        0        3        1
  M1C        2        1        6
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus        0  1
  subtype1 38 27
  subtype2 50 31
  subtype3 41 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   27
  subtype2   50   31
  subtype3   41   29
     clus
vv    subtype1 subtype2 subtype3
  NO        38       50       41
  YES       27       31       29
[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"
D1V10, binary
          cls
clus         0   1
  subtype1  13  81
  subtype2  15 118
  subtype3  15 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   81
  subtype2   15  118
  subtype3   15  105
     clus
vv    subtype1 subtype2 subtype3
  NO        13       15       15
  YES       81      118      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"
D1V11, continuous
D1V12, binary
          cls
clus        0  1
  subtype1 37 57
  subtype2 43 90
  subtype3 51 70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   57
  subtype2   43   90
  subtype3   51   70
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       37       43       51
  MALE         57       90       70
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    88
  subtype2     1                         1   127
  subtype3     3                         0   111
D1V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        3
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                           88      127      111
[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"
D1V14, binary
          cls
clus         0   1
  subtype1   2  90
  subtype2   2 130
  subtype3   3 114
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   90
  subtype2    2  130
  subtype3    3  114
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        3
  NOT HISPANIC OR LATINO       90      130      114
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 51 62
  subtype2 81 50
  subtype3 37 51
subtype1 subtype2 subtype3 
     113      131       88 
subtype1 subtype2 subtype3 
      62       50       51 
$subtype1
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JG 
        3.02         8.52        22.55        45.83        44.19         7.50 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       92.42        15.25         6.31        26.37        93.21        54.31 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       32.61        25.78       110.24        52.01        47.87        17.72 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       23.11        22.06         4.18        38.93        75.65        87.62 
TCGA-D3-A8GR TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
        5.56        11.31        13.22        14.60        48.79        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EB-A5KH 
       39.19        36.69        25.15         6.64        13.15         0.13 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I 
       11.57         8.12         5.13         4.31         4.34         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q 
        7.99         9.90        36.85         1.08        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GJ 
        9.99         8.09        36.30        51.12        34.29        19.43 
TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       28.31        36.33        98.27       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       25.08        26.99        21.60         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI 
       15.95        12.72        22.92        21.60        16.14        33.60 
TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A2NE 
       31.40        38.40        11.11       114.15         4.21         1.51 
TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZA 
       18.41         2.20         4.70        64.47        11.01         7.30 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZZ 
       20.38        11.08         7.17        47.38         8.65         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC 
       53.85         3.22         7.36        28.73        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A8LK TCGA-OD-A75X 
        0.99        44.28        31.33        15.42        14.50        11.05 
TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8JZ 
       18.05         0.69       164.19         2.99        71.01        11.84 
TCGA-WE-A8K5 TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-Z2-AA3S 
        6.48         3.42         5.36         6.18         6.67 

$subtype2
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
        6.97         6.97        70.16       110.79        28.08        81.24 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       11.41        36.16         6.31        56.19        64.44        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F 
      114.67        46.32        82.29        24.00       103.59        54.74 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
       31.30        21.44        13.68        29.72        10.22        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      142.45       124.47        24.07         4.01        21.93         9.90 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 
       35.80        10.03         9.99        44.52        22.36        19.36 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
       17.56        14.83        23.15        13.35        13.22         0.20 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        1.12        12.20        15.85        37.97        62.79         8.55 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
       39.62         9.50        30.44         2.43        11.31        49.22 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       36.33        17.98        60.00        47.21        30.08        16.01 
TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       35.54        34.98         8.84         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MU 
       29.46        44.25         7.96        63.42        60.49         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
      124.31       122.73        21.60         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19H 
       21.73        18.61        12.95         5.72        76.41        34.88 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 
       78.44        12.62        11.74        85.74         6.71         5.36 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZH TCGA-FS-A1ZT 
       13.28         3.29        15.52         3.39        30.87        40.64 
TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       27.39        14.20         0.16        17.33         9.90         7.23 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-HR-A2OH 
       11.61        84.72        10.13        12.16        11.84        15.81 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A828 TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN 
        5.79         0.33        60.03       185.16         5.49        21.07 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3V 
       21.83         1.08        19.96        12.07         5.98 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       16.47       111.09        32.42        10.29        46.98        61.38 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51K TCGA-D3-A8GK TCGA-D3-A8GQ 
       13.32         9.34        29.23        32.28       108.79        11.44 
TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SH 
        5.72        13.68         4.93         7.00         0.20        19.00 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29D 
       10.55         6.31         1.35        60.23         9.21        11.15 
TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
        8.84        32.15         9.67        33.83        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MS 
        1.15        13.02         2.70         2.73        14.56        53.16 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-ER-A19B TCGA-ER-A19C 
       52.67        51.62         3.22        22.22        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND 
        3.52        11.90        13.45         6.58        11.80         1.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       13.08         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       15.72         3.58         3.45        23.80        14.24         7.33 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR 
        8.22        19.53        12.92        12.89        52.08         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
       49.15         8.68         0.82         5.98         2.27         0.20 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LL 
        0.13         0.85        16.24        14.70        10.65        14.50 
TCGA-LH-A9QB TCGA-W3-A825 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        0.43         8.98         7.10        18.67        13.12         3.72 
TCGA-WE-A8ZR TCGA-WE-AAA3 TCGA-YG-AA3P TCGA-Z2-A8RT 
        3.58         1.94         4.70         8.22 

subtype1 subtype2 subtype3 
    0.13     0.16     0.13 
subtype1 subtype2 subtype3 
  164.19   185.16   111.09 
subtype1 subtype2 subtype3 
   15.95    21.14    10.42 
[1] "0.1 - 164.2 (15.9)" "0.2 - 185.2 (21.1)" "0.1 - 111.1 (10.4)"
D2V2, survival
          sevent
clus2       0  1
  subtype1 52 63
  subtype2 85 50
  subtype3 37 51
subtype1 subtype2 subtype3 
     115      135       88 
subtype1 subtype2 subtype3 
      63       50       51 
$subtype1
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JG 
       17.03        16.67        31.59        90.90        62.07       113.52 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
      171.58        58.06        13.87        39.75       174.84       145.12 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       63.81        26.89       125.79       135.75       137.92        18.18 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
      125.19        79.59        58.52        89.13        95.24       137.79 
TCGA-D3-A8GR TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
      129.63         6.41        18.12        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IC 
       48.89       117.21       194.83        61.18        53.92        68.09 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 
       13.87        17.85        29.82        94.98        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L 
      151.27        13.55        63.35        80.61        64.64         2.60 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GB 
       56.42        37.35        55.92        17.92        36.82        59.28 
TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MK 
       67.43        89.33        75.48        94.82       129.27       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AD 
      203.05       167.90        47.54       248.65        43.23         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 
       54.51        13.81        23.47       138.81       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19F TCGA-ER-A19G 
       34.32       148.08        31.40        50.76        26.37       268.93 
TCGA-ER-A19J TCGA-ER-A2NE TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
        6.44        20.15        92.98        34.82        29.46       216.92 
TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM 
      228.59        27.72       357.37        15.45         9.70       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
      133.55        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
       12.43        49.45        22.92       139.89       117.93        62.79 
TCGA-GN-A8LK TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O 
       50.10       294.77        18.05         0.69       212.22         4.01 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-YG-AA3O 
      105.04        24.03        54.38         3.75        43.73        36.03 
TCGA-Z2-AA3S 
       93.07 

$subtype2
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       61.02        12.99        71.80       133.25        28.08        95.74 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       11.87        42.08        12.10        56.19        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F 
      130.72        46.32       166.52        24.53       103.59        55.73 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
       56.35        22.62       178.32        30.84        11.61        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      228.99       161.00       117.17       151.53        54.67         3.65 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I4 
       11.34        22.29         9.90        36.03        20.38        35.93 
TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG 
      107.34        23.44        28.60       215.44        15.68        68.25 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A183 
       17.29        52.01         6.35        12.20        33.73        26.89 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N 
       91.56        47.84        63.78        72.07        56.84        18.61 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD 
      369.93        25.87        46.82       102.90        86.14       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT 
      161.03       208.04        48.72        54.74        79.66        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       16.96        96.23       134.40        53.26       124.31       122.73 
TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 
       36.95       201.80        27.35        51.35       109.58        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N 
       13.94         9.17        77.75       152.35        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG 
      162.08        50.89        37.25       148.18        79.99        31.27 
TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE 
       32.05       174.21       210.08         7.00        38.27        94.39 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZH TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 
       28.08        48.85        32.75        53.16        49.48       174.84 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 
        0.16        19.30         9.90         7.23        11.74        84.72 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A693 
       10.13        32.48        46.36        65.88         6.67         0.33 
TCGA-W3-A828 TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZX TCGA-WE-AA9Y 
      121.08       219.16        38.56        56.98        22.68         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-AA3V 
       30.18        15.16        11.74 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       16.57       112.04       112.57        43.43        46.98        86.93 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51K TCGA-D3-A8GK TCGA-D3-A8GQ 
       60.23         9.34        45.30        32.94       170.20        29.06 
TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SH 
       11.11       176.55        65.92        10.49        10.16        54.02 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29D 
       27.22         8.65        14.70       133.81       168.26        13.97 
TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       14.47       195.02        39.29        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MS 
       14.30        55.59        28.83       268.73       204.66       162.48 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-ER-A19B TCGA-ER-A19C 
       71.21        51.62       172.18        53.19        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND 
       12.59        13.02       131.51         8.88        43.82        23.34 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       16.37       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       15.72        15.16        48.59       202.65        20.91         7.79 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR 
       53.52        40.27        47.38        23.93        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 
      148.80        26.56        27.09        26.73        77.88         0.20 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LL 
       47.54         2.04        64.44        39.58        12.62        21.37 
TCGA-LH-A9QB TCGA-W3-A825 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      357.04        63.02         8.61        90.28        59.41        52.34 
TCGA-WE-A8ZR TCGA-WE-AAA3 TCGA-YG-AA3P TCGA-Z2-A8RT 
        4.37        10.36        14.43        23.64 

subtype1 subtype2 subtype3 
    0.69     0.16     0.20 
subtype1 subtype2 subtype3 
  357.37   369.93   357.04 
subtype1 subtype2 subtype3 
  58.520   49.480   43.625 
[1] "0.7 - 357.4 (58.5)" "0.2 - 369.9 (49.5)" "0.2 - 357.0 (43.6)"
D2V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 24             2
  subtype2                 15             1
  subtype3                 21             2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        26                  66
  subtype2                                        25                  97
  subtype3                                        21                  45
D2V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              24       15       21
  PRIMARY TUMOR                                    2        1        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       26       25       21
  REGIONAL LYMPH NODE                             66       97       45
[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"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           6       3       9        9       10        4         6
  subtype2           5       2      13        6        9        7         4
  subtype3           1       2       6        1        8       10         4
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         9         6        10          8          8         14
  subtype2         3         1        18          5         14         28
  subtype3         7         5         7          2         10         17
          vv
clus       STAGE IV
  subtype1        7
  subtype2        8
  subtype3        4
D2V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        6        5        1
  STAGE 0            3        2        2
  STAGE I            9       13        6
  STAGE IA           9        6        1
  STAGE IB          10        9        8
  STAGE II           4        7       10
  STAGE IIA          6        4        4
  STAGE IIB          9        3        7
  STAGE IIC          6        1        5
  STAGE III         10       18        7
  STAGE IIIA         8        5        2
  STAGE IIIB         8       14       10
  STAGE IIIC        14       28       17
  STAGE IV           7        8        4
[1] 14  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       T0+T1 T2 T3 T4
  subtype1    23 23 23 25
  subtype2    32 25 30 20
  subtype3     7 23 20 23
D2V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       23       32        7
  T2          23       25       23
  T3          23       30       20
  T4          25       20       23
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 64 15 15 13
  subtype2 56 29 15 25
  subtype3 47 18  8  9
D2V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       64       56       47
  N1       15       29       18
  N2       15       15        8
  N3       13       25        9
[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"
          vv
clus        M0  M1 M1A M1B M1C
  subtype1 106   1   0   1   5
  subtype2 120   1   1   3   4
  subtype3  79   2   2   0   0
D2V8, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       106      120       79
  M1         1        1        2
  M1A        0        1        2
  M1B        1        3        0
  M1C        5        4        0
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus        0  1
  subtype1 50 33
  subtype2 53 28
  subtype3 23 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   33
  subtype2   53   28
  subtype3   23   27
     clus
vv    subtype1 subtype2 subtype3
  NO        50       53       23
  YES       33       28       27
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
          cls
clus         0   1
  subtype1  12 106
  subtype2  23 116
  subtype3   8  80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  106
  subtype2   23  116
  subtype3    8   80
     clus
vv    subtype1 subtype2 subtype3
  NO        12       23        8
  YES      106      116       80
[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"
D2V11, continuous
D2V12, binary
          cls
clus        0  1
  subtype1 40 78
  subtype2 52 87
  subtype3 37 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   78
  subtype2   52   87
  subtype3   37   52
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       40       52       37
  MALE         78       87       52
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0   112
  subtype2     1                         1   130
  subtype3     2                         0    81
D2V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        2
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                          112      130       81
[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"
D2V14, binary
          cls
clus         0   1
  subtype1   2 112
  subtype2   3 134
  subtype3   2  86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  112
  subtype2    3  134
  subtype3    2   86
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        3        2
  NOT HISPANIC OR LATINO      112      134       86
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 22 23
  subtype2 23 32
  subtype3 10 15
  subtype4 13 23
subtype1 subtype2 subtype3 subtype4 
      45       55       25       36 
subtype1 subtype2 subtype3 subtype4 
      23       32       15       23 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2JO TCGA-D3-A3CB 
       16.47        70.16       110.79         8.38        64.44        82.29 
TCGA-D3-A3MR TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A3F2 TCGA-DA-A3F3 
      103.59        10.03         9.99        25.15        19.36         7.00 
TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R 
       17.56        15.85        37.97        62.79         8.55         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GH TCGA-EE-A2GU 
        9.99        30.44        32.15        11.31        47.21        36.33 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU 
        8.84        47.51        14.56       111.91        26.99         5.56 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19M 
       27.35        21.73        76.41         3.52        11.90        28.60 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FS-A1ZA TCGA-GF-A3OT TCGA-GN-A265 
       17.72        12.62        11.74         7.30         9.90        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       10.13        16.24        12.16 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A3CE 
      111.09        32.42        28.08        22.55        45.83        13.32 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29P TCGA-EE-A2A2 
        6.31         9.34         8.12         4.34        12.03        36.30 
TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD 
       34.29        16.01        35.54        13.02        98.27         9.53 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS 
       63.42       125.65        56.02        25.08        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
       52.67        51.62        15.95         3.22        21.60        22.22 
TCGA-EE-A3JE TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A1A1 
       18.41         5.72        25.18       114.15         4.21        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YW 
       11.80         1.51        13.08         9.04         1.71        64.47 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
       23.80        14.24        15.52        20.38         8.22         7.17 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
       40.64         8.68         0.20        44.28        31.33        15.42 
TCGA-GN-A26D 
       14.70 

$subtype3
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1IA 
       81.24        10.29        11.41        29.23         4.01         4.93 
TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A185 TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GI 
        6.64        14.83         4.31         2.43        36.33        30.08 
TCGA-EE-A2M8 TCGA-EE-A3AD TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19Q 
        6.18         3.68         3.78        34.88        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       36.07         1.87         6.58        18.41        47.38         8.65 
TCGA-FW-A3TV 
        0.16 

$subtype4
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       86.76        56.19        59.57        48.79        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       13.68        44.52        22.36        11.57         1.12         1.35 
TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
        5.13         9.90        36.85         1.08        39.62         9.50 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE 
        5.42         1.15        34.98       124.31       122.73        30.15 
TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19F 
       13.81        31.40        18.61        12.95        38.40        11.11 
TCGA-ER-A19L TCGA-ER-A19N TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       13.45        42.84        30.87        12.92        12.89        52.08 

subtype1 subtype2 subtype3 subtype4 
    3.52     0.20     0.16     1.08 
subtype1 subtype2 subtype3 subtype4 
  111.91   125.65    81.24   124.31 
subtype1 subtype2 subtype3 subtype4 
  17.560   20.380    9.570   26.255 
[1] "3.5 - 111.9 (17.6)" "0.2 - 125.7 (20.4)" "0.2 - 81.2 (9.6)"  
[4] "1.1 - 124.3 (26.3)"
D3V2, survival
          sevent
clus2       0  1
  subtype1 22 23
  subtype2 25 33
  subtype3 11 15
  subtype4 13 23
subtype1 subtype2 subtype3 subtype4 
      45       58       26       36 
subtype1 subtype2 subtype3 subtype4 
      23       33       15       23 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2JO TCGA-D3-A3CB 
       16.57        71.80       133.25        65.49        66.08       166.52 
TCGA-D3-A3MR TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A3F2 TCGA-DA-A3F3 
      103.59        20.38        35.93        53.92        28.60        10.49 
TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R 
      215.44        91.56        47.84        63.78        72.07        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GH TCGA-EE-A2GU 
       55.92       369.93       195.02        46.82       208.04        94.82 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU 
       21.67        61.51       204.66       203.05       248.65        53.26 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19M 
       27.35       109.58        77.75        12.59        13.02        61.05 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FS-A1ZA TCGA-GF-A3OT TCGA-GN-A265 
      148.18        31.27        32.05        27.72         9.90        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       10.13        64.44        32.48 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A3CE 
      112.04       112.57        28.08        31.59        90.90        60.23 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-EE-A180 
       13.87         9.34       151.53        54.67         6.41        94.98 
TCGA-EE-A20C TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL 
      151.27        56.42        36.82        67.43        54.74        79.66 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       55.59       129.27        47.28        96.23       158.63       167.90 
TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG 
       47.54       134.40       162.48        71.21        51.62        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A199 TCGA-ER-A19B 
      172.18        64.08        53.19        51.35         9.17        98.40 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
      268.93         6.44        79.99        43.82        20.15        16.37 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      247.04        33.21       216.92       202.65        20.91        28.08 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FW-A3I3 
      357.37        53.52         9.70        53.16        26.56         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
      139.89       117.93        62.79        39.58 

$subtype3
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-D9-A1JW TCGA-D9-A3Z1 
       95.74        43.43        11.87        45.30         3.65        11.34 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A185 TCGA-EE-A29V TCGA-EE-A2A6 
       65.92        68.09        15.68         4.96        25.87        86.14 
TCGA-EE-A2GI TCGA-EE-A2M8 TCGA-EE-A3AD TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19P 
       48.72        19.76         3.68        48.89       152.35       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FS-A1ZM 
       50.89        37.25        23.34        80.32        92.98       101.26 
TCGA-FS-A1ZQ TCGA-FW-A3TV 
      133.55         0.16 

$subtype4
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       86.76        56.19        59.57        48.89        36.03       117.21 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
      176.55       107.34        23.44        29.82        33.73        14.70 
TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       68.15        80.61        64.64         2.60        56.84        18.61 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE 
       13.91        14.30        44.88       124.31       122.73        54.51 
TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19F 
       13.81        31.40        35.44        13.94        50.76        26.37 
TCGA-ER-A19L TCGA-ER-A19N TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
      131.51        44.05        32.75        47.38        23.93        74.73 

subtype1 subtype2 subtype3 subtype4 
    9.90     0.20     0.16     2.60 
subtype1 subtype2 subtype3 subtype4 
  369.93   357.37   162.08   176.55 
subtype1 subtype2 subtype3 subtype4 
  61.510   56.005   47.010   46.130 
[1] "9.9 - 369.9 (61.5)" "0.2 - 357.4 (56.0)" "0.2 - 162.1 (47.0)"
[4] "2.6 - 176.6 (46.1)"
D3V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  2             0
  subtype2                 11             1
  subtype3                  4             0
  subtype4                  5             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        14                  31
  subtype2                                        10                  36
  subtype3                                         5                  17
  subtype4                                         3                  29
D3V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                               2       11        4        5
  PRIMARY TUMOR                                    0        1        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       14       10        5        3
  REGIONAL LYMPH NODE                             31       36       17       29
[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"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           2       1       5        2        7        1         2
  subtype2           2       2       7        1        7        2         2
  subtype3           1       0       1        2        1        0         0
  subtype4           3       0       1        3        2        4         1
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         1         0         3          3          5          9
  subtype2         2         3         8          1          2          6
  subtype3         1         0         5          1          4          5
  subtype4         2         0         4          0          4          7
          vv
clus       STAGE IV
  subtype1        2
  subtype2        5
  subtype3        0
  subtype4        2
D3V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        2        2        1        3
  STAGE 0            1        2        0        0
  STAGE I            5        7        1        1
  STAGE IA           2        1        2        3
  STAGE IB           7        7        1        2
  STAGE II           1        2        0        4
  STAGE IIA          2        2        0        1
  STAGE IIB          1        2        1        2
  STAGE IIC          0        3        0        0
  STAGE III          3        8        5        4
  STAGE IIIA         3        1        1        0
  STAGE IIIB         5        2        4        4
  STAGE IIIC         9        6        5        7
  STAGE IV           2        5        0        2
[1] 14  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       T0+T1 T2 T3 T4
  subtype1     8 12 10  9
  subtype2     9 13  7 13
  subtype3     7  7  5  2
  subtype4    12  5  6  7
D3V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        8        9        7       12
  T2          12       13        7        5
  T3          10        7        5        6
  T4           9       13        2        7
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 22  7  6  8
  subtype2 36  6  6  6
  subtype3  8  6  7  3
  subtype4 19  5  7  4
D3V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       22       36        8       19
  N1        7        6        6        5
  N2        6        6        7        7
  N3        8        6        3        4
[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"
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 42  1   1   0   0
  subtype2 48  3   1   2   0
  subtype3 25  0   0   0   0
  subtype4 34  0   0   0   2
D3V8, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        42       48       25       34
  M1         1        3        0        0
  M1A        1        1        0        0
  M1B        0        2        0        0
  M1C        0        0        0        2
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
          cls
clus        0  1
  subtype1 21  7
  subtype2 23 15
  subtype3 11  5
  subtype4 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    7
  subtype2   23   15
  subtype3   11    5
  subtype4   10   10
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        21       23       11       10
  YES        7       15        5       10
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
          cls
clus        0  1
  subtype1  6 41
  subtype2  8 50
  subtype3  3 23
  subtype4  8 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   41
  subtype2    8   50
  subtype3    3   23
  subtype4    8   30
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6        8        3        8
  YES       41       50       23       30
[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"
D3V11, continuous
D3V12, binary
          cls
clus        0  1
  subtype1 17 30
  subtype2 20 38
  subtype3 11 15
  subtype4 16 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   30
  subtype2   20   38
  subtype3   11   15
  subtype4   16   22
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17       20       11       16
  MALE         30       38       15       22
[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       WHITE
  subtype1    47
  subtype2    58
  subtype3    26
  subtype4    38
[1] "NOT AVAILABLE: table dimension [4x1]"
D3V14, binary
          cls
clus        0
  subtype1 47
  subtype2 58
  subtype3 26
  subtype4 37
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 11 14
  subtype2 26 31
  subtype3 12 22
  subtype4 19 26
subtype1 subtype2 subtype3 subtype4 
      25       57       34       45 
subtype1 subtype2 subtype3 subtype4 
      14       31       22       26 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A3F2 
       16.47        70.16         8.38        10.03         9.99        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        7.00        17.56         1.35        37.97        62.79         8.55 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GP TCGA-EE-A2M5 
        8.84         2.43        32.15        11.31         5.42         8.84 
TCGA-EE-A2MC TCGA-EE-A2MU TCGA-EE-A3JH TCGA-ER-A19A TCGA-GF-A3OT TCGA-GN-A265 
       47.51         5.56        21.73        76.41         9.90        84.72 
TCGA-GN-A267 
       16.24 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A3CE 
      111.09       110.79        28.08        86.76        64.44        13.32 
TCGA-D3-A3MO TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-EE-A29B TCGA-EE-A29P 
        9.34        48.79        51.12        25.15         9.90        12.03 
TCGA-EE-A2A2 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       36.30        16.01        35.54        34.98        36.33        98.27 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA 
       14.56       125.65        56.02        25.08        60.49       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J7 
      122.73        51.62        30.15        13.81        15.95        21.60 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
       22.22        27.35        31.40         5.72        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 
       11.90        11.11       114.15         4.21        42.84        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       11.80         1.51        13.08         9.04        23.80        15.52 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GN-A264 
        7.30        20.38         8.22        40.64         8.68        31.33 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
       10.13        15.42        14.70 

$subtype3
TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3ML 
       32.42        81.24        56.19        59.57        82.29         6.31 
TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A181 
        4.01        35.80        13.68        22.36        14.83         1.12 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
        5.13         4.34        15.85        36.85        39.62         9.50 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2GR TCGA-EE-A2M8 TCGA-ER-A195 TCGA-ER-A197 
        9.99        30.44         1.15         6.18        18.61        12.95 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3ET 
       34.88        13.45        28.60        17.72        12.62         6.58 
TCGA-FR-A3YN TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       18.41        30.87        12.92        52.08 

$subtype4
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MR TCGA-D3-A3MV 
       22.55        45.83        10.29        11.41       103.59        29.23 
TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A185 
       44.52         4.93         6.64        11.57         8.12         4.31 
TCGA-EE-A29L TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GS 
        1.08        36.33        34.29        47.21        30.08        13.02 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
        9.53        63.42       111.91        26.99        53.16        52.67 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19P 
        3.68         3.22        18.41        38.40         3.78        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FS-A1YW 
        9.57        36.07         1.87        11.74         1.71        64.47 
TCGA-FS-A1Z3 TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3I3 
       14.24         7.17        12.89        47.38         8.65         0.20 
TCGA-FW-A3TV TCGA-GN-A262 TCGA-GN-A26A 
        0.16        44.28        12.16 

subtype1 subtype2 subtype3 subtype4 
    1.35     1.51     1.12     0.16 
subtype1 subtype2 subtype3 subtype4 
   84.72   125.65    82.29   111.91 
subtype1 subtype2 subtype3 subtype4 
  11.310   25.080   16.785   13.020 
[1] "1.4 - 84.7 (11.3)"  "1.5 - 125.7 (25.1)" "1.1 - 82.3 (16.8)" 
[4] "0.2 - 111.9 (13.0)"
D4V2, survival
          sevent
clus2       0  1
  subtype1 11 14
  subtype2 26 31
  subtype3 12 22
  subtype4 22 27
subtype1 subtype2 subtype3 subtype4 
      25       57       34       49 
subtype1 subtype2 subtype3 subtype4 
      14       31       22       27 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A3F2 
       16.57        71.80        65.49        20.38        35.93        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       10.49       215.44        14.70        47.84        63.78        72.07 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GP TCGA-EE-A2M5 
       14.47        25.87       195.02        46.82        13.91        21.67 
TCGA-EE-A2MC TCGA-EE-A2MU TCGA-EE-A3JH TCGA-ER-A19A TCGA-GF-A3OT TCGA-GN-A265 
       61.51        53.26       109.58        77.75         9.90        84.72 
TCGA-GN-A267 
       64.44 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A3CE 
      112.04       133.25        28.08        86.76        66.08        60.23 
TCGA-D3-A3MO TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-EE-A29B TCGA-EE-A29P 
        9.34        48.89       117.21        53.92        80.61        56.42 
TCGA-EE-A2A2 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       36.82        54.74        79.66        44.88        94.82       129.27 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA 
      204.66       158.63       167.90        47.54       134.40       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J7 
      122.73        51.62        54.51        13.81        23.47        64.08 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
       53.19        27.35        31.40         9.17        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 
       13.02        26.37       268.93         6.44        44.05        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       43.82        20.15        16.37       247.04       202.65        28.08 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GN-A264 
       27.72       357.37        53.52        53.16        26.56       117.93 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
       10.13        62.79        39.58 

$subtype3
TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3ML 
      112.57        95.74        56.19        59.57       166.52        13.87 
TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A181 
       11.34        36.03       176.55        23.44        15.68        33.73 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       68.15       151.27        91.56        64.64        56.84        18.61 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2GR TCGA-EE-A2M8 TCGA-ER-A195 TCGA-ER-A197 
       55.92       369.93        14.30        19.76        35.44        13.94 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3ET 
      152.35       131.51        61.05       148.18        31.27        80.32 
TCGA-FR-A3YN TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       92.98        32.75        47.38        74.73 

$subtype4
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MR TCGA-D3-A3MV 
       31.59        90.90        43.43        11.87       103.59        45.30 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-DA-A1I5 TCGA-DA-A1IA 
      151.53        54.67         3.65         6.41       107.34        65.92 
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A2A6 
       68.09        29.82        94.98         4.96         2.60        86.14 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2MJ 
       67.43       208.04        48.72        55.59        47.28        96.23 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3J3 
      203.05       248.65       162.48        71.21         3.68       172.18 
TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       51.35        50.76        48.89       162.08        50.89        37.25 
TCGA-ER-A2ND TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZG 
       23.34        32.05        33.21       216.92        20.91         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GN-A262 
       23.93       101.26       133.55         0.20         0.16       139.89 
TCGA-GN-A26A 
       32.48 

subtype1 subtype2 subtype3 subtype4 
    9.90     6.44    11.34     0.16 
subtype1 subtype2 subtype3 subtype4 
  215.44   357.37   369.93   248.65 
subtype1 subtype2 subtype3 subtype4 
  47.840   53.920   58.205   50.890 
[1] "9.9 - 215.4 (47.8)"  "6.4 - 357.4 (53.9)"  "11.3 - 369.9 (58.2)"
[4] "0.2 - 248.7 (50.9)" 
D4V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  3             0
  subtype2                  9             1
  subtype3                  2             0
  subtype4                  8             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                         8                  16
  subtype2                                         8                  40
  subtype3                                         4                  28
  subtype4                                        12                  29
D4V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                               3        9        2        8
  PRIMARY TUMOR                                    0        1        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE        8        8        4       12
  REGIONAL LYMPH NODE                             16       40       28       29
[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"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       1       2        1        3        0         1
  subtype2           2       1       7        3        5        0         3
  subtype3           4       1       2        1        4        3         1
  subtype4           1       0       3        3        5        4         0
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0         0         1          2          5          7
  subtype2         4         3        10          0          2          9
  subtype3         0         0         3          2          3          5
  subtype4         2         0         6          1          5          6
          vv
clus       STAGE IV
  subtype1        2
  subtype2        2
  subtype3        1
  subtype4        4
D4V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        1        2        4        1
  STAGE 0            1        1        1        0
  STAGE I            2        7        2        3
  STAGE IA           1        3        1        3
  STAGE IB           3        5        4        5
  STAGE II           0        0        3        4
  STAGE IIA          1        3        1        0
  STAGE IIB          0        4        0        2
  STAGE IIC          0        3        0        0
  STAGE III          1       10        3        6
  STAGE IIIA         2        0        2        1
  STAGE IIIB         5        2        3        5
  STAGE IIIC         7        9        5        6
  STAGE IV           2        2        1        4
[1] 14  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       T0+T1 T2 T3 T4
  subtype1     4  6  7  7
  subtype2    16 12  4 11
  subtype3     6  9  8  3
  subtype4    10 10  9 10
D4V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        4       16        6       10
  T2           6       12        9       10
  T3           7        4        8        9
  T4           7       11        3       10
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 10  8  4  4
  subtype2 32  4  9  9
  subtype3 18  5  6  3
  subtype4 25  7  7  5
D4V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       10       32       18       25
  N1        8        4        5        7
  N2        4        9        6        7
  N3        4        9        3        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 24  1   1   0   0
  subtype2 51  1   0   1   0
  subtype3 32  0   0   0   1
  subtype4 42  2   1   1   1
D4V8, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        24       51       32       42
  M1         1        1        0        2
  M1A        1        0        0        1
  M1B        0        1        0        1
  M1C        0        0        1        1
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
          cls
clus        0  1
  subtype1 11  6
  subtype2 19 14
  subtype3 12  5
  subtype4 23 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    6
  subtype2   19   14
  subtype3   12    5
  subtype4   23   12
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        11       19       12       23
  YES        6       14        5       12
[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"
D4V10, binary
          cls
clus        0  1
  subtype1  3 24
  subtype2 14 44
  subtype3  3 32
  subtype4  5 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   24
  subtype2   14   44
  subtype3    3   32
  subtype4    5   44
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3       14        3        5
  YES       24       44       32       44
[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"
D4V11, continuous
D4V12, binary
          cls
clus        0  1
  subtype1  6 21
  subtype2 25 33
  subtype3 15 20
  subtype4 18 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   21
  subtype2   25   33
  subtype3   15   20
  subtype4   18   31
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6       25       15       18
  MALE         21       33       20       31
[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       WHITE
  subtype1    27
  subtype2    58
  subtype3    35
  subtype4    49
[1] "NOT AVAILABLE: table dimension [4x1]"
D4V14, binary
          cls
clus        0
  subtype1 27
  subtype2 58
  subtype3 35
  subtype4 48
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 56 71
  subtype2 64 32
  subtype3 49 61
subtype1 subtype2 subtype3 
     127       96      110 
subtype1 subtype2 subtype3 
      71       32       61 
$subtype1
TCGA-3N-A9WB TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD 
        3.02        22.55        45.83        81.24        10.29        11.41 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU 
        7.50         6.31       114.67        61.38         6.31        26.37 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GK 
       93.21        32.28       110.24        22.06         4.18       108.79 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       38.93        75.65        87.62         5.56         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
        5.72         9.90        11.31        13.22        14.60        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EB-A44R 
       10.03         9.99         4.93         6.64        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z 
        0.13        19.00        13.35        13.22        11.57         6.31 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20I 
        8.12         1.35        12.20         5.13         4.31         1.18 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        9.90        37.97        11.15        62.79        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GR 
       39.62         2.43         8.09        51.12        28.31         1.15 
TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AC 
       36.33         9.53        25.08        21.60        52.67        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 
        3.68        13.81        22.92        33.60        12.95        38.40 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE 
        3.78        11.11         9.57         6.58         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A7U8 
       13.08        12.62         9.04        22.49        18.41         3.58 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
        4.70        64.47        11.01         3.39        19.53         7.17 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       12.92        12.89         8.65         8.68         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        3.22         7.36        10.78         0.99         0.13         0.16 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A8LL 
       31.33        16.24        15.42        14.70        14.50        14.50 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA21 
        5.79        18.05         0.69       164.19         2.99        71.01 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZX 
        5.49         6.48        21.07        13.12         3.58        21.83 
TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
        5.36         1.94        12.07         6.18         4.70         6.67 
TCGA-Z2-AA3V 
        5.98 

$subtype2
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 
        6.97         6.97         8.52       110.79        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO 
       21.14        68.22        44.19        36.16        92.42        64.44 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H 
       46.32        82.29        24.00       103.59        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GJ 
       54.31        25.78        47.87        29.72        10.22       142.45 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IB 
      124.47        24.07        48.79        39.19        44.52        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A20F 
       19.36        14.83        23.15         0.20         1.12        15.85 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.50        12.03         9.99        11.31        49.22        36.30 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       36.33        34.29        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       35.54        34.98         6.18        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
        7.96        63.42       111.91        60.49         5.56       124.31 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       30.15        21.60        22.22        27.35        18.41        21.73 
TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A19P 
       31.40         5.72        76.41       114.15        42.84        34.68 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 
       36.07        17.72        78.44        11.74        85.74         6.71 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZT TCGA-FS-A1ZW 
        5.36        13.28         3.29        15.52        40.64        27.39 
TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A4U8 
       14.20        17.33         7.23        11.61        84.72        11.84 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A693 TCGA-W3-AA1W TCGA-WE-AAA0 TCGA-Z2-A8RT 
       14.50        15.81         0.33       185.16        19.96         8.22 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2JA 
       16.47       111.09        32.42        70.16        28.08        88.50 
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
       86.76        56.19        59.57        15.25        46.98        13.32 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
        9.34        29.23        21.44        32.61        52.01        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GE TCGA-D3-A8GQ TCGA-DA-A1HY TCGA-DA-A1I2 
       17.72        23.11        15.19        11.44        51.12        13.68 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B 
       36.69        25.15         7.00        17.56        10.55        60.23 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R 
        4.34         9.21         7.99         8.55         8.09         8.84 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GN 
       30.44        32.15         9.67        17.98        60.00        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.69         5.42        13.02         8.84        98.27         2.70 
TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       47.51        14.56       125.65        56.02        26.99        53.16 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
      122.73        15.95        12.72         3.22        21.60        16.14 
TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
        0.95        18.61        25.18         3.52        11.90        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3PL 
        4.21        13.45        28.60        11.80         6.58         1.71 
TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.62        15.72         2.20         3.45        23.80        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.33         7.30        20.38         8.22        11.08        30.87 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A4F5 
       47.38        52.08         8.81        49.15         0.82        28.73 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A3OT TCGA-GF-A6C8 
        5.98         6.41         2.27         0.20         9.90         0.85 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-LH-A9QB TCGA-OD-A75X 
       44.28        10.13        12.16        10.65         0.43        11.05 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
        8.98        10.98        11.84         7.10        18.67         3.72 
TCGA-WE-A8ZT TCGA-WE-AA9Y 
        3.42         1.08 

subtype1 subtype2 subtype3 
    0.13     0.20     0.20 
subtype1 subtype2 subtype3 
  164.19   185.16   125.65 
subtype1 subtype2 subtype3 
  11.310   26.565   13.960 
[1] "0.1 - 164.2 (11.3)" "0.2 - 185.2 (26.6)" "0.2 - 125.7 (14.0)"
D5V2, survival
          sevent
clus2       0  1
  subtype1 59 71
  subtype2 66 33
  subtype3 49 61
subtype1 subtype2 subtype3 
     130       99      110 
subtype1 subtype2 subtype3 
      71       33       61 
$subtype1
TCGA-3N-A9WB TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD 
       17.03        31.59        90.90        95.74        43.43        11.87 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU 
      113.52        12.10       130.72        86.93        13.87        39.75 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GK 
      174.84        32.94       125.79        79.59        58.52       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1JW 
       89.13        95.24       137.79       129.63       151.53         3.65 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       18.12        11.34        22.29        11.11         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IA 
       66.25        22.95        36.03        20.38        35.93        65.92 
TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL 
       68.09        13.87        10.16        17.85        54.02        17.29 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       52.01        29.82         8.65        94.98        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       68.15         4.96        13.55        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A29X 
       63.78        64.64         2.60        56.84        25.87        17.92 
TCGA-EE-A2GB TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MN 
       59.28        75.48        14.30        94.82        47.28        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
       43.23        71.21        51.62         3.68        13.81       127.20 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19Q 
      148.08        13.94        50.76        48.89        26.37        50.89 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
        8.88        23.34        20.15        16.37        31.27       247.04 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY 
       46.98        92.98        15.16        29.46       216.92       228.59 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ 
       48.85        40.27         9.70        47.38        23.93       133.55 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F9 
       26.56        27.02        77.82        50.14        66.67        12.43 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       22.92        47.54         0.16       117.93        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A8LL TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 
       39.58        50.10        21.37         6.67        18.05         0.69 
TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
      212.22         4.01       105.04        38.56        54.38        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 
       59.41         4.37        22.68        43.73        10.36        15.16 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        93.07        11.74 

$subtype2
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 
       61.02        12.99        16.67       133.25       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO 
       23.77       168.00        62.07        42.08       171.58        66.08 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H 
       46.32       166.52        24.53       103.59        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GJ 
      145.12        26.89       137.92        30.84        11.61       228.99 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX TCGA-DA-A1HV TCGA-DA-A1I1 
      161.00       117.17        54.67         6.41        48.89       194.83 
TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5VV 
      107.34        23.44        28.60        15.68        68.25         6.35 
TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       12.20        33.73        91.56        18.61        56.42        55.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH 
       46.82       102.90        36.82        86.14        67.43       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M8 
       48.72        89.33        54.74        79.66        44.88        19.76 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML 
      103.27       268.73       103.20        16.96        96.23       203.05 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA 
      134.40        53.26       124.31        54.51        36.95        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19A 
       27.35        51.35       109.58        31.40         9.17        77.75 
TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
      268.93        44.05       162.08        37.25       148.18        79.99 
TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE 
       32.05       174.21       210.08         7.00        38.27        94.39 
TCGA-FS-A1Z4 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO 
       28.08        53.16        49.48       174.84        19.30         7.23 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A693 
       11.74        84.72        46.36        59.41        65.88         0.33 
TCGA-W3-AA1W TCGA-WE-AAA0 TCGA-Z2-A8RT 
      219.16        30.18        23.64 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2JA 
       16.57       112.04       112.57        71.80        28.08       115.53 
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
       86.76        56.19        59.57        58.06        46.98        60.23 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
        9.34        45.30        22.62        63.81       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GE TCGA-D3-A8GQ TCGA-DA-A1HY TCGA-DA-A1I2 
       18.18       125.19        15.19        29.06       117.21       176.55 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B 
       61.18        53.92        10.49       215.44        27.22       133.81 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R 
      151.27       168.26        63.35        72.07        37.35        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GN 
      369.93       195.02        39.29       314.56       161.03        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      126.81        13.91        55.59        21.67       129.27        28.83 
TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS 
       61.51       204.66       158.63       167.90       248.65       162.48 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
      122.73        23.47       138.81       172.18        64.08        34.32 
TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
      201.80        35.44        98.40        12.59        13.02       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A3ET TCGA-ER-A3PL 
        6.44       131.51        61.05        43.82        80.32        33.21 
TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        6.77        15.72        34.82        48.59       202.65        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.79        27.72       357.37        53.52        15.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A4F5 
      101.26        74.73        11.41       148.80        27.09        28.73 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A3OT TCGA-GF-A6C8 
       26.73        49.45        77.88         0.20         9.90         2.04 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-LH-A9QB TCGA-OD-A75X 
      139.89        10.13        32.48        12.62       357.04       294.77 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       63.02        42.08        24.03         8.61        90.28        52.34 
TCGA-WE-A8ZT TCGA-WE-AA9Y 
        3.75         2.20 

subtype1 subtype2 subtype3 
    0.16     0.33     0.20 
subtype1 subtype2 subtype3 
  247.04   268.93   369.93 
subtype1 subtype2 subtype3 
  40.010   55.730   57.125 
[1] "0.2 - 247.0 (40.0)" "0.3 - 268.9 (55.7)" "0.2 - 369.9 (57.1)"
D5V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 30             5
  subtype2                 12             0
  subtype3                 18             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        21                  75
  subtype2                                        14                  74
  subtype3                                        37                  61
D5V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              30       12       18
  PRIMARY TUMOR                                    5        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       21       14       37
  REGIONAL LYMPH NODE                             75       74       61
[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"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           3       3       6        7       10        5         4
  subtype2           4       1      11        9        7        6         5
  subtype3           5       3      11        1       10       10         5
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1        10         9        12          8         13         26
  subtype2         3         2        10          1         10         18
  subtype3         6         1        13          6          9         15
          vv
clus       STAGE IV
  subtype1        6
  subtype2        3
  subtype3       10
D5V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        3        4        5
  STAGE 0            3        1        3
  STAGE I            6       11       11
  STAGE IA           7        9        1
  STAGE IB          10        7       10
  STAGE II           5        6       10
  STAGE IIA          4        5        5
  STAGE IIB         10        3        6
  STAGE IIC          9        2        1
  STAGE III         12       10       13
  STAGE IIIA         8        1        6
  STAGE IIIB        13       10        9
  STAGE IIIC        26       18       15
  STAGE IV           6        3       10
[1] 14  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       T0+T1 T2 T3 T4
  subtype1    19 23 26 38
  subtype2    25 17 21 15
  subtype3    19 31 26 15
D5V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       19       25       19
  T2          23       17       31
  T3          26       21       26
  T4          38       15       15
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 56 23 19 20
  subtype2 52 17  7 13
  subtype3 59 22 12 14
D5V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       56       52       59
  N1       23       17       22
  N2       19        7       12
  N3       20       13       14
[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"
          vv
clus        M0  M1 M1A M1B M1C
  subtype1 118   0   2   1   4
  subtype2  89   1   0   0   2
  subtype3  99   3   1   3   3
D5V8, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       118       89       99
  M1         0        1        3
  M1A        2        0        1
  M1B        1        0        3
  M1C        4        2        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
          cls
clus        0  1
  subtype1 55 41
  subtype2 42 22
  subtype3 32 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55   41
  subtype2   42   22
  subtype3   32   25
     clus
vv    subtype1 subtype2 subtype3
  NO        55       42       32
  YES       41       22       25
[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"
D5V10, binary
          cls
clus         0   1
  subtype1  11 121
  subtype2  15  85
  subtype3  17  98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11  121
  subtype2   15   85
  subtype3   17   98
     clus
vv    subtype1 subtype2 subtype3
  NO        11       15       17
  YES      121       85       98
[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"
D5V11, continuous
D5V12, binary
          cls
clus        0  1
  subtype1 44 88
  subtype2 38 62
  subtype3 49 67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   88
  subtype2   38   62
  subtype3   49   67
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       44       38       49
  MALE         88       62       67
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         0   120
  subtype2     1                         1    96
  subtype3     1                         0   109
D5V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        1        1
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                          120       96      109
[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"
D5V14, binary
          cls
clus         0   1
  subtype1   5 125
  subtype2   0  99
  subtype3   2 110
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  125
  subtype2    0   99
  subtype3    2  110
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        0        2
  NOT HISPANIC OR LATINO      125       99      110
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 38 60
  subtype2 92 59
  subtype3 39 45
subtype1 subtype2 subtype3 
      98      151       84 
subtype1 subtype2 subtype3 
      60       59       45 
$subtype1
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JK 
        3.02         6.97        16.47        10.29         7.50         6.31 
TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GU 
       61.38         6.31        26.37        32.28       110.24        23.11 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
       22.06         4.18       108.79        38.93        87.62         5.56 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I4 TCGA-DA-A1IA 
        5.72        11.31        13.22        14.60         9.99         4.93 
TCGA-DA-A1IC TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
        6.64         0.20         0.13        19.00        13.22        11.57 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A29B TCGA-EE-A29C 
        6.31         8.12         1.35         4.31         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29V 
       11.15        62.79         8.55         1.08         8.09         2.43 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF 
       28.31        33.83         1.15        52.67         3.68        13.81 
TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19T TCGA-ER-A2ND 
       21.60        12.95         3.78         4.21         6.58         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 
        1.51        13.08         9.04         6.58        22.49         3.58 
TCGA-FR-A8YD TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
        4.70        11.01        14.24         3.39        19.53         7.17 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU 
       12.92        12.89        52.08         8.65         8.81         8.68 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F9 
        0.82         5.23        53.85         3.22        28.73        10.78 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A264 
        6.41         2.27         0.20         0.99         0.13        31.33 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A8LL TCGA-OD-A75X 
       16.24        15.42        14.70        14.50        14.50        11.05 
TCGA-W3-AA1O TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
        2.99         3.58         5.36         1.08         1.94         6.18 
TCGA-YG-AA3P TCGA-Z2-AA3V 
        4.70         5.98 

$subtype2
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
        6.97         8.52       110.79        22.55        45.83        81.24 
TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH 
       85.32        21.14        68.22        11.41        44.19        36.16 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
       92.42        64.44        59.57       114.67        46.32        82.29 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       24.00       103.59        93.21        54.74        31.30        54.31 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM 
       25.78        47.87        29.72        10.22       142.45        75.65 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV 
      124.47        24.07         4.01        21.93         9.90        48.79 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB 
       35.80        10.03        39.19        13.68        44.52        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UL 
       19.36         7.00        14.83        13.15        23.15        13.35 
TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A20I 
        0.20         1.12        12.20         5.13        15.85         1.18 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T 
       36.85        39.62         9.50        12.03         9.99        30.44 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        36.30        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MD 
       35.54         5.42        34.98        36.33         6.18         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML 
       29.46         2.73        44.25         7.96        63.42       111.91 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       25.08        21.60        60.49         5.56       124.31        51.62 
TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
       30.15         3.22        22.92        21.60        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 
       18.41        21.73        33.60        31.40        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       76.41        11.11       114.15        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH 
        9.57        36.07        17.72        78.44        12.62        11.74 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC 
        1.71        18.41        85.74         6.71        13.28         2.20 
TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FS-A4F8 
       64.47        15.52        40.64        27.39         7.36        14.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A4U8 
        0.16        17.33         7.23        11.61        84.72        11.84 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
       14.50        15.81         5.79        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
      164.19       185.16        71.01        11.84         5.49         6.48 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT 
       21.07        13.12        21.83        19.96        12.07         8.22 
TCGA-Z2-AA3S 
        6.67 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2JA 
      111.09        32.42        70.16        28.08         8.38        88.50 
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MO 
       86.76        56.19        15.25        46.98        13.32         9.34 
TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       29.23        21.44        32.61        52.01        13.68        17.72 
TCGA-D3-A8GE TCGA-D3-A8GQ TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       15.19        11.44        51.12        36.69        25.15        17.56 
TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29R 
       10.55        60.23         4.34         9.21         7.99         8.84 
TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M5 
       32.15         9.67        60.00        55.69        13.02         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
       98.27         2.70        47.51        14.56       125.65        56.02 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J8 
       26.99        53.16       122.73        15.95        12.72        16.14 
TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
        0.95        18.61        25.18         3.52        11.90        34.88 
TCGA-ER-A19L TCGA-ER-A2NC TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE 
       13.45        11.80         5.62        15.72         5.36         3.29 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
        3.45        23.80         7.33         7.30        20.38         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A4FB TCGA-GF-A3OT 
       11.08        30.87        47.38        49.15         5.98         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-LH-A9QB 
        0.85        44.28        10.13        12.16        10.65         0.43 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.98        10.98         7.10        18.67         3.72         3.42 

subtype1 subtype2 subtype3 
    0.13     0.16     0.43 
subtype1 subtype2 subtype3 
  110.24   185.16   125.65 
subtype1 subtype2 subtype3 
   8.665   22.220   15.220 
[1] "0.1 - 110.2 (8.7)"  "0.2 - 185.2 (22.2)" "0.4 - 125.7 (15.2)"
D6V2, survival
          sevent
clus2       0  1
  subtype1 39 60
  subtype2 96 60
  subtype3 39 45
subtype1 subtype2 subtype3 
      99      156       84 
subtype1 subtype2 subtype3 
      60       60       45 
$subtype1
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JK 
       17.03        12.99        16.57        43.43       113.52        12.10 
TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GU 
       86.93        13.87        39.75        32.94       125.79       125.19 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
       79.59        58.52       170.20        89.13       137.79       129.63 
TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I4 
       18.12        11.11        25.18        66.25        22.95        35.93 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN 
       65.92        68.09        10.16        17.85        54.02        52.01 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A29B 
       29.82         8.65        94.98        14.70         4.96        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29Q 
       47.84        13.97        63.78        72.07         2.60        37.35 
TCGA-EE-A29V TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MT TCGA-EE-A3AD 
       25.87        75.48        90.97        14.30        71.21         3.68 
TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19T 
       13.81        64.08        13.94        48.89         6.44         8.88 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       23.34        20.15        16.37       247.04        80.32        46.98 
TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE 
       15.16        29.46       228.59        20.91        48.85        40.27 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        47.38        23.93        74.73       133.55        11.41 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 
       26.56        27.09        27.02        77.82        50.14        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        49.45        77.88         0.20        22.92        47.54 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A8LL 
      117.93        64.44        62.79        39.58        50.10        21.37 
TCGA-OD-A75X TCGA-W3-AA1O TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 
      294.77         4.01         4.37        43.73         2.20        10.36 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3V 
       36.03        14.43        11.74 

$subtype2
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       61.02        16.67       133.25        31.59        90.90        95.74 
TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH 
      103.10        23.77       168.00        11.87        62.07        42.08 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
      171.58        66.08        59.57       130.72        46.32       166.52 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       24.53       103.59       174.84        55.73        56.35       145.12 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GM 
       26.89       137.92        30.84        11.61       228.99        95.24 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      161.00       117.17       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
       11.34        22.29         9.90        48.89        36.03        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
      194.83       176.55       107.34        23.44        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 
       15.68        13.87        68.25        17.29         6.35        12.20 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29H 
       33.73        26.89        68.15        91.56        13.55        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
       56.84        18.61        56.42        55.92       369.93        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       13.91        44.88        94.82        19.76        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      268.73       103.20        16.96        96.23       203.05        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
       43.23       134.40        53.26       124.31        51.62        54.51 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      172.18       127.20        36.95        53.19        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      109.58       148.08        31.40        50.76         9.17        77.75 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       26.37       268.93        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3PL 
       37.25       148.18        79.99        31.27        32.05        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YW 
       92.98       174.21       210.08        38.27        34.82       216.92 
TCGA-FS-A1Z4 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FW-A3TV 
       28.08        53.16        49.48        66.67       174.84         0.16 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A4U8 TCGA-GN-A9SD 
       19.30         7.23        11.74        84.72        46.36        59.41 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       65.88         6.67        18.05         0.33         0.69       212.22 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
      219.16       105.04        24.03        38.56        54.38        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S 
       59.41        22.68        30.18        15.16        23.64        93.07 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2JA 
      112.04       112.57        71.80        28.08        65.49       115.53 
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MO 
       86.76        56.19        58.06        46.98        60.23         9.34 
TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       45.30        22.62        63.81       135.75       178.32        18.18 
TCGA-D3-A8GE TCGA-D3-A8GQ TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       15.19        29.06       117.21        61.18        53.92       215.44 
TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29R 
       27.22       133.81       151.27       168.26        63.35        14.47 
TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GE TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M5 
      195.02        39.29       161.03       126.81        55.59        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM 
      129.27        28.83        61.51       204.66       158.63       167.90 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J8 
      248.65       162.48       122.73        23.47       138.81        34.32 
TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
      201.80        35.44        98.40        12.59        13.02       152.35 
TCGA-ER-A19L TCGA-ER-A2NC TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE 
      131.51        43.82         6.77        15.72         7.00        94.39 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
       48.59       202.65         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A4FB TCGA-GF-A3OT 
       15.45        32.75       101.26       148.80        26.73         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-LH-A9QB 
        2.04       139.89        10.13        32.48        12.62       357.04 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       63.02        42.08         8.61        90.28        52.34         3.75 

subtype1 subtype2 subtype3 
    0.20     0.16     2.04 
subtype1 subtype2 subtype3 
  294.77   369.93   357.37 
subtype1 subtype2 subtype3 
  36.030   54.445   59.145 
[1] "0.2 - 294.8 (36.0)" "0.2 - 369.9 (54.4)" "2.0 - 357.4 (59.1)"
D6V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 32             4
  subtype2                 16             1
  subtype3                 12             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        19                  45
  subtype2                                        28                 114
  subtype3                                        25                  51
D6V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              32       16       12
  PRIMARY TUMOR                                    4        1        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       19       28       25
  REGIONAL LYMPH NODE                             45      114       51
[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"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           2       2       3        4        6        5         5
  subtype2           6       2      15       11       14        8         6
  subtype3           4       3      10        2        7        8         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         9         9         8          9          7         21
  subtype2         8         2        14          2         19         27
  subtype3         2         1        13          4          6         11
          vv
clus       STAGE IV
  subtype1        5
  subtype2        8
  subtype3        6
D6V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        2        6        4
  STAGE 0            2        2        3
  STAGE I            3       15       10
  STAGE IA           4       11        2
  STAGE IB           6       14        7
  STAGE II           5        8        8
  STAGE IIA          5        6        3
  STAGE IIB          9        8        2
  STAGE IIC          9        2        1
  STAGE III          8       14       13
  STAGE IIIA         9        2        4
  STAGE IIIB         7       19        6
  STAGE IIIC        21       27       11
  STAGE IV           5        8        6
[1] 14  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       T0+T1 T2 T3 T4
  subtype1    11 16 22 35
  subtype2    36 31 31 24
  subtype3    16 24 20  9
D6V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       11       36       16
  T2          16       31       24
  T3          22       31       20
  T4          35       24        9
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 44 17 14 14
  subtype2 79 26 15 23
  subtype3 44 19  9 10
D6V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       44       79       44
  N1       17       26       19
  N2       14       15        9
  N3       14       23       10
[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"
          vv
clus        M0  M1 M1A M1B M1C
  subtype1  89   3   1   0   1
  subtype2 141   1   2   1   5
  subtype3  76   0   0   3   3
D6V8, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        89      141       76
  M1         3        1        0
  M1A        1        2        0
  M1B        0        1        3
  M1C        1        5        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus        0  1
  subtype1 39 32
  subtype2 64 40
  subtype3 26 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   32
  subtype2   64   40
  subtype3   26   16
     clus
vv    subtype1 subtype2 subtype3
  NO        39       64       26
  YES       32       40       16
[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"
D6V10, binary
          cls
clus         0   1
  subtype1   8  93
  subtype2  23 136
  subtype3  12  75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   93
  subtype2   23  136
  subtype3   12   75
     clus
vv    subtype1 subtype2 subtype3
  NO         8       23       12
  YES       93      136       75
[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"
D6V11, continuous
D6V12, binary
          cls
clus         0   1
  subtype1  35  66
  subtype2  57 102
  subtype3  39  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   66
  subtype2   57  102
  subtype3   39   49
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       35       57       39
  MALE         66      102       49
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0    93
  subtype2     2                         1   149
  subtype3     1                         0    83
D6V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        2        1
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                           93      149       83
[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"
D6V14, binary
          cls
clus         0   1
  subtype1   4  96
  subtype2   1 155
  subtype3   2  83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   96
  subtype2    1  155
  subtype3    2   83
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        1        2
  NOT HISPANIC OR LATINO       96      155       83
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 25 17
  subtype2 46 49
  subtype3 39 31
  subtype4 42 62
  subtype5  6  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      42       95       70      104        7 
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       49       31       62        1 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CE 
        6.97        28.08        22.55        36.16        64.44        13.32 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      103.59        26.37        29.23        32.61        25.78        52.01 
TCGA-D3-A8GQ TCGA-DA-A1I0 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R 
       11.44        10.03        19.36        17.56        14.83         0.20 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB 
        1.35        60.23        12.03        11.31        36.30        51.12 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A3AB 
       36.33         2.70         9.53       111.91        26.99       122.73 
TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-ER-A19F TCGA-ER-A19G TCGA-FR-A7UA TCGA-FR-A8YC 
       15.95        16.14        11.11       114.15        13.28         2.20 
TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 
       20.38        30.87         0.20        84.72        14.70        11.84 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 
        6.97       111.09        70.16       110.79        85.32         8.38 
TCGA-D3-A2JA TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CC 
       88.50         6.31        56.19       114.67        46.32        61.38 
TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GL TCGA-D3-A8GN 
        9.34        54.74        29.72        15.19        38.93       124.47 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y 
       51.12        39.19         9.99        44.52        36.69        10.55 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29S 
        9.21         7.99        37.97         8.55         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE 
        2.43        32.15        49.22         9.67        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       47.21         5.42        13.02         8.84         6.18        47.51 
TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
       29.46        14.56         5.56         3.22        21.60        21.60 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
        0.95        18.41        21.73        31.40        18.61        76.41 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19W 
       25.18         3.52        34.88         4.21        28.60        17.72 
TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P 
       11.80        12.62        11.74         6.58        22.49        15.72 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
        5.36         3.45        11.01         7.33         3.39         8.22 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV 
       47.38        49.15        40.64         2.27         0.99         0.16 
TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-LH-A9QB 
        9.90        10.13        12.16        10.65        14.50         0.43 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZN 
        8.98        60.03         2.99        11.84         7.10        21.07 
TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.72         5.36         1.08         1.94        12.07 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JB 
       16.47        32.42        81.24        10.29        21.14        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A51H TCGA-D3-A8GD 
       86.76        11.41        44.19        82.29        31.30        10.22 
TCGA-D3-A8GS TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1IA TCGA-DA-A1IB 
       24.07         9.90        11.31        13.22         4.93        22.36 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A183 
       13.15         0.13        23.15         0.20        11.57        12.20 
TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29X 
        4.34        62.79         9.50         8.09        30.44         8.09 
TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GT TCGA-EE-A2M6 
       36.33        16.01        28.31        55.69        34.98        98.27 
TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       44.25        56.02        25.08        60.49        53.16        52.67 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3JD TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19L 
       51.62        30.15        27.35         5.72        11.90        13.45 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-FR-A8YE TCGA-FS-A1Z0 
       42.84        78.44         1.51        13.08         3.29        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZU 
       15.52         7.30        19.53        12.89         8.65         8.68 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A262 TCGA-OD-A75X TCGA-W3-AA1V 
       14.20         0.13         7.23        44.28        11.05        10.98 
TCGA-W3-AA1W TCGA-WE-A8ZR TCGA-WE-AAA0 TCGA-Z2-AA3V 
      185.16         3.58        19.96         5.98 

$subtype4
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CF 
        8.52        45.83         7.50        92.42        15.25        24.00 
TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU 
        6.31        93.21        32.28       110.24        17.72        23.11 
TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 
       22.06       142.45        75.65        87.62         5.56         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IC 
       21.93         5.72        48.79        35.80        13.68         6.64 
TCGA-DA-A3F3 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 
        7.00        19.00        13.35        13.22         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B 
        1.12         5.13         4.31        15.85         1.18         9.90 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A2GC TCGA-EE-A2GI 
       11.15        36.85         1.08        39.62        34.29        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MF TCGA-EE-A2MH 
       19.43        35.54        33.83         1.15         2.73         7.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF 
       63.42       125.65        21.60       124.31         3.68        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 
       12.72        22.92        22.22        33.60        12.95        38.40 
TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ES 
        3.78        34.68         9.57        36.07         1.87         9.04 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z3 
        1.71        18.41         3.58         4.70        64.47        14.24 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZW 
       11.08         7.17        12.92        52.08         8.81        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB 
        0.82         5.23        53.85         7.36        28.73         5.98 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH 
       31.33        16.24        15.42        14.50        14.50        15.81 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA21 
        5.79        18.05         0.33         0.69       164.19        71.01 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-YG-AA3O TCGA-YG-AA3P 
        5.49         6.48        13.12         3.42         6.18         4.70 
TCGA-Z2-A8RT TCGA-Z2-AA3S 
        8.22         6.67 

$subtype5
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A51J TCGA-D3-A51N TCGA-DA-A1I8 TCGA-ER-A42K 
       59.57        46.98        54.31        21.44        25.15         5.62 
TCGA-WE-A8ZM 
       18.67 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     0.16     0.13     0.33     5.62 
subtype1 subtype2 subtype3 subtype4 subtype5 
  122.73   124.47   185.16   164.19    59.57 
subtype1 subtype2 subtype3 subtype4 subtype5 
  19.870   12.620   16.240   13.745   25.150 
[1] "0.2 - 122.7 (19.9)" "0.2 - 124.5 (12.6)" "0.1 - 185.2 (16.2)"
[4] "0.3 - 164.2 (13.7)" "5.6 - 59.6 (25.1)" 
D7V2, survival
          sevent
clus2       0  1
  subtype1 25 18
  subtype2 46 49
  subtype3 40 31
  subtype4 46 62
  subtype5  6  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      43       95       71      108        7 
subtype1 subtype2 subtype3 subtype4 subtype5 
      18       49       31       62        1 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CE 
       61.02        28.08        31.59        42.08        66.08        60.23 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN 
      103.59        39.75        45.30        63.81        26.89       135.75 
TCGA-D3-A8GQ TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       29.06         6.41        20.38        28.60       215.44        15.68 
TCGA-EB-A44R TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 
       10.16        14.70       133.81        56.42        46.82        36.82 
TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MP 
       59.28        94.82        28.83        47.28       203.05       248.65 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-ER-A19F TCGA-ER-A19G TCGA-FR-A7UA 
      122.73        23.47        34.32        26.37       268.93        38.27 
TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A26D 
       34.82       357.37        32.75         0.20        84.72        39.58 
TCGA-GN-A4U8 
       46.36 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 
       12.99       112.04        71.80       133.25       103.10        65.49 
TCGA-D3-A2JA TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CC 
      115.53        12.10        56.19       130.72        46.32        86.93 
TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GL TCGA-D3-A8GN 
        9.34        55.73        30.84        15.19        89.13       161.00 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y 
      117.21       194.83        35.93       107.34        61.18        27.22 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29S 
      168.26        63.35        47.84        72.07        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE 
       25.87       195.02       102.90        39.29       314.56       161.03 
TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
      208.04        13.91        55.59        21.67        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
      103.27       204.66        53.26       172.18        36.95        64.08 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
      201.80        51.35       109.58        31.40        35.44        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19W 
       98.40        12.59       152.35         6.44        61.05       148.18 
TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P 
       43.82        31.27        32.05        80.32        46.98        15.72 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
        7.00        48.59       228.59         7.79        48.85        53.52 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV 
      101.26       148.80        53.16        77.88        22.92         0.16 
TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-LH-A9QB 
        9.90        10.13        32.48        12.62        21.37       357.04 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZN 
       63.02       121.08         4.01        24.03         8.61        56.98 
TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
       52.34        43.73         2.20        10.36        15.16 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JB 
       16.57       112.57        95.74        43.43        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A51H TCGA-D3-A8GD 
       86.76        11.87        62.07       166.52        56.35        11.61 
TCGA-D3-A8GS TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1IA TCGA-DA-A1IB 
      117.17         9.90        25.18        66.25        65.92        23.44 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.87        17.85        68.25         6.35        12.20        29.82 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T 
       26.89       151.27        63.78        18.61        37.35       369.93 
TCGA-EE-A29X TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GT 
       17.92        86.14        54.74        75.48       126.81        44.88 
TCGA-EE-A2M6 TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS 
      129.27       103.20       167.90        47.54       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3JD TCGA-ER-A199 TCGA-ER-A19E 
       71.21        51.62        54.51        27.35         9.17        13.02 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-FR-A8YE 
      131.51        44.05        79.99        20.15        16.37        94.39 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZQ 
      202.65        28.08        27.72        40.27        23.93       133.55 
TCGA-FS-A1ZU TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A262 TCGA-OD-A75X 
       26.56       174.84        47.54         7.23       139.89       294.77 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8ZR TCGA-WE-AAA0 TCGA-Z2-AA3V 
       42.08       219.16         4.37        30.18        11.74 

$subtype4
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3CF 
       16.67        90.90       113.52       171.58        58.06        24.53 
TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU 
       13.87       174.84        32.94       125.79        18.18       125.19 
TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A148 
       79.59       228.99        95.24       137.79       129.63       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         3.65        18.12        11.34        22.29        11.11 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A5SH 
       48.89        36.03       176.55        68.09        10.49        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 
       17.29        52.01         8.65        94.98        33.73        68.15 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H 
        4.96        91.56        13.55        80.61        13.97        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL 
        2.60        56.84        67.43        48.72        89.33        79.66 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
       90.97        14.30       268.73        16.96        96.23       158.63 
TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
       43.23       124.31         3.68        13.81       138.81       127.20 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19P 
       53.19       148.08        13.94        50.76        48.89       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN 
       50.89        37.25        23.34       247.04        33.21        92.98 
TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG 
       15.16        29.46       216.92        20.91        15.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       47.38        74.73        11.41        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-GN-A264 TCGA-GN-A267 
       77.82        66.67        28.73        26.73       117.93        64.44 
TCGA-GN-A268 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O 
       62.79        50.10        59.41        65.88         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
        0.33         0.69       212.22       105.04        38.56        54.38 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       59.41         3.75        36.03        14.43        23.64        93.07 

$subtype5
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A51J TCGA-D3-A51N TCGA-DA-A1I8 TCGA-ER-A42K 
       59.57        46.98       145.12        22.62        53.92         6.77 
TCGA-WE-A8ZM 
       90.28 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     0.16     4.37     0.33     6.77 
subtype1 subtype2 subtype3 subtype4 subtype5 
  357.37   357.04   369.93   268.73   145.12 
subtype1 subtype2 subtype3 subtype4 subtype5 
  42.080   53.520   47.540   50.825   53.920 
[1] "0.2 - 357.4 (42.1)" "0.2 - 357.0 (53.5)" "4.4 - 369.9 (47.5)"
[4] "0.3 - 268.7 (50.8)" "6.8 - 145.1 (53.9)"
D7V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  6             0
  subtype2                 16             0
  subtype3                 14             4
  subtype4                 21             0
  subtype5                  0             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                         9                  29
  subtype2                                        35                  48
  subtype3                                         5                  50
  subtype4                                        17                  70
  subtype5                                         3                   5
D7V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                               6       16       14       21
  PRIMARY TUMOR                                    0        0        4        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE        9       35        5       17
  REGIONAL LYMPH NODE                             29       48       50       70
                                           clus
vv                                          subtype5
  DISTANT METASTASIS                               0
  PRIMARY TUMOR                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE        3
  REGIONAL LYMPH NODE                              5
[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"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       0       2        1        2        5         3
  subtype2           3       1       9        1       11        3         5
  subtype3           5       5       9        8        3        5         1
  subtype4           2       1       7        5       11        7         3
  subtype5           1       0       0        0        0        0         0
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         1         2         4          2          7          5
  subtype2         5         2        12          6          8         21
  subtype3         2         3         5          2          4         14
  subtype4        10         4        10          4         10         15
  subtype5         0         0         2          0          1          3
          vv
clus       STAGE IV
  subtype1        4
  subtype2        4
  subtype3        0
  subtype4        9
  subtype5        1
D7V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  I OR II NOS        1        3        5        2        1
  STAGE 0            0        1        5        1        0
  STAGE I            2        9        9        7        0
  STAGE IA           1        1        8        5        0
  STAGE IB           2       11        3       11        0
  STAGE II           5        3        5        7        0
  STAGE IIA          3        5        1        3        0
  STAGE IIB          1        5        2       10        0
  STAGE IIC          2        2        3        4        0
  STAGE III          4       12        5       10        2
  STAGE IIIA         2        6        2        4        0
  STAGE IIIB         7        8        4       10        1
  STAGE IIIC         5       21       14       15        3
  STAGE IV           4        4        0        9        1
[1] 14  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       T0+T1 T2 T3 T4
  subtype1     9  6 11 10
  subtype2     7 31 23 17
  subtype3    20 10 11 12
  subtype4    19 23 24 22
  subtype5     4  1  0  2
D7V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        9        7       20       19        4
  T2           6       31       10       23        1
  T3          11       23       11       24        0
  T4          10       17       12       22        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"
          vv
clus       N0 N1 N2 N3
  subtype1 19  8  9  4
  subtype2 44 24 10 13
  subtype3 41  8  6 11
  subtype4 56 15 13 13
  subtype5  1  3  0  4
D7V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       19       44       41       56        1
  N1        8       24        8       15        3
  N2        9       10        6       13        0
  N3        4       13       11       13        4
[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"
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 37  1   1   1   1
  subtype2 89  2   0   1   1
  subtype3 68  0   0   0   0
  subtype4 93  1   1   2   6
  subtype5  7  0   0   0   1
D7V8, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0        37       89       68       93        7
  M1         1        2        0        1        0
  M1A        1        0        0        1        0
  M1B        1        1        0        2        0
  M1C        1        1        0        6        1
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus        0  1
  subtype1 12 14
  subtype2 37 22
  subtype3 27 17
  subtype4 46 29
  subtype5  0  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   14
  subtype2   37   22
  subtype3   27   17
  subtype4   46   29
  subtype5    0    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        12       37       27       46        0
  YES       14       22       17       29        2
[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"
D7V10, binary
          cls
clus        0  1
  subtype1  7 37
  subtype2 10 89
  subtype3  7 66
  subtype4 13 96
  subtype5  4  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   37
  subtype2   10   89
  subtype3    7   66
  subtype4   13   96
  subtype5    4    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         7       10        7       13        4
  YES       37       89       66       96        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"
D7V11, continuous
D7V12, binary
          cls
clus        0  1
  subtype1 17 27
  subtype2 31 68
  subtype3 30 43
  subtype4 41 68
  subtype5  5  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   27
  subtype2   31   68
  subtype3   30   43
  subtype4   41   68
  subtype5    5    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       17       31       30       41        5
  MALE         27       68       43       68        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    43
  subtype2     1                         0    90
  subtype3     3                         1    67
  subtype4     0                         0   104
  subtype5     0                         0     7
D7V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        3        0        0
  BLACK OR AFRICAN AMERICAN        0        0        1        0        0
  WHITE                           43       90       67      104        7
[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"
D7V14, binary
          cls
clus         0   1
  subtype1   0  44
  subtype2   2  93
  subtype3   0  72
  subtype4   4 103
  subtype5   1   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   44
  subtype2    2   93
  subtype3    0   72
  subtype4    4  103
  subtype5    1    7
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        2        0        4        1
  NOT HISPANIC OR LATINO       44       93       72      103        7
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 37 48
  subtype2 69 62
  subtype3 32 35
  subtype4 20 15
subtype1 subtype2 subtype3 subtype4 
      85      131       67       35 
subtype1 subtype2 subtype3 subtype4 
      48       62       35       15 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2J7 
        6.97        16.47         8.52       110.79        10.29        85.32 
TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A5GL 
       68.22        44.19        61.38        24.00         6.31       110.24 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       17.72        29.72        75.65         5.56        21.93         5.72 
TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.90        35.80        13.68         9.99         4.93        22.36 
TCGA-DA-A1IC TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A183 
        6.64        13.35        13.22         0.20         8.12        12.20 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
        9.90        62.79         8.55        36.85        39.62         9.50 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GL 
        2.43         8.09         9.67        36.33        17.98        35.54 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MJ TCGA-EE-A2MM 
        1.15        13.02        34.98         6.18        63.42        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
       25.08        21.60        53.16        52.67       124.31        51.62 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A198 
       13.81        22.92        21.60        21.60        27.35        38.40 
TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
        3.78        13.45         1.87         1.51        13.08        12.62 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A1ZR TCGA-FS-A1ZT 
        9.04         1.71        23.80        12.89         8.81        40.64 
TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A8LK 
        7.36         2.27         0.13        16.24        14.70        14.50 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-WE-A8ZR TCGA-YG-AA3O 
       15.81         5.79         0.33       164.19         3.58         6.18 
TCGA-YG-AA3P 
        4.70 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
        6.97        45.83         7.50         6.31        92.42        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3MO TCGA-D3-A3MU 
      114.67        15.25        46.32        82.29         9.34        26.37 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
       93.21        54.74        54.31        32.28        21.44        25.78 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP 
       23.11        22.06        10.22       142.45        38.93        87.62 
TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 
        4.01        11.31        13.22        48.79        39.19        44.52 
TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Z 
       36.69         7.00        13.15        23.15        19.00         6.31 
TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        1.12         5.13         4.31        15.85         9.21         1.18 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A1 
       37.97        11.15         1.08         8.84         9.99        49.22 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GN 
       34.29        60.00        47.21        30.08        19.43        33.83 
TCGA-EE-A2GP TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK 
        5.42         9.53        29.46         2.73         7.96       125.65 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 
       26.99         5.56         3.68        30.15        12.72         3.22 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19A 
       22.22        21.73        33.60        31.40        12.95        76.41 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       11.11         4.21        28.60        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P 
       17.72         6.58        22.49         5.62        18.41        15.72 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        3.58        13.28         4.70        64.47         3.45        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       14.24         7.33         3.39        11.08         7.17        12.92 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       47.38        52.08         8.65         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TV 
        5.23        53.85        28.73         5.98         0.99         0.16 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-OD-A75X 
       44.28        31.33        15.42        14.50        14.50        11.05 
TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       18.05         0.69         2.99        71.01         5.49         6.48 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       21.07        13.12         3.72         3.42         5.36         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S 
       19.96         1.94        12.07         8.22         6.67 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
      111.09        32.42        70.16        81.24         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3CE 
       88.50        86.76        11.41        56.19        46.98        13.32 
TCGA-D3-A51H TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS TCGA-DA-A1HY TCGA-DA-A1I8 
       31.30        15.19       124.47        24.07        51.12        25.15 
TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29Q TCGA-EE-A29T 
        0.13        11.57         4.34         7.99         8.09        30.44 
TCGA-EE-A29W TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 
       32.15        16.01        28.31        55.69         8.84        98.27 
TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A3JB TCGA-ER-A195 
       47.51        44.25        14.56        60.49         0.95        18.61 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19N 
        5.72        25.18         3.52        11.90        34.88        42.84 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NH TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1Z4 
       78.44        11.80        11.74         5.36         3.29        15.52 
TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-GF-A3OT 
        7.30         8.22        19.53        49.15        14.20         9.90 
TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-LH-A9QB TCGA-W3-A825 
        7.23        10.13        12.16        10.65         0.43         8.98 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM 
       60.03        10.98       185.16        11.84         7.10        18.67 
TCGA-Z2-AA3V 
        5.98 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A3MV 
       28.08        22.55        36.16        64.44       103.59        29.23 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GQ TCGA-DA-A1I0 TCGA-DA-A3F2 TCGA-DA-A3F5 
       32.61        52.01        11.44        10.03        19.36        17.56 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29P 
       14.83         0.20        10.55         1.35        60.23        12.03 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML 
       11.31        36.30        51.12        36.33         2.70       111.91 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A19G TCGA-FR-A8YC 
      122.73        15.95        16.14        18.41       114.15         2.20 
TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U8 
       20.38        30.87         0.20        84.72        11.84 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.16     0.13     0.20 
subtype1 subtype2 subtype3 subtype4 
  164.19   142.45   185.16   122.73 
subtype1 subtype2 subtype3 subtype4 
   13.68    14.24    15.52    20.38 
[1] "0.1 - 164.2 (13.7)" "0.2 - 142.4 (14.2)" "0.1 - 185.2 (15.5)"
[4] "0.2 - 122.7 (20.4)"
D8V2, survival
          sevent
clus2       0  1
  subtype1 40 48
  subtype2 70 62
  subtype3 33 35
  subtype4 20 16
subtype1 subtype2 subtype3 subtype4 
      88      132       68       36 
subtype1 subtype2 subtype3 subtype4 
      48       62       35       16 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2J7 
       61.02        16.57        16.67       133.25        43.43       103.10 
TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A5GL 
      168.00        62.07        86.93        24.53        13.87       125.79 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 
       18.18        30.84        95.24       129.63       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I2 
        3.65        22.29        11.11         9.90        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-EB-A5UL TCGA-EB-A5UN 
       35.93        65.92        23.44        68.09        17.29        52.01 
TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
       12.20        94.98        26.89        80.61        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 
       64.64        56.84        18.61        25.87        17.92        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       86.14       314.56        79.66        14.30        55.59        44.88 
TCGA-EE-A2M8 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS 
       19.76        96.23       167.90        47.54        43.23       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 
       71.21       124.31        51.62        13.81       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2ND 
       64.08        27.35        50.76        48.89       131.51        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1Z0 
       20.15        16.37        31.27       247.04        33.21       202.65 
TCGA-FS-A1ZK TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TU 
       23.93        11.41        53.16        66.67        77.88        47.54 
TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A8LK TCGA-HR-A2OH TCGA-QB-A6FS TCGA-RP-A693 
       64.44        39.58        50.10        65.88         6.67         0.33 
TCGA-W3-A824 TCGA-WE-A8ZR TCGA-YG-AA3O TCGA-YG-AA3P 
      212.22         4.37        36.03        14.43 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       12.99        90.90       113.52        12.10       171.58        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3MO TCGA-D3-A3MU 
      130.72        58.06        46.32       166.52         9.34        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T 
      174.84        55.73       145.12        32.94        22.62        26.89 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP 
      125.19        79.59        11.61       228.99        89.13       137.79 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 
       18.12        11.34        25.18        66.25        48.89       194.83 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
      107.34        61.18        10.49        13.87        68.25        54.02 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H 
        8.65        33.73        68.15         4.96        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S 
       13.55        47.84        13.97         2.60        14.47        55.92 
TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
      102.90        67.43       161.03       208.04        48.72        89.33 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
       90.97        13.91        47.28       103.27       268.73        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH 
      158.63       248.65        53.26         3.68        54.51       138.81 
TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
      172.18        53.19       109.58       148.08        31.40        13.94 
TCGA-ER-A19A TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
       77.75        26.37         6.44        61.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       37.25       148.18        80.32        46.98         6.77        92.98 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX 
       15.72        15.16        38.27        29.46       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZG 
      228.59        20.91         7.79        48.85        15.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38       101.26        74.73       133.55        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3R5 
       27.09        27.02        77.82        28.73        26.73        22.92 
TCGA-FW-A3TV TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A8LL TCGA-GN-A9SD 
        0.16       139.89       117.93        62.79        21.37        59.41 
TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8K1 
      294.77        18.05         0.69         4.01       105.04        38.56 
TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       54.38        56.98        59.41        52.34         3.75        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S 
        2.20        30.18        10.36        15.16        23.64        93.07 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
      112.04       112.57        71.80        95.74        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A3C7 TCGA-D3-A3CE 
      115.53        86.76        11.87        56.19        46.98        60.23 
TCGA-D3-A51H TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS TCGA-DA-A1HY TCGA-DA-A1I8 
       56.35        15.19       161.00       117.17       117.21        53.92 
TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29Q 
       17.85         6.35        29.82       151.27        63.35        37.35 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 
      369.93       195.02        54.74        75.48       126.81        21.67 
TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A3JB 
      129.27        61.51       103.20       204.66       134.40       201.80 
TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
       35.44         9.17        98.40        12.59        13.02       152.35 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NH TCGA-FR-A7U9 TCGA-FR-A8YE 
       44.05        79.99        43.82        32.05         7.00        94.39 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZS TCGA-FS-A4F8 
       28.08        27.72        53.52        40.27       148.80       174.84 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-LH-A9QB 
        9.90         7.23        10.13        32.48        12.62       357.04 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K6 
       63.02       121.08        42.08       219.16        24.03         8.61 
TCGA-WE-A8ZM TCGA-Z2-AA3V 
       90.28        11.74 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A3MV 
       28.08        31.59        42.08        66.08       103.59        45.30 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GQ TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A3F2 
       63.81       135.75        29.06         6.41        20.38        28.60 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20B 
      215.44        15.68        10.16        27.22        14.70       133.81 
TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 
       56.42        46.82        36.82        59.28        94.82        28.83 
TCGA-EE-A2ML TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A19G 
      203.05       122.73        23.47        34.32        51.35       268.93 
TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U8 
       34.82       357.37        32.75         0.20        84.72        46.36 

subtype1 subtype2 subtype3 subtype4 
    0.33     0.16     6.35     0.20 
subtype1 subtype2 subtype3 subtype4 
  314.56   294.77   369.93   357.37 
subtype1 subtype2 subtype3 subtype4 
  49.495   50.185   58.290   43.690 
[1] "0.3 - 314.6 (49.5)" "0.2 - 294.8 (50.2)" "6.3 - 369.9 (58.3)"
[4] "0.2 - 357.4 (43.7)"
D8V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 19             2
  subtype2                 21             2
  subtype3                 12             0
  subtype4                  5             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        16                  51
  subtype2                                        27                  87
  subtype3                                        15                  43
  subtype4                                        11                  21
D8V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                              19       21       12        5
  PRIMARY TUMOR                                    2        2        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       16       27       15       11
  REGIONAL LYMPH NODE                             51       87       43       21
[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"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       4       5        4        8        5         4
  subtype2           8       0      11        7       14        6         5
  subtype3           2       3      10        3        4        5         1
  subtype4           1       0       1        1        1        4         2
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         5         4         9          5          7         16
  subtype2        10         4        13          5          9         25
  subtype3         2         2         8          3          5         13
  subtype4         1         1         3          1          9          4
          vv
clus       STAGE IV
  subtype1        3
  subtype2       10
  subtype3        1
  subtype4        4
D8V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        1        8        2        1
  STAGE 0            4        0        3        0
  STAGE I            5       11       10        1
  STAGE IA           4        7        3        1
  STAGE IB           8       14        4        1
  STAGE II           5        6        5        4
  STAGE IIA          4        5        1        2
  STAGE IIB          5       10        2        1
  STAGE IIC          4        4        2        1
  STAGE III          9       13        8        3
  STAGE IIIA         5        5        3        1
  STAGE IIIB         7        9        5        9
  STAGE IIIC        16       25       13        4
  STAGE IV           3       10        1        4
[1] 14  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       T0+T1 T2 T3 T4
  subtype1    15 18 22 17
  subtype2    20 36 24 27
  subtype3    16 14 12 11
  subtype4     8  3 11  8
D8V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       15       20       16        8
  T2          18       36       14        3
  T3          22       24       12       11
  T4          17       27       11        8
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 39 17 12 10
  subtype2 72 18 15 20
  subtype3 36 15  3 11
  subtype4 14  8  8  4
D8V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       39       72       36       14
  N1       17       18       15        8
  N2       12       15        3        8
  N3       10       20       11        4
[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"
          vv
clus        M0  M1 M1A M1B M1C
  subtype1  78   0   1   1   2
  subtype2 120   3   0   1   6
  subtype3  65   0   0   1   0
  subtype4  31   1   1   1   1
D8V8, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        78      120       65       31
  M1         0        3        0        1
  M1A        1        0        0        1
  M1B        1        1        1        1
  M1C        2        6        0        1
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus        0  1
  subtype1 39 25
  subtype2 54 31
  subtype3 19 16
  subtype4 10 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   25
  subtype2   54   31
  subtype3   19   16
  subtype4   10   12
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        39       54       19       10
  YES       25       31       16       12
[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"
D8V10, binary
          cls
clus         0   1
  subtype1   6  82
  subtype2  18 119
  subtype3  11  59
  subtype4   6  31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   82
  subtype2   18  119
  subtype3   11   59
  subtype4    6   31
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6       18       11        6
  YES       82      119       59       31
[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"
D8V11, continuous
D8V12, binary
          cls
clus        0  1
  subtype1 29 59
  subtype2 56 82
  subtype3 27 43
  subtype4 12 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   59
  subtype2   56   82
  subtype3   27   43
  subtype4   12   25
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       29       56       27       12
  MALE         59       82       43       25
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    82
  subtype2     1                         0   128
  subtype3     1                         0    66
  subtype4     2                         0    35
D8V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        1        2
  BLACK OR AFRICAN AMERICAN        1        0        0        0
  WHITE                           82      128       66       35
[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"
D8V14, binary
          cls
clus         0   1
  subtype1   2  84
  subtype2   4 134
  subtype3   1  65
  subtype4   0  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   84
  subtype2    4  134
  subtype3    1   65
  subtype4    0   36
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        4        1        0
  NOT HISPANIC OR LATINO       84      134       65       36
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 45 36
  subtype2 45 54
  subtype3 59 65
subtype1 subtype2 subtype3 
      81       99      124 
subtype1 subtype2 subtype3 
      36       54       65 
$subtype1
TCGA-3N-A9WC TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
        6.97        21.14        68.22        86.76        11.41        44.19 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR 
       59.57        46.98        46.32        82.29        24.00       103.59 
TCGA-D3-A51N TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       21.44        29.72        10.22        24.07         4.01        21.93 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB 
       48.79        35.80        39.19        13.68         9.99        22.36 
TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A183 
        6.64        14.83         0.20        11.57         8.12        12.20 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GJ 
       15.85         1.18         9.50         2.43        36.33        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 
       16.01        35.54        55.69        34.98        36.33         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MR 
        6.18         7.96        63.42       125.65        21.60        60.49 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 
       52.67       124.31        30.15        13.81        22.92        21.60 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A19G TCGA-ER-A19L 
       22.22        27.35        21.73        12.95       114.15        13.45 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
        9.57        36.07        78.44         1.87        12.62        11.74 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FW-A3R5 
       13.28         3.29        15.52         8.65        40.64         0.99 
TCGA-FW-A3TU TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-AAA0 
        0.13        14.50        18.05       185.16         5.49        19.96 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3V 
       12.07         6.18         5.98 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J7 
        6.97       111.09        70.16       110.79        28.08        85.32 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
        8.38        88.50        36.16         6.31        56.19        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H 
      114.67        15.25         9.34        29.23        54.74        31.30 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-DA-A1HY 
       32.61        52.01        15.19       124.47        11.44        51.12 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A182 
       44.52        36.69        17.56        13.22        10.55         1.35 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29S 
       60.23         9.21         7.99        37.97         8.55         9.99 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       32.15        11.31        49.22        17.98        60.00        47.21 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
        5.42        13.02         8.84        47.51        29.46        44.25 
TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-EE-A3JE 
       14.56         5.56       122.73         3.22         0.95        18.41 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       31.40        18.61        76.41        25.18         3.52        11.90 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A3ET 
       34.88         4.21        28.60        17.72        11.80         6.58 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       22.49        15.72         5.36         3.45        11.01         7.33 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH 
        3.39        20.38         8.22        19.53        11.08        30.87 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GF-A3OT 
       47.38         8.81        49.15        14.20         0.16         9.90 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-LH-A9QB 
       31.33        84.72        10.13        12.16        10.65         0.43 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZN 
        8.98        60.03         2.99        11.84         7.10        21.07 
TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 
        3.72         1.08         1.94 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       16.47         8.52        32.42        22.55        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       10.29         7.50        92.42        61.38        13.32         6.31 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS 
       93.21        54.31        32.28        25.78       110.24        17.72 
TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
       23.11       142.45        38.93        75.65        87.62         5.56 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I8 TCGA-DA-A1IA 
        5.72         9.90        11.31        13.22        25.15         4.93 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL 
        7.00        13.15         0.20         0.13        19.00        13.35 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29B 
        6.31         1.12         5.13         4.31         4.34         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P 
       11.15        62.79        36.85         1.08        39.62        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.09         8.84        30.44        36.30         9.67        51.12 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2M6 
       34.29        30.08        28.31        33.83         1.15        98.27 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
        9.53         2.73       111.91        56.02        25.08        26.99 
TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J7 
       53.16        51.62         3.68        15.95        12.72        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19F 
       16.14        33.60        38.40         5.72         3.78        11.11 
TCGA-ER-A19P TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN 
       34.68         1.51        13.08         9.04         1.71        18.41 
TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.58         2.20         4.70        64.47        23.80        14.24 
TCGA-FS-A1ZA TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZW 
        7.30        12.92        12.89        52.08         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FD 
        0.82         5.23         7.36        28.73         5.98         2.27 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 
        0.20        44.28        16.24        15.42        14.70        11.84 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       14.50        14.50        11.05         0.33         0.69       164.19 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZR 
       10.98        71.01         6.48        18.67        13.12         3.58 
TCGA-WE-A8ZY TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        5.36         4.70         8.22         6.67 

subtype1 subtype2 subtype3 
    0.13     0.16     0.13 
subtype1 subtype2 subtype3 
  185.16   124.47   164.19 
subtype1 subtype2 subtype3 
  19.960   15.720   13.185 
[1] "0.1 - 185.2 (20.0)" "0.2 - 124.5 (15.7)" "0.1 - 164.2 (13.2)"
D9V2, survival
          sevent
clus2       0  1
  subtype1 49 36
  subtype2 45 54
  subtype3 60 66
subtype1 subtype2 subtype3 
      85       99      126 
subtype1 subtype2 subtype3 
      36       54       66 
$subtype1
TCGA-3N-A9WC TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       61.02        23.77       168.00        86.76        11.87        62.07 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR 
       59.57        46.98        46.32       166.52        24.53       103.59 
TCGA-D3-A51N TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
       22.62        30.84        11.61       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
        3.65        11.34        22.29        48.89        36.03       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EB-A5VV 
      176.55        35.93        23.44        68.09        15.68         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20I 
       12.20        29.82        94.98        26.89        91.56        13.55 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       18.61        25.87        86.14        89.33        54.74        79.66 
TCGA-EE-A2GO TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH 
      126.81        44.88        94.82        28.83        19.76        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA 
       96.23       158.63        43.23       134.40        71.21       124.31 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
       54.51        13.81       127.20        36.95        53.19        27.35 
TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S 
      109.58        13.94       268.93       131.51        50.89        37.25 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A7UA TCGA-FR-A8YE 
       79.99        23.34        31.27        32.05        38.27        94.39 
TCGA-FS-A1Z4 TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A9SD 
       28.08       133.55        53.16        22.92        47.54        59.41 
TCGA-QB-AA9O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       18.05       219.16        38.56        30.18        15.16        36.03 
TCGA-Z2-AA3V 
       11.74 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J7 
       12.99       112.04        71.80       133.25        28.08       103.10 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       65.49       115.53        42.08        12.10        56.19        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H 
      130.72        58.06         9.34        45.30        55.73        56.35 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-DA-A1HY 
       63.81       135.75        15.19       161.00        29.06       117.21 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A182 
      107.34        61.18       215.44        52.01        27.22        14.70 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29S 
      133.81       168.26        63.35        47.84        72.07        55.92 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
      195.02        46.82       102.90       314.56       161.03       208.04 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       13.91        55.59        21.67        61.51       103.27       103.20 
TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3JB TCGA-EE-A3JE 
      204.66        53.26       122.73       172.18       201.80        51.35 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       31.40        35.44        77.75        98.40        12.59        13.02 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A3ET 
      152.35         6.44        61.05       148.18        43.82        80.32 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       46.98        15.72         7.00        48.59       228.59         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH 
       48.85       357.37        53.52        40.27        15.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GF-A3OT 
      101.26        11.41       148.80       174.84         0.16         9.90 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-LH-A9QB 
      117.93        84.72        10.13        32.48        12.62       357.04 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZN 
       63.02       121.08         4.01        24.03         8.61        56.98 
TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 
       52.34         2.20        10.36 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       16.57        16.67       112.57        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       43.43       113.52       171.58        86.93        60.23        13.87 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS 
      174.84       145.12        32.94        26.89       125.79        18.18 
TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR 
      125.19       228.99        89.13        95.24       137.79       129.63 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        18.12        11.11         9.90        25.18        66.25 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       53.92        65.92        10.49        13.87        10.16        17.85 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 
       54.02        17.29         8.65        33.73        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
      151.27        80.61        13.97        63.78        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A2 
       56.84        56.42        37.35        14.47       369.93        36.82 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN 
       39.29        59.28        67.43        48.72        75.48        90.97 
TCGA-EE-A2GR TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2ML TCGA-EE-A2MM 
       14.30       129.27        47.28       268.73       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG 
       47.54       248.65       162.48        51.62         3.68        23.47 
TCGA-EE-A3AH TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A198 TCGA-ER-A199 
      138.81        64.08        34.32       148.08        50.76         9.17 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
       48.89        26.37       162.08        20.15        16.37       247.04 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW 
       33.21        92.98        15.16        34.82        29.46       216.92 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
      202.65        20.91        27.72        47.38        23.93        74.73 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        27.02        66.67        28.73 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 
       26.73        77.88         0.20       139.89        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A693 
       39.58        46.36        50.10        21.37       294.77         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM 
        0.69       212.22        42.08       105.04        54.38        90.28 
TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       59.41         4.37        43.73        14.43        23.64        93.07 

subtype1 subtype2 subtype3 
    3.65     0.16     0.20 
subtype1 subtype2 subtype3 
  268.93   357.37   369.93 
subtype1 subtype2 subtype3 
  46.320   56.350   49.185 
[1] "3.6 - 268.9 (46.3)" "0.2 - 357.4 (56.4)" "0.2 - 369.9 (49.2)"
D9V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 11             0
  subtype2                 19             0
  subtype3                 26             4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        12                  66
  subtype2                                        31                  52
  subtype3                                        23                  74
D9V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              11       19       26
  PRIMARY TUMOR                                    0        0        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       12       31       23
  REGIONAL LYMPH NODE                             66       52       74
[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"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           7       2       5       10        4        4         3
  subtype2           2       2      11        1       12        6         6
  subtype3           3       3      11        4       10       10         3
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0         0        13          1          9         21
  subtype2         5         3         9          6          7         16
  subtype3        12         8        11          6         12         16
          vv
clus       STAGE IV
  subtype1        2
  subtype2        6
  subtype3        8
D9V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        7        2        3
  STAGE 0            2        2        3
  STAGE I            5       11       11
  STAGE IA          10        1        4
  STAGE IB           4       12       10
  STAGE II           4        6       10
  STAGE IIA          3        6        3
  STAGE IIB          0        5       12
  STAGE IIC          0        3        8
  STAGE III         13        9       11
  STAGE IIIA         1        6        6
  STAGE IIIB         9        7       12
  STAGE IIIC        21       16       16
  STAGE IV           2        6        8
[1] 14  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       T0+T1 T2 T3 T4
  subtype1    26 13 17 12
  subtype2    13 29 21 17
  subtype3    18 28 28 29
D9V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       26       13       18
  T2          13       29       28
  T3          17       21       28
  T4          12       17       29
[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"
          vv
clus       N0 N1 N2 N3
  subtype1 40 14 12 18
  subtype2 53 18 11 11
  subtype3 66 25 11 11
D9V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       40       53       66
  N1       14       18       25
  N2       12       11       11
  N3       18       11       11
[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"
          vv
clus        M0  M1 M1A M1B M1C
  subtype1  83   0   0   1   2
  subtype2  88   2   0   2   2
  subtype3 113   2   1   0   5
D9V8, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        83       88      113
  M1         0        2        2
  M1A        0        0        1
  M1B        1        2        0
  M1C        2        2        5
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
          cls
clus        0  1
  subtype1 38 16
  subtype2 36 23
  subtype3 43 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   16
  subtype2   36   23
  subtype3   43   40
     clus
vv    subtype1 subtype2 subtype3
  NO        38       36       43
  YES       16       23       40
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
          cls
clus         0   1
  subtype1  13  77
  subtype2  12  90
  subtype3  12 115
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   77
  subtype2   12   90
  subtype3   12  115
     clus
vv    subtype1 subtype2 subtype3
  NO        13       12       12
  YES       77       90      115
[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"
D9V11, continuous
D9V12, binary
          cls
clus        0  1
  subtype1 36 54
  subtype2 33 69
  subtype3 47 80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   54
  subtype2   33   69
  subtype3   47   80
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       36       33       47
  MALE         54       69       80
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    85
  subtype2     1                         0    95
  subtype3     3                         0   119
D9V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        3
  BLACK OR AFRICAN AMERICAN        1        0        0
  WHITE                           85       95      119
[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"
D9V14, binary
          cls
clus         0   1
  subtype1   2  87
  subtype2   2  96
  subtype3   3 123
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   87
  subtype2    2   96
  subtype3    3  123
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        3
  NOT HISPANIC OR LATINO       87       96      123
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 77 74
  subtype2 57 68
  subtype3 15 13
subtype1 subtype2 subtype3 
     151      125       28 
subtype1 subtype2 subtype3 
      74       68       13 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
        6.97        16.47         8.52       110.79        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK 
       10.29        68.22        11.41        44.19         7.50         6.31 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E 
       92.42        59.57        82.29        24.00         6.31        93.21 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD 
       32.28        25.78       110.24        17.72        23.11        10.22 
TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A3Z1 
      142.45        38.93        75.65        87.62         5.56         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
       21.93         5.72         9.90        11.31        13.22        48.79 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F3 
       35.80        39.19        13.68         4.93        22.36         7.00 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       14.83        13.15         0.13        19.00        13.35        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
        0.20        11.57         6.31         8.12         1.12        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
        5.13         4.31        15.85         9.90        11.15        62.79 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2A6 TCGA-EE-A2GC 
       36.85         1.08        39.62         9.50        36.33        34.29 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       30.08        19.43        35.54        28.31        33.83         1.15 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH 
       34.98        98.27         6.18         9.53         2.73         7.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       63.42       125.65        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.16        52.67       124.31        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
       13.81        12.72        22.92        21.60        22.22        27.35 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19F 
       33.60        12.95        38.40         5.72         3.78        11.11 
TCGA-ER-A19J TCGA-ER-A19S TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
        4.21        36.07         1.51        13.08        12.62         9.04 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW 
        1.71        18.41         3.58        13.28         4.70        64.47 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       23.80        14.24        19.53        12.92        12.89        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.65        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 
        7.36        28.73         5.98         0.13        44.28        16.24 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LK TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 
       15.42        14.70        14.50        11.05        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZR 
        0.69       164.19       185.16        71.01        13.12         3.58 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        5.36        19.96         6.18         4.70         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2J8 
        6.97       111.09        32.42        70.16        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 
       21.14        88.50        86.76        56.19       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98        46.32        61.38        13.32         9.34       103.59 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A8GB TCGA-D3-A8GE 
       54.74        31.30        54.31        21.44        29.72        15.19 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      124.47        24.07        51.12         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20H 
       25.15         6.64        17.56        10.55         4.34         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R 
        1.18         7.99        37.97         8.55         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A5 
        9.99        30.44         2.43        32.15        49.22         9.67 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GP 
       17.98        60.00        47.21        16.01        55.69         5.42 
TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
       13.02         8.84        47.51        29.46        44.25        14.56 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JE 
       60.49         5.56         3.22        21.60         0.95        18.41 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       21.73        31.40        18.61        76.41        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
       11.90        34.88        13.45        28.60        34.68         9.57 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NH TCGA-ER-A3ET 
       17.72        78.44        11.80         1.87        11.74         6.58 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1YY 
       22.49        15.72         5.36         3.29         3.45        11.01 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF 
       15.52         7.33         7.30         3.39         8.22        11.08 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3R5 
       47.38         8.81        49.15        14.20         2.27         0.99 
TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 
        0.16         9.90        31.33        10.13        12.16        10.65 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
       14.50        14.50         0.43         8.98        60.03         2.99 
TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       10.98        11.84         5.49         6.48         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
       21.07         3.72         1.08         1.94        12.07 

$subtype3
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MV TCGA-D3-A51R 
       28.08        22.55        36.16        64.44        29.23        32.61 
TCGA-D3-A5GN TCGA-D3-A8GQ TCGA-EB-A44R TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29P 
       52.01        11.44         0.20         1.35        60.23        12.03 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML 
       11.31        36.30        51.12        36.33         2.70       111.91 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-ER-A19G TCGA-FR-A8YC TCGA-FS-A1ZC 
      122.73        15.95        16.14       114.15         2.20        20.38 
TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U8 
       30.87         0.20        84.72        11.84 

subtype1 subtype2 subtype3 
    0.13     0.16     0.20 
subtype1 subtype2 subtype3 
  185.16   124.47   122.73 
subtype1 subtype2 subtype3 
  14.500   14.500   28.655 
[1] "0.1 - 185.2 (14.5)" "0.2 - 124.5 (14.5)" "0.2 - 122.7 (28.7)"
D10V2, survival
          sevent
clus2       0  1
  subtype1 81 74
  subtype2 58 68
  subtype3 15 14
subtype1 subtype2 subtype3 
     155      126       29 
subtype1 subtype2 subtype3 
      74       68       14 
$subtype1
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
       61.02        16.57        16.67       133.25        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK 
       43.43       168.00        11.87        62.07       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E 
      171.58        59.57       166.52        24.53        13.87       174.84 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD 
       32.94        26.89       125.79        18.18       125.19        11.61 
TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A148 
      228.99        89.13        95.24       137.79       129.63       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         3.65        18.12        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
        9.90        25.18        66.25        48.89        36.03       194.83 
TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
      176.55        65.92        23.44        10.49        15.68        13.87 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       17.85        54.02        17.29        52.01        12.20        29.82 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        26.89        68.15         4.96 
TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       91.56        80.61        13.97        63.78        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ 
       56.84        18.61        86.14        67.43        48.72        89.33 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M6 
       79.66        75.48        90.97        14.30        44.88       129.27 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
       19.76        47.28       268.73        16.96        96.23       158.63 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       162.48        71.21 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      124.31        51.62         3.68        54.51        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A197 
      127.20        36.95        53.19        27.35       148.08        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19S 
       50.76         9.17        48.89        26.37         6.44        37.25 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN 
       20.15        16.37        31.27       247.04        33.21        92.98 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.16        38.27        29.46       216.92       202.65        20.91 
TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       40.27        47.38        23.93        74.73       133.55        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        49.48        27.09        27.02        66.67        28.73 
TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       26.73        47.54       139.89        64.44        62.79        39.58 
TCGA-GN-A8LK TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       50.10       294.77        18.05         0.33         0.69       212.22 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZR TCGA-WE-A8ZY TCGA-WE-AAA0 
      219.16       105.04        59.41         4.37        43.73        30.18 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        23.64        93.07        11.74 

$subtype2
TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       12.99       112.04       112.57        71.80       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 
       23.77       115.53        86.76        56.19       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98        46.32        86.93        60.23         9.34       103.59 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A8GB TCGA-D3-A8GE 
       55.73        56.35       145.12        22.62        30.84        15.19 
TCGA-D3-A8GN TCGA-D3-A8GS TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      161.00       117.17       117.21        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A5VV TCGA-EE-A17Y TCGA-EE-A20C 
       53.92        68.09       215.44         6.35        27.22       151.27 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29Q 
      168.26        13.55        63.35        47.84        72.07        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 
       14.47        55.92       369.93        25.87       195.02       102.90 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GO 
       39.29       314.56       161.03       208.04        54.74       126.81 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       13.91        55.59        21.67        61.51       103.27       103.20 
TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB 
      204.66       134.40        53.26       172.18        64.08       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19B 
       51.35       109.58        31.40        35.44        77.75        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       12.59        13.02       152.35       131.51        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NH 
       50.89       148.18        79.99        43.82        23.34        32.05 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1YX 
       80.32        46.98        15.72         7.00        94.39        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD 
      228.59        28.08         7.79        27.72        48.85        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FS-A4FD 
       15.45       101.26        11.41       148.80       174.84        77.88 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A 
       22.92         0.16         9.90       117.93        10.13        32.48 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-W3-A825 TCGA-W3-A828 
       12.62        21.37        59.41       357.04        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
        4.01        42.08        24.03        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 
       90.28        56.98        52.34         2.20        10.36        15.16 

$subtype3
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MV TCGA-D3-A51R 
       28.08        31.59        42.08        66.08        45.30        63.81 
TCGA-D3-A5GN TCGA-D3-A8GQ TCGA-D9-A1JX TCGA-EB-A44R TCGA-EE-A182 TCGA-EE-A20B 
      135.75        29.06         6.41        10.16        14.70       133.81 
TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 
       56.42        46.82        36.82        59.28        94.82        28.83 
TCGA-EE-A2ML TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-ER-A19G TCGA-FR-A8YC 
      203.05       122.73        23.47        34.32       268.93        34.82 
TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U8 
      357.37        32.75         0.20        84.72        46.36 

subtype1 subtype2 subtype3 
    0.33     0.16     0.20 
subtype1 subtype2 subtype3 
  294.77   369.93   357.37 
subtype1 subtype2 subtype3 
   47.54    56.27    45.30 
[1] "0.3 - 294.8 (47.5)" "0.2 - 369.9 (56.3)" "0.2 - 357.4 (45.3)"
D10V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 31             4
  subtype2                 20             0
  subtype3                  5             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        17                 104
  subtype2                                        43                  70
  subtype3                                         6                  18
D10V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              31       20        5
  PRIMARY TUMOR                                    4        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       17       43        6
  REGIONAL LYMPH NODE                            104       70       18
[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"
          vv
clus       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           5       4      11       11       13       10         6
  subtype2           6       3      15        3       12        6         4
  subtype3           1       0       1        1        1        4         2
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1        10         7        17          6         13         25
  subtype2         6         3        14          6         11         25
  subtype3         1         1         2          1          4          3
          vv
clus       STAGE IV
  subtype1        7
  subtype2        6
  subtype3        3
D10V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        5        6        1
  STAGE 0            4        3        0
  STAGE I           11       15        1
  STAGE IA          11        3        1
  STAGE IB          13       12        1
  STAGE II          10        6        4
  STAGE IIA          6        4        2
  STAGE IIB         10        6        1
  STAGE IIC          7        3        1
  STAGE III         17       14        2
  STAGE IIIA         6        6        1
  STAGE IIIB        13       11        4
  STAGE IIIC        25       25        3
  STAGE IV           7        6        3
[1] 14  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       T0+T1 T2 T3 T4
  subtype1    31 32 32 33
  subtype2    20 36 26 19
  subtype3     6  2  8  6
D10V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       31       20        6
  T2          32       36        2
  T3          32       26        8
  T4          33       19        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"
          vv
clus       N0 N1 N2 N3
  subtype1 80 27 16 19
  subtype2 65 26 12 19
  subtype3 14  4  6  2
D10V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       80       65       14
  N1       27       26        4
  N2       16       12        6
  N3       19       19        2
[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"
          vv
clus        M0  M1 M1A M1B M1C
  subtype1 141   2   1   1   4
  subtype2 119   1   0   1   4
  subtype3  24   1   0   1   1
D10V8, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       141      119       24
  M1         2        1        1
  M1A        1        0        0
  M1B        1        1        1
  M1C        4        4        1
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus        0  1
  subtype1 64 41
  subtype2 45 29
  subtype3  8  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64   41
  subtype2   45   29
  subtype3    8    9
     clus
vv    subtype1 subtype2 subtype3
  NO        64       45        8
  YES       41       29        9
[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"
D10V10, binary
          cls
clus         0   1
  subtype1  17 140
  subtype2  15 118
  subtype3   5  24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17  140
  subtype2   15  118
  subtype3    5   24
     clus
vv    subtype1 subtype2 subtype3
  NO        17       15        5
  YES      140      118       24
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
D10V12, binary
          cls
clus         0   1
  subtype1  56 101
  subtype2  48  85
  subtype3  12  17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56  101
  subtype2   48   85
  subtype3   12   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       56       48       12
  MALE        101       85       17
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1   147
  subtype2     1                         0   124
  subtype3     1                         0    28
D10V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        1        1
  BLACK OR AFRICAN AMERICAN        1        0        0
  WHITE                          147      124       28
[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"
D10V14, binary
          cls
clus         0   1
  subtype1   4 151
  subtype2   3 126
  subtype3   0  29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  151
  subtype2    3  126
  subtype3    0   29
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        3        0
  NOT HISPANIC OR LATINO      151      126       29
[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"
