
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.84.4098/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.84.4098/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/THCA-TP/2909296/1.GDAC_mergedClustering.Finished/THCA-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2844384/1.GDAC_clinicalDataPicker.Finished/THCA-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=318, in cluster file=500, common to both=318
[1]   8 318
[1] "CN_CNMF"
[1] 3
  1   2   3 
 21 238  50 
  1   2   3 
 21 238  50 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
101  46 171 
  1   2   3 
101  46 171 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
46 59 59 
 1  2  3 
46 59 59 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
70 26 68 
 1  2  3 
70 26 68 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
95 32 70 92 
 1  2  3  4 
95 32 70 92 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
105 128  56 
  1   2   3 
105 128  56 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
 89 112 101 
  1   2   3 
 89 112 101 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
115 104  83 
  1   2   3 
115 104  83 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "RADIATIONTHERAPY"                      
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "RADIATIONEXPOSURE"                     
[13] "DISTANT.METASTASIS"                    
[14] "EXTRATHYROIDAL.EXTENSION"              
[15] "LYMPH.NODE.METASTASIS"                 
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "TUMOR.STAGECODE"                       
[19] "NEOPLASM.DISEASESTAGE"                 
[20] "MULTIFOCALITY"                         
[21] "TUMOR.SIZE"                            
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 318 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
         479          356          232          182          197          251 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZF TCGA-BJ-A0ZG 
         264          122          183          237          210          230 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
          22          152           85           13          235          246 
TCGA-BJ-A28R TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A290 TCGA-BJ-A3PR 
         148           84          155          532          626          244 
TCGA-BJ-A3PT TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-DE-A0XZ 
         367           16            3            6            7          402 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13O 
         231          952          161          286          274          215 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
        4199           92          265          758          393          362 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
         454          243          334         3041          549          212 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
         243          151          212           30          273           31 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
         181          304          242          152          623          318 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
          59          292          312          242          234          153 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
         267          256          247          284          206          280 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
         287          301          262          291          215          315 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
         378          330          304          251          524          380 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
         480          167          277          721          630          469 
TCGA-DJ-A3UU TCGA-DJ-A3UV TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
         538          590         1308          345          405          388 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V6 TCGA-DJ-A3V7 
         761          225          540          443          454          299 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
         259          217          363          350          134          235 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VM TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
         253          528          481         1225           93           70 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
         945          365         1544         1222         1421          635 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
         427           34           11           NA           45           10 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
           7            5           22            8           45           NA 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
          16            5            7           35          234          210 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
          12           12          580          153          214           NA 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
         245          217          284         1421         1209          650 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
          81          207          202          138          106          209 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
         189          174          192          348          249          209 
TCGA-EM-A2CM TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR 
         357          344          183           90          199          218 
TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
         284          319          176          353          219           88 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
         347          284          191          194          224           10 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
         201          397          282          341          336          161 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3O8 TCGA-EM-A3OB TCGA-ET-A25G TCGA-ET-A25I 
         262          207           15           71         1088           10 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
         903          589          450          375           75          135 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
          15          621         1643          579          373         1049 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
         449          198           43         1182            9          362 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
        2058           59         2266         2535         1309          406 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
        1413           20          237           51          177          127 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
          74          168          752           39           56           72 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
         137         2095         1536         1366           65            9 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40S 
         145          138         3424          751           98          152 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
        1565         1442          374         1346          751         1333 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
        3130         2031         2292         1215           NA         1907 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SE 
        2872         2589         1868         1913         1401          669 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
          28         1463           38           35           34           50 
TCGA-FY-A3NM TCGA-FY-A3NN TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
          30           NA           18           46           23            1 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
         141           66          278           NA           23           29 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-GE-A2C6 
         208          126          199          138           27          206 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
         106          145          148           90           67           88 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 
        1070          939           80           99           68          392 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
         415           41          968          846          751          678 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
         174           75         3680          485          477         2637 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
         182          366          204          376          530         1963 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EU TCGA-MK-A4N7 TCGA-MK-A4N9 
         447          623           18           22          440          265 
Variable 1:'AGE':	nDistinctValues=67,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=254,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONEXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'EXTRATHYROIDAL.EXTENSION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'LYMPH.NODE.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR.SIZE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=28,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "HISTOLOGICAL.TYPE"                     
 [4] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [5] "RADIATIONEXPOSURE"                     
 [6] "DISTANT.METASTASIS"                    
 [7] "EXTRATHYROIDAL.EXTENSION"              
 [8] "LYMPH.NODE.METASTASIS"                 
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "TUMOR.STAGECODE"                       
[12] "NEOPLASM.DISEASESTAGE"                 
[13] "MULTIFOCALITY"                         
[14] "TUMOR.SIZE"                            
[1] "TUMOR.?STAGE" "11"          
[1] "stage2"
vv
 T1 T1A T1B  T2  T3  T4 T4A  TX 
 28  11  63 109  97   1   8   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 318 columns, 1 survival variables, and 14 non-survival variables.
AGE, nv=67, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RADIATIONEXPOSURE, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL.EXTENSION, nv=3, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=26, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR.SIZE, nv=59, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1  20   1
  subtype2 238   0
  subtype3  50   0
subtype1 subtype2 subtype3 
      21      238       50 
subtype1 subtype2 subtype3 
       1        0        0 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A290 TCGA-DJ-A2PV TCGA-DJ-A2Q0 
       15.75         0.43         8.09        20.58         7.96         8.12 
TCGA-E8-A432 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22N TCGA-EM-A2CO 
        0.53        46.72        39.75        21.37         6.87         6.02 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-ET-A2MZ TCGA-ET-A39M TCGA-ET-A39N TCGA-FE-A231 
       11.41         6.61        12.26        65.88        65.88        12.30 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       65.92         1.64         0.99 

$subtype2
TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       11.70         5.98         8.25         8.68         4.01         6.02 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28T 
        7.79         7.56         5.00         7.73         4.87         2.76 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A3PR TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        5.10        17.49         8.02         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DJ-A13O 
        0.23         7.59        31.30         5.29         9.40         7.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       65.72         3.02         8.71        12.92        11.90        14.93 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI 
        7.99        10.98        65.85        18.05         7.99         4.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.97         0.99         1.02         5.95         9.99         7.96 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PW 
        5.00        20.48        10.45         9.60        10.26         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.03         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QC 
        9.44         9.90         8.61         7.07        10.36         9.99 
TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       17.23         9.11        23.70        20.71        15.42        17.69 
TCGA-DJ-A3UV TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       19.40        43.00        11.34        13.32        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V6 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
        7.40        17.75        14.56        14.93         9.83         8.52 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
        7.13        11.93        11.51         4.41         7.73         8.32 
TCGA-DJ-A3VJ TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 
       17.36        40.27         3.06         2.30        31.07        50.76 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
       40.18        46.72        20.88         1.12         0.36        66.12 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
        1.48         0.33         0.23         0.16         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
        1.48        66.15         0.16         1.15         7.69         6.90 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
        0.39         0.39         5.03         7.04        66.08         8.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22O TCGA-EM-A22Q 
        7.13         9.34         2.66         6.81         6.21         6.31 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
        8.19         6.87        11.31         2.96         6.54         9.34 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49         5.79        11.61         7.20         2.89         9.34 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
        6.28         6.38         7.36         0.33        13.05         9.27 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3O8 TCGA-EM-A3OB 
       11.21        11.05         8.61         6.81         0.49         2.33 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N 
       35.77         0.33        29.69        19.36        12.33         2.47 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
        0.49        20.42        54.02        19.04        34.49        14.76 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O 
        6.51        38.86         0.30        11.90        65.95        43.04 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       13.35        46.45         0.66         7.79         1.68         5.82 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.52        24.72         1.28         1.84         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT 
        4.50        65.92        50.50        44.91         2.14         4.77 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-FE-A22Z TCGA-FE-A230 
        4.54        65.79        24.69         5.00        51.45        47.41 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 
       44.25        24.69        43.82        65.82        65.88        39.95 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SE 
       62.70        65.82        61.41        62.89        46.06        21.99 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NN 
        0.92        48.10         1.25         1.15         1.12        66.12 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        1.51         0.76         4.64         2.17         9.14        66.15 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-H2-A26U 
        6.84         4.14         6.54         4.54         0.89         3.48 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
        4.77         4.87         2.96         2.20         2.89        35.18 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE 
       30.87         2.63         2.24        13.64         1.35        27.81 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L 
       24.69        22.29         2.47        65.82        15.68        65.88 
TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-L6-A4EU TCGA-MK-A4N7 
        6.71        17.42         0.72        14.47 

$subtype3
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A3PT TCGA-DE-A0XZ 
        7.63         6.48         0.72         2.79        12.07        13.22 
TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q7 
        9.01        24.92         6.97         8.98         1.94         9.57 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       12.43        10.85         8.25        12.49        15.78         5.49 
TCGA-DJ-A3VM TCGA-E3-A3DZ TCGA-E3-A3E5 TCGA-E8-A434 TCGA-EM-A1CS TCGA-EM-A22K 
       15.81        12.00        14.04         0.23        19.07         6.64 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CM TCGA-EM-A3AP 
        4.54         3.48         5.72        11.44        11.74         5.29 
TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L TCGA-ET-A3BP TCGA-ET-A3DS 
       14.79         4.44         1.41         1.94         4.18         0.30 
TCGA-ET-A40P TCGA-FE-A237 TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA 
        3.22        65.92        65.88         0.03         0.76         0.95 
TCGA-GE-A2C6 TCGA-IM-A3U3 TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH TCGA-KS-A41I 
        6.77         3.25        12.89        31.82         5.72        15.95 
TCGA-KS-A4I7 TCGA-KS-A4IB 
       12.36        64.54 

subtype1 subtype2 subtype3 
    0.43     0.10     0.03 
subtype1 subtype2 subtype3 
   65.92    66.15    65.92 
subtype1 subtype2 subtype3 
   11.41     8.22     7.94 
[1] "0.4 - 65.9 (11.4)" "0.1 - 66.2 (8.2)"  "0.0 - 65.9 (7.9)" 
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
  [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
 [25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [31] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [61] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [73] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [79] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [85] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[103] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[109] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[115] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[121] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[133] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[145] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[151] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[157] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[163] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[169] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[175] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[181] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[187] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[193] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[199] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[205] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[211] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[217] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[223] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[229] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[235] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[241] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[247] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[253] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[259] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[265] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[271] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[277] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[283] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[289] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[295] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[301] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[307] "subtype3" "subtype2" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
  [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
 [25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [31] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [61] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [73] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [79] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [85] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[103] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[109] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[115] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[121] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[133] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[145] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[151] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[157] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[163] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[169] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[175] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[181] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[187] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[193] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[199] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[205] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[211] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[217] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[223] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[229] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[235] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[241] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[247] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[253] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[259] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[265] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[271] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[277] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[283] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[289] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[295] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[301] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[307] "subtype3" "subtype2" "subtype2"
  [1] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
  [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [13] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [19] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype3"
 [25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [31] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [37] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [55] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [61] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [67] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
 [73] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [79] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [85] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [91] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [97] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[103] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[109] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[115] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[121] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[133] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[139] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[145] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[151] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[157] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[163] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[169] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[175] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[181] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[187] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[193] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[199] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[205] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[211] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[217] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[223] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[229] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[235] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[241] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[247] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[253] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[259] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[265] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[271] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[277] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[283] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[289] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[295] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[301] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[307] "subtype3" "subtype2" "subtype2"
D1V2, continuous
D1V3, binary
          cls
clus         0   1
  subtype1  14   7
  subtype2 179  59
  subtype3  40  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    7
  subtype2  179   59
  subtype3   40   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14      179       40
  MALE          7       59       10
          vv
clus       OTHER THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1     5                                             9
  subtype2    12                                           151
  subtype3     3                                            23
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      6
  subtype2                                                                     49
  subtype3                                                                     20
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   1
  subtype2                                                                  26
  subtype3                                                                   4
D1V4, multiclass
D1V5, binary
          cls
clus         0   1
  subtype1   2  19
  subtype2  11 227
  subtype3   1  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   19
  subtype2   11  227
  subtype3    1   49
     clus
vv    subtype1 subtype2 subtype3
  NO         2       11        1
  YES       19      227       49
D1V6, binary
          cls
clus         0   1
  subtype1  18   1
  subtype2 194  12
  subtype3  46   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    1
  subtype2  194   12
  subtype3   46    0
     clus
vv    subtype1 subtype2 subtype3
  NO        18      194       46
  YES        1       12        0
          vv
clus        M0  M1  MX
  subtype1   6   0  15
  subtype2 117   3 117
  subtype3  24   1  25
D1V7, multiclass
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1            3                       0   18
  subtype2           57                       6  163
  subtype3           10                       0   38
D1V8, multiclass
          vv
clus        N0  N1 N1A N1B  NX
  subtype1  14   0   1   1   5
  subtype2 110  16  56  33  23
  subtype3  27   2   9   9   3
D1V9, multiclass
          vv
clus        R0  R1  R2  RX
  subtype1  17   0   0   3
  subtype2 191  18   1  11
  subtype3  37   4   0   6
D1V10, multiclass
D1V11, continuous
D1V12, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1       4       10         6         1         0
  subtype2     143       20        51        21         2
  subtype3      30        3        10         6         1
D1V13, multiclass
D1V14, binary
          cls
clus         0   1
  subtype1   8  13
  subtype2 113 118
  subtype3  29  19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   13
  subtype2  113  118
  subtype3   29   19
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL        8      113       29
  UNIFOCAL         13      118       19
D1V15, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1 100   1
  subtype2  46   0
  subtype3 171   0
subtype1 subtype2 subtype3 
     101       46      171 
subtype1 subtype2 subtype3 
       1        0        0 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       15.75        11.70         7.63         8.68         6.02         7.79 
TCGA-BJ-A0ZF TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
        6.90         7.56         2.79         0.43         7.73         8.09 
TCGA-BJ-A28V TCGA-BJ-A3PT TCGA-CE-A3ME TCGA-DE-A2OL TCGA-DJ-A13M TCGA-DJ-A13S 
        5.10        12.07         0.23         5.29         9.01         8.71 
TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP TCGA-DJ-A2PS 
       14.93         6.97         6.97         0.99         5.00         1.94 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3UV 
        8.12         6.77        10.85         5.49        15.42        19.40 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3VG TCGA-DJ-A3VM TCGA-E3-A3DZ 
       11.34        13.32        12.76         8.32        15.81        12.00 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A434 TCGA-EM-A1CW TCGA-EM-A1YA 
        0.33         0.16         0.72         0.23         8.05         7.13 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K 
        9.34        46.72        39.75        21.37         6.81         6.64 
TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
        4.54         6.87         6.31        11.44         8.19         6.87 
TCGA-EM-A2CM TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT 
       11.74        11.31         6.02         6.54         7.17        10.49 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AP 
       11.61         7.20        11.41         7.36         6.61         5.29 
TCGA-EM-A3AR TCGA-EM-A3O8 TCGA-EM-A3OB TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N1 
        6.81         0.49         2.33         0.33         0.49        14.76 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3DS 
        6.51        38.86         0.30         1.94        65.88         0.30 
TCGA-ET-A3DV TCGA-ET-A40P TCGA-FE-A239 TCGA-FY-A2QD TCGA-FY-A3I4 TCGA-FY-A3I5 
       65.79         3.22        65.92         1.25         1.12         1.64 
TCGA-FY-A3NM TCGA-FY-A3NN TCGA-FY-A3NP TCGA-FY-A3R7 TCGA-FY-A3R9 TCGA-FY-A3W9 
        0.99        66.12         0.59         0.03         2.17         0.76 
TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A40N TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-J8-A3O0 
        0.95         4.54         0.89         4.77         4.87        12.89 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4I3 
       31.82        27.81        15.95        65.88        12.03 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ TCGA-BJ-A28T TCGA-BJ-A28X TCGA-BJ-A3PR TCGA-CE-A27D 
        5.98         5.00         2.76        17.49         8.02         0.10 
TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A2PT TCGA-DJ-A2PX TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 
        7.07         3.02         9.60         5.03         9.34         9.21 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q9 TCGA-DJ-A3US TCGA-DJ-A3UW TCGA-DJ-A3VD TCGA-DJ-A3VF 
        9.90        10.36        20.71        43.00        11.51         7.73 
TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A414 TCGA-E8-A419 
        2.30         1.12         0.36        66.12         0.23        66.15 
TCGA-E8-A44M TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CP TCGA-EM-A2P1 TCGA-EM-A3AJ 
        0.39         3.48         5.72         2.96         6.38        13.05 
TCGA-ET-A39M TCGA-ET-A39R TCGA-ET-A3BV TCGA-ET-A3DO TCGA-ET-A3DQ TCGA-ET-A3DT 
       65.88        46.45         1.84        65.92        44.91         4.77 
TCGA-ET-A3DU TCGA-ET-A40S TCGA-FE-A230 TCGA-FE-A23A TCGA-FY-A3R6 TCGA-FY-A3TY 
        4.54         5.00        47.41        62.70         0.76        66.15 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3EB TCGA-KS-A4ID 
        6.77         3.48        35.18        20.48 

$subtype3
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A28R TCGA-BJ-A290 
        6.48         8.25         4.01         0.72         4.87        20.58 
TCGA-CE-A13K TCGA-CE-A3MD TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN 
        0.53         0.20        13.22         7.59        31.30         9.40 
TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QD 
       65.72        24.92        12.92        11.90         7.99        10.98 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A1QO 
       65.85        18.05         7.99         4.96         8.98         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU 
        5.95         9.99         7.96        20.48        10.45        10.26 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q4 TCGA-DJ-A2Q6 
        7.96         7.69         8.78         8.42         9.44         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
        9.57         7.07        12.43         9.99         8.25        17.23 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3UU TCGA-DJ-A3V0 
       12.49        15.78         9.11        23.70        17.69        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V6 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
        7.40        17.75        14.56        14.93         9.83         8.52 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VE TCGA-DJ-A3VJ TCGA-DO-A1JZ TCGA-DO-A1K0 
        7.13        11.93         4.41        17.36        40.27         3.06 
TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       31.07        50.76        40.18        46.72        20.88        14.04 
TCGA-E8-A3X7 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A436 
        1.48         0.26         1.48         0.53         0.16         1.15 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
        7.69         6.90         0.39        19.07         5.03         7.04 
TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2CU TCGA-EM-A2OX 
       66.08         2.66         6.21         9.34         5.79         2.89 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P3 TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO 
        9.34         6.28         0.33         9.27        11.21        11.05 
TCGA-EM-A3AQ TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
        8.61        35.77        29.69        19.36        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
        2.47         4.44        20.42        54.02        19.04        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39P 
       34.49         1.41        11.90        65.95        43.04        13.35 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
        0.66         7.79         1.68         5.82         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DP 
        5.52        24.72         1.28         2.37         4.50        50.50 
TCGA-ET-A3DR TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        2.14        24.69        51.45        12.30        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A3PA 
       43.82        65.82        65.88        65.92        39.95        65.82 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SE TCGA-FK-A3SG 
       65.88        61.41        62.89        46.06        21.99         0.92 
TCGA-FK-A3SH TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A3YR 
       48.10         1.15         1.51         4.64         9.14         6.84 
TCGA-FY-A40K TCGA-FY-A40L TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED 
        4.14         6.54         2.96         2.20         2.89        30.87 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YF 
        2.63         3.25         2.24        13.64         1.35        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 
       22.29         5.72         2.47        65.82        15.68         5.98 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-L6-A4EP 
        6.71        12.36        17.42        64.54        14.70         0.59 
TCGA-L6-A4EU TCGA-MK-A4N7 TCGA-MK-A4N9 
        0.72        14.47         8.71 

subtype1 subtype2 subtype3 
    0.03     0.10     0.16 
subtype1 subtype2 subtype3 
   66.12    66.15    66.08 
subtype1 subtype2 subtype3 
    6.97     7.40     9.40 
[1] "0.0 - 66.1 (7.0)" "0.1 - 66.2 (7.4)" "0.2 - 66.1 (9.4)"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [37] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [43] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [67] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [73] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [91] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [97] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[109] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[121] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[127] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[133] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[139] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[145] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[151] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[157] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[169] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[175] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[181] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[187] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[193] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[199] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[205] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[211] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
[217] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[223] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[229] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[235] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[241] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[247] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[253] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[259] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[265] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[271] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
[277] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[283] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[289] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[295] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[301] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[307] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[313] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [37] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [43] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [67] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [73] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [91] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [97] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[109] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[121] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[127] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[133] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[139] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[145] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[151] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[157] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[169] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[175] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[181] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[187] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[193] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[199] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[205] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[211] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
[217] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[223] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[229] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[235] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[241] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[247] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[253] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[259] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[265] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[271] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
[277] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[283] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[289] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[295] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[301] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[307] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[313] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype3"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
 [25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [37] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
 [43] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [49] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
 [55] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [67] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype2"
 [73] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [79] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [85] "subtype3" "subtype1" "subtype3" "subtype3" "subtype2" "subtype1"
 [91] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [97] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[103] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[109] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[115] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[121] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[127] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[133] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[139] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[145] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[151] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[157] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[169] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[175] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
[181] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[187] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[193] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[199] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[205] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[211] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
[217] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[223] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[229] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[235] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[241] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[247] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[253] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[259] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[265] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[271] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
[277] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[283] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[289] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[295] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[301] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[307] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[313] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
D2V2, continuous
D2V3, binary
          cls
clus         0   1
  subtype1  78  23
  subtype2  35  11
  subtype3 127  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78   23
  subtype2   35   11
  subtype3  127   44
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       78       35      127
  MALE         23       11       44
          vv
clus       OTHER THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1    15                                            26
  subtype2     2                                            30
  subtype3     3                                           132
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     58
  subtype2                                                                      8
  subtype3                                                                     13
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   2
  subtype2                                                                   6
  subtype3                                                                  23
D2V4, multiclass
D2V5, binary
          cls
clus         0   1
  subtype1   1 100
  subtype2   2  44
  subtype3  11 160
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  100
  subtype2    2   44
  subtype3   11  160
     clus
vv    subtype1 subtype2 subtype3
  NO         1        2       11
  YES      100       44      160
D2V6, binary
          cls
clus         0   1
  subtype1  82   5
  subtype2  39   2
  subtype3 144   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   82    5
  subtype2   39    2
  subtype3  144    6
     clus
vv    subtype1 subtype2 subtype3
  NO        82       39      144
  YES        5        2        6
          vv
clus       M0 M1 MX
  subtype1 43  2 55
  subtype2 24  0 22
  subtype3 88  2 81
D2V7, multiclass
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1           10                       0   85
  subtype2            9                       0   35
  subtype3           51                       6  106
D2V8, multiclass
          vv
clus       N0 N1 N1A N1B NX
  subtype1 72  2   7   5 15
  subtype2 21  2  13   8  2
  subtype3 64 16  47  30 14
D2V9, multiclass
          vv
clus        R0  R1  R2  RX
  subtype1  83   4   0   7
  subtype2  34   4   0   4
  subtype3 134  16   1  10
D2V10, multiclass
D2V11, continuous
D2V12, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      56       21        19         2         2
  subtype2      29        3         9         5         0
  subtype3      98       11        40        21         1
D2V13, multiclass
D2V14, binary
          cls
clus        0  1
  subtype1 45 54
  subtype2 19 25
  subtype3 88 78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   54
  subtype2   19   25
  subtype3   88   78
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       45       19       88
  UNIFOCAL         54       25       78
D2V15, continuous

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 46  0
  subtype2 59  0
  subtype3 58  1
subtype1 subtype2 subtype3 
      46       59       59 
subtype1 subtype2 subtype3 
       0        0        1 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0ZA TCGA-BJ-A0ZC 
       15.75        11.70         7.63         5.98         8.68         6.02 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-DE-A3KN 
        7.79         7.56         5.00         2.79         0.43         9.40 
TCGA-DJ-A13M TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QM TCGA-DJ-A2PN 
        9.01        14.93         7.99        18.05         0.99         9.99 
TCGA-DJ-A2PO TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q2 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        7.96         7.96         8.42         6.77         8.61         9.57 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-E3-A3DZ TCGA-EM-A1CW TCGA-EM-A1YD 
       10.36        12.43         9.99        12.00         8.05        39.75 
TCGA-EM-A22L TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CQ TCGA-EM-A2CU 
        4.54        11.44         8.19         6.87         6.54         5.79 
TCGA-EM-A2OV TCGA-EM-A3AJ TCGA-EM-A3AN TCGA-EM-A3AP TCGA-ET-A2N5 TCGA-ET-A39I 
       11.61        13.05        11.21         5.29        38.86         0.30 
TCGA-ET-A3BP TCGA-ET-A3DP TCGA-FY-A2QD TCGA-J8-A3O0 
        4.18        50.50         1.25        12.89 

$subtype2
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A290 
        6.48         8.25         4.01         8.09         4.87        20.58 
TCGA-CE-A3ME TCGA-DE-A0Y2 TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QD 
        0.23         7.59         7.07         3.02         8.71        10.98 
TCGA-DJ-A1QE TCGA-DJ-A1QG TCGA-DJ-A1QO TCGA-DJ-A2PP TCGA-DJ-A2PY TCGA-DJ-A2Q0 
       65.85         6.97         1.02         5.00         8.78         8.12 
TCGA-DJ-A2Q8 TCGA-DJ-A2QB TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E1 TCGA-E3-A3E3 
        7.07        10.85         3.06        31.07        40.18        20.88 
TCGA-E3-A3E5 TCGA-E8-A2EA TCGA-EM-A1CT TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       14.04         0.36         5.03         7.13         9.34        46.72 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22O TCGA-EM-A2CM TCGA-EM-A2CO TCGA-EM-A2OY 
        2.66         6.81         6.21        11.74         6.02        11.41 
TCGA-EM-A2P1 TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25O TCGA-ET-A2MY 
        6.38        35.77        14.79        12.33         4.44        19.04 
TCGA-ET-A2N0 TCGA-ET-A39P TCGA-ET-A39T TCGA-ET-A3BT TCGA-ET-A3DO TCGA-ET-A3DW 
       34.49        13.35         7.79        24.72        65.92        24.69 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A234 TCGA-FE-A236 
       51.45        47.41        12.30        44.25        43.82        65.88 
TCGA-FE-A237 TCGA-FE-A23A TCGA-FY-A3BL TCGA-IM-A3EB TCGA-J8-A3NZ 
       65.92        62.70         1.15        35.18         2.24 

$subtype3
TCGA-BJ-A0ZF TCGA-BJ-A191 TCGA-BJ-A28T TCGA-BJ-A28V TCGA-CE-A13K TCGA-CE-A27D 
        6.90         7.73         2.76         5.10         0.53         0.10 
TCGA-CE-A3MD TCGA-DE-A2OL TCGA-DJ-A13V TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QN 
        0.20         5.29        11.90         4.96         6.97         8.98 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2Q1 
       20.48        10.45         1.94        10.26         7.69         9.34 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DO-A1JZ TCGA-E3-A3E0 TCGA-E8-A2JQ TCGA-EM-A1CU 
        9.44         9.90        40.27        50.76        66.12         7.04 
TCGA-EM-A1CV TCGA-EM-A1YE TCGA-EM-A22M TCGA-EM-A22Q TCGA-EM-A2CN TCGA-EM-A2CP 
       66.08        21.37         3.48         6.31        11.31         2.96 
TCGA-EM-A2CR TCGA-EM-A2CS TCGA-EM-A3AI TCGA-EM-A3AO TCGA-ET-A2MZ TCGA-ET-A2N1 
        7.17         9.34         6.61        11.05        12.26        14.76 
TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39R 
        1.41        11.90         1.94        65.88        65.88        46.45 
TCGA-ET-A3BN TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        1.68         5.52         1.28         1.84         2.37         4.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DV TCGA-FE-A233 TCGA-FE-A235 TCGA-FE-A239 
        0.30         4.77        65.79        24.69        65.82        65.92 
TCGA-FY-A3ON TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-IM-A3ED TCGA-J8-A3O1 
        1.51         6.77         4.77        30.87        13.64 

subtype1 subtype2 subtype3 
    0.30     0.23     0.10 
subtype1 subtype2 subtype3 
   50.50    65.92    66.12 
subtype1 subtype2 subtype3 
   8.305    9.340    7.690 
[1] "0.3 - 50.5 (8.3)" "0.2 - 65.9 (9.3)" "0.1 - 66.1 (7.7)"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
  [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
 [31] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
 [37] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [43] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [55] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
 [73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[109] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[115] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[121] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[127] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[133] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[139] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[145] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[151] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[157] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[163] "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
  [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
 [31] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
 [37] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [43] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [55] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
 [73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[109] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[115] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[121] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[127] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[133] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[139] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[145] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[151] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[157] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[163] "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
  [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
 [19] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [25] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
 [31] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
 [37] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [43] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
 [49] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [55] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
 [73] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[103] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[109] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
[115] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[121] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[127] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[133] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[139] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[145] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[151] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[157] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[163] "subtype1" "subtype3"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1 31 15
  subtype2 41 18
  subtype3 39 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   15
  subtype2   41   18
  subtype3   39   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       31       41       39
  MALE         15       18       20
          vv
clus       OTHER THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1     1                                            12
  subtype2    10                                            30
  subtype3     2                                            42
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     31
  subtype2                                                                      8
  subtype3                                                                     14
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   2
  subtype2                                                                  11
  subtype3                                                                   1
D3V4, multiclass
D3V5, binary
          cls
clus        0  1
  subtype1  0 46
  subtype2  9 50
  subtype3  4 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   46
  subtype2    9   50
  subtype3    4   55
     clus
vv    subtype1 subtype2 subtype3
  NO         0        9        4
  YES       46       50       55
D3V6, binary
          cls
clus        0  1
  subtype1 41  1
  subtype2 49  3
  subtype3 48  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41    1
  subtype2   49    3
  subtype3   48    3
     clus
vv    subtype1 subtype2 subtype3
  NO        41       49       48
  YES        1        3        3
          vv
clus       M0 M1 MX
  subtype1 25  1 19
  subtype2 25  0 34
  subtype3 21  1 37
D3V7, multiclass
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1            8                       0   38
  subtype2           17                       3   36
  subtype3            8                       0   46
D3V8, multiclass
          vv
clus       N0 N1 N1A N1B NX
  subtype1 29  0   7   4  6
  subtype2 24  6  11  10  8
  subtype3 23  5  15   7  9
D3V9, multiclass
          vv
clus       R0 R1 RX
  subtype1 38  3  4
  subtype2 45  6  3
  subtype3 46  2  3
D3V10, multiclass
D3V11, continuous
D3V12, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      24        9        10         1         1
  subtype2      22       12        16         9         0
  subtype3      40        7         8         3         1
D3V13, multiclass
D3V14, binary
          cls
clus        0  1
  subtype1 28 15
  subtype2 20 37
  subtype3 29 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   15
  subtype2   20   37
  subtype3   29   27
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       28       20       29
  UNIFOCAL         15       37       27
D3V15, continuous

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 69  1
  subtype2 26  0
  subtype3 68  0
subtype1 subtype2 subtype3 
      70       26       68 
subtype1 subtype2 subtype3 
       1        0        0 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0ZA TCGA-BJ-A0ZC 
       15.75        11.70         7.63         5.98         8.68         6.02 
TCGA-BJ-A0ZE TCGA-BJ-A0ZF TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 
        7.79         6.90         7.56         5.00         2.79         0.43 
TCGA-BJ-A28V TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13W 
        5.10         5.29         9.40         9.01         7.07        14.93 
TCGA-DJ-A13X TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ 
        7.99         6.97         0.99         9.99         7.96        20.48 
TCGA-DJ-A2PS TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q2 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        1.94         7.96         8.42         6.77         8.61         9.57 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-E3-A3DZ TCGA-EM-A1CT TCGA-EM-A1CW 
       10.36        12.43         9.99        12.00         5.03         8.05 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22L TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       39.75        21.37         4.54         6.31        11.44         8.19 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CU 
        6.87        11.31         2.96         6.54         7.17         5.79 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AN TCGA-EM-A3AP TCGA-ET-A25M TCGA-ET-A2MZ 
        6.61        13.05        11.21         5.29        12.33        12.26 
TCGA-ET-A2N1 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39P 
       14.76        38.86         0.30         1.94        65.88        13.35 
TCGA-ET-A3BP TCGA-ET-A3DP TCGA-ET-A3DS TCGA-ET-A3DV TCGA-FE-A232 TCGA-FE-A236 
        4.18        50.50         0.30        65.79        44.25        65.88 
TCGA-FE-A239 TCGA-FY-A2QD TCGA-H2-A2K9 TCGA-J8-A3O0 
       65.92         1.25         4.77        12.89 

$subtype2
TCGA-BJ-A192 TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A2PP TCGA-DJ-A2Q0 
        8.09         3.02         8.71         6.97         5.00         8.12 
TCGA-DJ-A2QB TCGA-E3-A3DY TCGA-E3-A3E5 TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       10.85        31.07        14.04         7.13         9.34        46.72 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A2CM TCGA-EM-A2CO TCGA-EM-A2OV TCGA-EM-A2OY 
        2.66         6.81        11.74         6.02        11.61        11.41 
TCGA-ET-A25O TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39T TCGA-ET-A3BT TCGA-FE-A231 
        4.44        19.04        34.49         7.79        24.72        12.30 
TCGA-FE-A237 TCGA-FY-A3BL 
       65.92         1.15 

$subtype3
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28T 
        6.48         8.25         4.01         7.73         4.87         2.76 
TCGA-BJ-A290 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-DE-A0Y2 
       20.58         0.53         0.10         0.20         0.23         7.59 
TCGA-DJ-A13V TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN 
       11.90        10.98        65.85        18.05         4.96         8.98 
TCGA-DJ-A1QO TCGA-DJ-A2PR TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2PY TCGA-DJ-A2Q1 
        1.02        10.45        10.26         7.69         8.78         9.34 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q8 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3E0 
        9.44         9.90         7.07        40.27         3.06        50.76 
TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-EM-A1CU TCGA-EM-A1CV 
       40.18        20.88         0.36        66.12         7.04        66.08 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2P1 TCGA-EM-A3AO TCGA-ET-A25G 
        3.48         6.21         9.34         6.38        11.05        35.77 
TCGA-ET-A25L TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39M TCGA-ET-A39R TCGA-ET-A3BN 
       14.79         1.41        11.90        65.88        46.45         1.68 
TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.52         1.28         1.84         2.37         4.50        65.92 
TCGA-ET-A3DT TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A233 TCGA-FE-A234 
        4.77        24.69        51.45        47.41        24.69        43.82 
TCGA-FE-A235 TCGA-FE-A23A TCGA-FY-A3ON TCGA-GE-A2C6 TCGA-IM-A3EB TCGA-IM-A3ED 
       65.82        62.70         1.51         6.77        35.18        30.87 
TCGA-J8-A3NZ TCGA-J8-A3O1 
        2.24        13.64 

subtype1 subtype2 subtype3 
    0.30     1.15     0.10 
subtype1 subtype2 subtype3 
   65.92    65.92    66.12 
subtype1 subtype2 subtype3 
   8.020    9.025    9.160 
[1] "0.3 - 65.9 (8.0)" "1.1 - 65.9 (9.0)" "0.1 - 66.1 (9.2)"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [31] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [49] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
 [55] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [73] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [97] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[103] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[109] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[121] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[127] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[133] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[139] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[145] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[151] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[157] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[163] "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [31] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [49] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
 [55] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [73] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [97] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[103] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[109] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[121] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[127] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[133] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[139] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[145] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[151] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[157] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[163] "subtype1" "subtype3"
  [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
 [25] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [31] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype3"
 [37] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
 [43] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
 [49] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
 [55] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
 [61] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
 [67] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [73] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
 [79] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype2"
 [85] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
 [91] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [97] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[103] "subtype1" "subtype2" "subtype2" "subtype3" "subtype1" "subtype1"
[109] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[115] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
[121] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[127] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
[133] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[139] "subtype1" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[145] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[151] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
[157] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[163] "subtype1" "subtype3"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 44 26
  subtype2 19  7
  subtype3 48 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   26
  subtype2   19    7
  subtype3   48   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       44       19       48
  MALE         26        7       20
          vv
clus       OTHER THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1     0                                            24
  subtype2    10                                             8
  subtype3     3                                            52
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     42
  subtype2                                                                      7
  subtype3                                                                      4
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   4
  subtype2                                                                   1
  subtype3                                                                   9
D4V4, multiclass
D4V5, binary
          cls
clus        0  1
  subtype1  3 67
  subtype2  2 24
  subtype3  8 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   67
  subtype2    2   24
  subtype3    8   60
     clus
vv    subtype1 subtype2 subtype3
  NO         3        2        8
  YES       67       24       60
D4V6, binary
          cls
clus        0  1
  subtype1 63  1
  subtype2 22  3
  subtype3 53  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    1
  subtype2   22    3
  subtype3   53    3
     clus
vv    subtype1 subtype2 subtype3
  NO        63       22       53
  YES        1        3        3
          vv
clus       M0 M1 MX
  subtype1 29  2 38
  subtype2  9  0 17
  subtype3 33  0 35
D4V7, multiclass
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1           11                       0   57
  subtype2            5                       0   21
  subtype3           17                       3   42
D4V8, multiclass
          vv
clus       N0 N1 N1A N1B NX
  subtype1 42  2  10   6 10
  subtype2 12  1   3   4  6
  subtype3 22  8  20  11  7
D4V9, multiclass
          vv
clus       R0 R1 RX
  subtype1 57  4  5
  subtype2 22  1  3
  subtype3 50  6  2
D4V10, multiclass
D4V11, continuous
D4V12, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      38       12        15         2         2
  subtype2       7        8         7         4         0
  subtype3      41        8        12         7         0
D4V13, multiclass
D4V14, binary
          cls
clus        0  1
  subtype1 34 33
  subtype2 11 14
  subtype3 32 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   33
  subtype2   11   14
  subtype3   32   32
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       34       11       32
  UNIFOCAL         33       14       32
D4V15, continuous

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 94  1
  subtype2 32  0
  subtype3 70  0
  subtype4 92  0
subtype1 subtype2 subtype3 subtype4 
      95       32       70       92 
subtype1 subtype2 subtype3 subtype4 
       1        0        0        0 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       15.75        11.70         7.63         8.68         6.02         7.79 
TCGA-BJ-A0ZF TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A28V 
        6.90         7.56         2.79         0.43         8.09         5.10 
TCGA-BJ-A3PT TCGA-DE-A2OL TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13W TCGA-DJ-A1QG 
       12.07         5.29         9.01         3.02        14.93         6.97 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QA 
        6.97         0.99         5.00         8.12         6.77        12.43 
TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UV TCGA-DJ-A3UZ 
       10.85         5.49        20.71        15.42        19.40        12.76 
TCGA-DJ-A3V4 TCGA-DJ-A3VG TCGA-DJ-A3VM TCGA-E3-A3DZ TCGA-E8-A415 TCGA-E8-A416 
       14.56         8.32        15.81        12.00         0.16         0.72 
TCGA-E8-A434 TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
        0.23         8.05         7.13         9.34        46.72        39.75 
TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A2CK 
       21.37         6.81         6.64         4.54         6.87         8.19 
TCGA-EM-A2CL TCGA-EM-A2CM TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
        6.87        11.74        11.31         6.02         2.96         6.54 
TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI 
       10.49        11.61         7.20        11.41         7.36         6.61 
TCGA-EM-A3AJ TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3O8 TCGA-EM-A3OB TCGA-ET-A25I 
       13.05         5.29         6.81         0.49         2.33         0.33 
TCGA-ET-A25P TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N 
        0.49         6.51        38.86         0.30         1.94        65.88 
TCGA-ET-A39S TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P 
        0.66        44.91         2.14         0.30        65.79         3.22 
TCGA-FE-A239 TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R7 
       65.92         1.25         1.64         0.99         0.59         0.03 
TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A40N TCGA-H2-A2K9 
        2.17         0.76         0.95         4.54         0.89         4.77 
TCGA-H2-A3RH TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-KS-A41I TCGA-KS-A41L 
        4.87        12.89        31.82        15.95        65.88 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ TCGA-BJ-A28T TCGA-BJ-A28X TCGA-BJ-A3PR TCGA-CE-A27D 
        5.98         5.00         2.76        17.49         8.02         0.10 
TCGA-DJ-A13O TCGA-DJ-A2PX TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q9 TCGA-DJ-A3UW 
        7.07         5.03         9.34         9.21        10.36        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3VD TCGA-DO-A2HM TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A413 
       11.34        11.51         2.30         0.36        66.12         0.33 
TCGA-E8-A414 TCGA-E8-A417 TCGA-E8-A44M TCGA-EM-A22P TCGA-EM-A2P1 TCGA-ET-A39R 
        0.23         0.26         0.39         5.72         6.38        46.45 
TCGA-ET-A3BO TCGA-ET-A40S TCGA-FE-A3PB TCGA-FY-A3R6 TCGA-FY-A3TY TCGA-GE-A2C6 
        5.82         5.00        65.88         0.76        66.15         6.77 
TCGA-H2-A26U TCGA-J8-A3O2 
        3.48         1.35 

$subtype3
TCGA-BJ-A0Z5 TCGA-BJ-A290 TCGA-CE-A13K TCGA-CE-A3MD TCGA-DE-A0XZ TCGA-DE-A3KN 
        6.48        20.58         0.53         0.20        13.22         9.40 
TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI 
       65.72        24.92        11.90         7.99        18.05         4.96 
TCGA-DJ-A1QN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU 
        8.98         7.96        20.48        10.45         1.94        10.26 
TCGA-DJ-A2PV TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.96         9.90         8.61         9.57         9.99         8.25 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3UU TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       12.49        15.78        23.70        17.69         7.40        17.75 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VE TCGA-DO-A1JZ TCGA-E3-A3DY TCGA-E3-A3E0 
        7.13        11.93         4.41        40.27        31.07        50.76 
TCGA-E3-A3E2 TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A438 TCGA-EM-A1CS TCGA-EM-A1CV 
       46.72        14.04         0.53         6.90        19.07        66.08 
TCGA-EM-A2CS TCGA-EM-A2OX TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ 
        9.34         2.89         9.27        11.21        11.05         8.61 
TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A3BP 
       19.36         4.44        12.26         1.41        11.90         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BW TCGA-ET-A3DP TCGA-FE-A3PA TCGA-FE-A3PC 
        2.43         5.52         2.37        50.50        65.82        61.41 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A3NN TCGA-FY-A40K 
       62.89        46.06         0.92        48.10        66.12         4.14 
TCGA-H2-A3RI TCGA-J8-A3YH TCGA-J8-A42S TCGA-KS-A41F 
        2.96         5.72         2.47        65.82 

$subtype4
TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A28R TCGA-CE-A3ME TCGA-DE-A0Y2 
        8.25         4.01         0.72         4.87         0.23         7.59 
TCGA-DE-A0Y3 TCGA-DJ-A13U TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QO 
       31.30        12.92        10.98        65.85         7.99         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PT TCGA-DJ-A2PW TCGA-DJ-A2PY TCGA-DJ-A2PZ 
        5.95         9.99         9.60         7.69         8.78         8.42 
TCGA-DJ-A2Q4 TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UY TCGA-DJ-A3V0 TCGA-DJ-A3V6 
        9.44        17.23         9.11        13.32        25.02        14.93 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DO-A1K0 TCGA-E3-A3E1 
        9.83         8.52         7.73        17.36         3.06        40.18 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A3X7 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       20.88         1.12         1.48         1.48        66.15         0.16 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A22I 
        1.15         7.69         0.39         5.03         7.04         2.66 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P3 TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25L 
        9.34         6.28         0.33        35.77        29.69        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       12.33         2.47        20.42        54.02        19.04        34.49 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BU 
       43.04        13.35         7.79         1.68        24.72         1.28 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        4.50        65.92        24.69        51.45        47.41        12.30 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       24.69        43.82        65.88        65.92        39.95        62.70 
TCGA-FK-A3SE TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA 
       21.99         1.15         1.12         1.51         4.64         9.14 
TCGA-FY-A3YR TCGA-FY-A40L TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
        6.84         6.54         2.20         2.89        35.18        30.87 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A3YF 
        2.63         3.25         2.24        13.64        27.81        24.69 
TCGA-J8-A3YG TCGA-KS-A41J 
       22.29        15.68 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.10     0.20     0.16 
subtype1 subtype2 subtype3 subtype4 
   65.92    66.15    66.12    66.15 
subtype1 subtype2 subtype3 subtype4 
   6.900    5.900   10.125    9.390 
[1] "0.0 - 65.9 (6.9)"  "0.1 - 66.2 (5.9)"  "0.2 - 66.1 (10.1)"
[4] "0.2 - 66.2 (9.4)" 
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype4"
  [7] "subtype1" "subtype4" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype4" "subtype2" "subtype1" "subtype1" "subtype1" "subtype4"
 [19] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype2" "subtype3" "subtype4" "subtype3" "subtype4"
 [31] "subtype4" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
 [37] "subtype1" "subtype3" "subtype4" "subtype3" "subtype1" "subtype3"
 [43] "subtype4" "subtype4" "subtype3" "subtype1" "subtype4" "subtype3"
 [49] "subtype1" "subtype1" "subtype3" "subtype4" "subtype4" "subtype4"
 [55] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype4"
 [61] "subtype3" "subtype3" "subtype4" "subtype2" "subtype4" "subtype4"
 [67] "subtype1" "subtype2" "subtype1" "subtype2" "subtype4" "subtype3"
 [73] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [79] "subtype3" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [85] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype4" "subtype1" "subtype4" "subtype3" "subtype3"
 [97] "subtype1" "subtype4" "subtype4" "subtype4" "subtype3" "subtype3"
[103] "subtype2" "subtype3" "subtype4" "subtype1" "subtype4" "subtype1"
[109] "subtype3" "subtype4" "subtype2" "subtype3" "subtype1" "subtype3"
[115] "subtype4" "subtype3" "subtype4" "subtype3" "subtype4" "subtype2"
[121] "subtype2" "subtype4" "subtype2" "subtype2" "subtype1" "subtype1"
[127] "subtype2" "subtype4" "subtype4" "subtype3" "subtype4" "subtype1"
[133] "subtype4" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
[139] "subtype4" "subtype4" "subtype3" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype1" "subtype1" "subtype4" "subtype1" "subtype1"
[151] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[163] "subtype1" "subtype1" "subtype3" "subtype1" "subtype4" "subtype4"
[169] "subtype2" "subtype1" "subtype4" "subtype1" "subtype1" "subtype3"
[175] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[181] "subtype1" "subtype4" "subtype1" "subtype4" "subtype3" "subtype4"
[187] "subtype4" "subtype4" "subtype3" "subtype1" "subtype4" "subtype4"
[193] "subtype4" "subtype3" "subtype4" "subtype1" "subtype3" "subtype1"
[199] "subtype1" "subtype3" "subtype1" "subtype1" "subtype4" "subtype4"
[205] "subtype2" "subtype1" "subtype4" "subtype4" "subtype2" "subtype3"
[211] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3" "subtype4"
[217] "subtype4" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[223] "subtype4" "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
[229] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype1"
[235] "subtype4" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[241] "subtype4" "subtype3" "subtype3" "subtype1" "subtype4" "subtype4"
[247] "subtype1" "subtype1" "subtype3" "subtype1" "subtype4" "subtype2"
[253] "subtype1" "subtype4" "subtype1" "subtype4" "subtype2" "subtype1"
[259] "subtype1" "subtype4" "subtype3" "subtype4" "subtype1" "subtype1"
[265] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype4"
[271] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[277] "subtype1" "subtype4" "subtype2" "subtype1" "subtype4" "subtype4"
[283] "subtype4" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
[289] "subtype1"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype4"
  [7] "subtype1" "subtype4" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype4" "subtype2" "subtype1" "subtype1" "subtype1" "subtype4"
 [19] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype2" "subtype3" "subtype4" "subtype3" "subtype4"
 [31] "subtype4" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
 [37] "subtype1" "subtype3" "subtype4" "subtype3" "subtype1" "subtype3"
 [43] "subtype4" "subtype4" "subtype3" "subtype1" "subtype4" "subtype3"
 [49] "subtype1" "subtype1" "subtype3" "subtype4" "subtype4" "subtype4"
 [55] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype4"
 [61] "subtype3" "subtype3" "subtype4" "subtype2" "subtype4" "subtype4"
 [67] "subtype1" "subtype2" "subtype1" "subtype2" "subtype4" "subtype3"
 [73] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [79] "subtype3" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [85] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype4" "subtype1" "subtype4" "subtype3" "subtype3"
 [97] "subtype1" "subtype4" "subtype4" "subtype4" "subtype3" "subtype3"
[103] "subtype2" "subtype3" "subtype4" "subtype1" "subtype4" "subtype1"
[109] "subtype3" "subtype4" "subtype2" "subtype3" "subtype1" "subtype3"
[115] "subtype4" "subtype3" "subtype4" "subtype3" "subtype4" "subtype2"
[121] "subtype2" "subtype4" "subtype2" "subtype2" "subtype1" "subtype1"
[127] "subtype2" "subtype4" "subtype4" "subtype3" "subtype4" "subtype1"
[133] "subtype4" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
[139] "subtype4" "subtype4" "subtype3" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype1" "subtype1" "subtype4" "subtype1" "subtype1"
[151] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[163] "subtype1" "subtype1" "subtype3" "subtype1" "subtype4" "subtype4"
[169] "subtype2" "subtype1" "subtype4" "subtype1" "subtype1" "subtype3"
[175] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[181] "subtype1" "subtype4" "subtype1" "subtype4" "subtype3" "subtype4"
[187] "subtype4" "subtype4" "subtype3" "subtype1" "subtype4" "subtype4"
[193] "subtype4" "subtype3" "subtype4" "subtype1" "subtype3" "subtype1"
[199] "subtype1" "subtype3" "subtype1" "subtype1" "subtype4" "subtype4"
[205] "subtype2" "subtype1" "subtype4" "subtype4" "subtype2" "subtype3"
[211] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3" "subtype4"
[217] "subtype4" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[223] "subtype4" "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
[229] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype1"
[235] "subtype4" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[241] "subtype4" "subtype3" "subtype3" "subtype1" "subtype4" "subtype4"
[247] "subtype1" "subtype1" "subtype3" "subtype1" "subtype4" "subtype2"
[253] "subtype1" "subtype4" "subtype1" "subtype4" "subtype2" "subtype1"
[259] "subtype1" "subtype4" "subtype3" "subtype4" "subtype1" "subtype1"
[265] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype4"
[271] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[277] "subtype1" "subtype4" "subtype2" "subtype1" "subtype4" "subtype4"
[283] "subtype4" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
[289] "subtype1"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype4"
  [7] "subtype1" "subtype4" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype4" "subtype2" "subtype1" "subtype1" "subtype1" "subtype4"
 [19] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype2" "subtype3" "subtype4" "subtype3" "subtype4"
 [31] "subtype4" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
 [37] "subtype1" "subtype3" "subtype4" "subtype3" "subtype1" "subtype3"
 [43] "subtype4" "subtype4" "subtype3" "subtype1" "subtype4" "subtype3"
 [49] "subtype1" "subtype1" "subtype3" "subtype4" "subtype4" "subtype4"
 [55] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype4"
 [61] "subtype3" "subtype3" "subtype4" "subtype2" "subtype4" "subtype4"
 [67] "subtype1" "subtype2" "subtype1" "subtype2" "subtype4" "subtype3"
 [73] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [79] "subtype3" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [85] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
 [91] "subtype2" "subtype4" "subtype1" "subtype4" "subtype3" "subtype3"
 [97] "subtype1" "subtype4" "subtype4" "subtype4" "subtype3" "subtype3"
[103] "subtype2" "subtype3" "subtype4" "subtype1" "subtype4" "subtype1"
[109] "subtype3" "subtype4" "subtype2" "subtype3" "subtype1" "subtype3"
[115] "subtype4" "subtype3" "subtype4" "subtype3" "subtype4" "subtype2"
[121] "subtype2" "subtype4" "subtype2" "subtype2" "subtype1" "subtype1"
[127] "subtype2" "subtype4" "subtype4" "subtype3" "subtype4" "subtype1"
[133] "subtype4" "subtype4" "subtype3" "subtype4" "subtype2" "subtype3"
[139] "subtype4" "subtype4" "subtype3" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype1" "subtype1" "subtype4" "subtype1" "subtype1"
[151] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[163] "subtype1" "subtype1" "subtype3" "subtype1" "subtype4" "subtype4"
[169] "subtype2" "subtype1" "subtype4" "subtype1" "subtype1" "subtype3"
[175] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[181] "subtype1" "subtype4" "subtype1" "subtype4" "subtype3" "subtype4"
[187] "subtype4" "subtype4" "subtype3" "subtype1" "subtype4" "subtype4"
[193] "subtype4" "subtype3" "subtype4" "subtype1" "subtype3" "subtype1"
[199] "subtype1" "subtype3" "subtype1" "subtype1" "subtype4" "subtype4"
[205] "subtype2" "subtype1" "subtype4" "subtype4" "subtype2" "subtype3"
[211] "subtype3" "subtype3" "subtype4" "subtype4" "subtype3" "subtype4"
[217] "subtype4" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[223] "subtype4" "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
[229] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype1"
[235] "subtype4" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[241] "subtype4" "subtype3" "subtype3" "subtype1" "subtype4" "subtype4"
[247] "subtype1" "subtype1" "subtype3" "subtype1" "subtype4" "subtype2"
[253] "subtype1" "subtype4" "subtype1" "subtype4" "subtype2" "subtype1"
[259] "subtype1" "subtype4" "subtype3" "subtype4" "subtype1" "subtype1"
[265] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype4"
[271] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[277] "subtype1" "subtype4" "subtype2" "subtype1" "subtype4" "subtype4"
[283] "subtype4" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
[289] "subtype1"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 72 23
  subtype2 25  7
  subtype3 52 18
  subtype4 67 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72   23
  subtype2   25    7
  subtype3   52   18
  subtype4   67   25
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       72       25       52       67
  MALE         23        7       18       25
          vv
clus       OTHER THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1    14                                            21
  subtype2     1                                            23
  subtype3     1                                            58
  subtype4     2                                            67
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     58
  subtype2                                                                      3
  subtype3                                                                      9
  subtype4                                                                      3
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   2
  subtype2                                                                   5
  subtype3                                                                   2
  subtype4                                                                  20
D5V4, multiclass
D5V5, binary
          cls
clus        0  1
  subtype1  1 94
  subtype2  0 32
  subtype3  1 69
  subtype4 10 82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   94
  subtype2    0   32
  subtype3    1   69
  subtype4   10   82
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        1       10
  YES       94       32       69       82
D5V6, binary
          cls
clus        0  1
  subtype1 80  5
  subtype2 25  1
  subtype3 58  3
  subtype4 78  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   80    5
  subtype2   25    1
  subtype3   58    3
  subtype4   78    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        80       25       58       78
  YES        5        1        3        3
          vv
clus       M0 M1 MX
  subtype1 37  2 55
  subtype2 21  0 11
  subtype3 38  1 31
  subtype4 44  1 47
D5V7, multiclass
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1           10                       0   81
  subtype2            8                       0   22
  subtype3           17                       0   51
  subtype4           32                       5   49
D5V8, multiclass
          vv
clus       N0 N1 N1A N1B NX
  subtype1 69  0   7   5 14
  subtype2 14  1  10   7  0
  subtype3 29  4  20  13  4
  subtype4 33 11  21  17 10
D5V9, multiclass
          vv
clus       R0 R1 R2 RX
  subtype1 78  4  0  7
  subtype2 22  2  0  4
  subtype3 57  4  1  3
  subtype4 72  8  0  6
D5V10, multiclass
D5V11, continuous
D5V12, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      51       19        20         2         2
  subtype2      22        2         5         3         0
  subtype3      42        8        12         8         0
  subtype4      48        5        25        13         1
D5V13, multiclass
D5V14, binary
          cls
clus        0  1
  subtype1 47 46
  subtype2 14 16
  subtype3 45 22
  subtype4 37 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47   46
  subtype2   14   16
  subtype3   45   22
  subtype4   37   53
            clus
vv           subtype1 subtype2 subtype3 subtype4
  MULTIFOCAL       47       14       45       37
  UNIFOCAL         46       16       22       53
D5V15, continuous

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1 104   1
  subtype2 128   0
  subtype3  56   0
subtype1 subtype2 subtype3 
     105      128       56 
subtype1 subtype2 subtype3 
       1        0        0 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       15.75        11.70         7.63         8.68         6.02         7.79 
TCGA-BJ-A0ZF TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A192 
        6.90         7.56         5.00         2.79         0.43         8.09 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A3PT TCGA-CE-A27D TCGA-DE-A2OL TCGA-DJ-A13M 
        2.76         5.10        12.07         0.10         5.29         9.01 
TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM 
        7.07         3.02        14.93         6.97         6.97         0.99 
TCGA-DJ-A2PP TCGA-DJ-A2PS TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP 
        5.00         1.94         8.12         6.77        10.85         5.49 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       20.71        15.42        17.69        11.34        13.32        12.76 
TCGA-DJ-A3V4 TCGA-DJ-A3VG TCGA-DJ-A3VM TCGA-E3-A3DZ TCGA-E8-A413 TCGA-E8-A414 
       14.56         8.32        15.81        12.00         0.33         0.23 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A434 TCGA-E8-A436 TCGA-EM-A1CW TCGA-EM-A1YA 
        0.16         0.72         0.23         1.15         8.05         7.13 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K 
        9.34        46.72        39.75        21.37         6.81         6.64 
TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CM TCGA-EM-A2CN 
        4.54         6.87         8.19         6.87        11.74        11.31 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW 
        6.02         2.96         6.54        10.49        11.61         7.20 
TCGA-EM-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AP TCGA-EM-A3AR 
       11.41         7.36         6.61        13.05         5.29         6.81 
TCGA-EM-A3O8 TCGA-EM-A3OB TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N3 TCGA-ET-A2N5 
        0.49         2.33         0.33         0.49         6.51        38.86 
TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39S TCGA-ET-A3DQ TCGA-ET-A3DS 
        0.30         1.94        65.88         0.66        44.91         0.30 
TCGA-ET-A3DV TCGA-ET-A40P TCGA-FE-A239 TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM 
       65.79         3.22        65.92         1.25         1.64         0.99 
TCGA-FY-A3NP TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R9 TCGA-FY-A3TY TCGA-FY-A3W9 
        0.59         0.76         0.03         2.17        66.15         0.76 
TCGA-FY-A3WA TCGA-FY-A40N TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-J8-A3O0 TCGA-J8-A3O2 
        0.95         0.89         4.77         4.87        12.89         1.35 
TCGA-J8-A3YD TCGA-KS-A41I TCGA-KS-A41L 
       31.82        15.95        65.88 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A28R 
        5.98         6.48         8.25         4.01         0.72         4.87 
TCGA-BJ-A28X TCGA-BJ-A3PR TCGA-CE-A3ME TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       17.49         8.02         0.23        13.22         7.59        31.30 
TCGA-DJ-A13U TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       12.92        10.98        65.85         7.99         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PW TCGA-DJ-A2PX 
        9.99         7.96        10.45         9.60         7.69         5.03 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.78         8.42         9.34         9.21         9.44         9.90 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q9 TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UW TCGA-DJ-A3V0 
        8.61        10.36        17.23         9.11        43.00        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V6 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3VA 
        7.40        17.75        14.93         9.83         8.52        11.93 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DO-A1K0 TCGA-DO-A2HM 
       11.51         4.41         7.73        17.36         3.06         2.30 
TCGA-E3-A3DY TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       31.07        40.18        46.72        20.88         1.12         0.36 
TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       66.12         1.48         0.26         1.48        66.15         0.16 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A22I TCGA-EM-A22P 
        0.39         0.39         5.03         7.04         2.66         5.72 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-ET-A25G TCGA-ET-A25J 
        9.34         6.28         6.38         0.33        35.77        29.69 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        12.33         2.47        20.42        54.02        19.04 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       43.04        13.35        46.45         7.79         1.68         5.82 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
        5.52        24.72         1.28         4.50        65.92        50.50 
TCGA-ET-A3DR TCGA-ET-A3DW TCGA-ET-A40S TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14        24.69         5.00        51.45        47.41        12.30 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       24.69        43.82        65.88        65.92        39.95        62.70 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FK-A3SE TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NN 
       65.88        61.41        21.99         1.15         1.12        66.12 
TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A3YR TCGA-FY-A40L TCGA-GE-A2C6 
        1.51         4.64         9.14         6.84         6.54         6.77 
TCGA-H2-A26U TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
        3.48         2.96         2.20         2.89        35.18        30.87 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A3YF 
        2.63         3.25         2.24        13.64        27.81        24.69 
TCGA-J8-A3YG TCGA-KS-A41J 
       22.29        15.68 

$subtype3
TCGA-BJ-A290 TCGA-CE-A13K TCGA-CE-A3MD TCGA-DE-A3KN TCGA-DJ-A13P TCGA-DJ-A13T 
       20.58         0.53         0.20         9.40        65.72        24.92 
TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PQ 
       11.90         7.99        18.05         4.96         8.98        20.48 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-DJ-A3UK 
       10.26         7.96         9.57        12.43         9.99         8.25 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3UV TCGA-DJ-A3V9 TCGA-DO-A1JZ 
       12.49        15.78        23.70        19.40         7.13        40.27 
TCGA-E3-A3E0 TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A437 TCGA-E8-A438 TCGA-EM-A1CS 
       50.76        14.04         0.53         7.69         6.90        19.07 
TCGA-EM-A1CV TCGA-EM-A2CS TCGA-EM-A2OX TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO 
       66.08         9.34         2.89         9.27        11.21        11.05 
TCGA-EM-A3AQ TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N4 
        8.61        19.36         4.44        12.26        34.49         1.41 
TCGA-ET-A39J TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BW TCGA-FE-A3PA TCGA-FE-A3PD 
       11.90         4.18         2.43         2.37        65.82        62.89 
TCGA-FK-A3S3 TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A40K TCGA-FY-A40M TCGA-J8-A3YH 
       46.06         0.92        48.10         4.14         4.54         5.72 
TCGA-J8-A42S TCGA-KS-A41F 
        2.47        65.82 

subtype1 subtype2 subtype3 
    0.03     0.16     0.20 
subtype1 subtype2 subtype3 
   66.15    66.15    66.08 
subtype1 subtype2 subtype3 
   6.870    9.175   10.125 
[1] "0.0 - 66.2 (6.9)"  "0.2 - 66.2 (9.2)"  "0.2 - 66.1 (10.1)"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
  [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [31] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [43] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [67] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [79] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
 [85] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[103] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[109] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[115] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[121] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[127] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[133] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[139] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[151] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[163] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype2"
[169] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[175] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[181] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[187] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[193] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[199] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[205] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[211] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[217] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[223] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[229] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[235] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[241] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[247] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[253] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[259] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[265] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[271] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[277] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[283] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[289] "subtype1"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
  [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [31] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [43] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [67] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [79] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
 [85] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[103] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[109] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[115] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[121] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[127] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[133] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[139] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[151] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[163] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype2"
[169] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[175] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[181] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[187] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[193] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[199] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[205] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[211] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[217] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[223] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[229] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[235] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[241] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[247] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[253] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[259] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[265] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[271] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[277] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[283] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[289] "subtype1"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
  [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
 [19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
 [25] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [31] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
 [37] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [43] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [49] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [55] "subtype2" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
 [61] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [67] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
 [73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype1" "subtype3"
 [79] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
 [85] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype2"
 [91] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [97] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[103] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[109] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[115] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
[121] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[127] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[133] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[139] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[151] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[163] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype2"
[169] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[175] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[181] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype2"
[187] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
[193] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[199] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[205] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[211] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[217] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[223] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[229] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[235] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[241] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
[247] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[253] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[259] "subtype1" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[265] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[271] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[277] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[283] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[289] "subtype1"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 79 26
  subtype2 92 36
  subtype3 45 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   79   26
  subtype2   92   36
  subtype3   45   11
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       79       92       45
  MALE         26       36       11
          vv
clus       OTHER THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1    14                                            29
  subtype2     4                                            93
  subtype3     0                                            47
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     58
  subtype2                                                                      7
  subtype3                                                                      8
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   4
  subtype2                                                                  24
  subtype3                                                                   1
D6V4, multiclass
D6V5, binary
          cls
clus         0   1
  subtype1   1 104
  subtype2  10 118
  subtype3   1  55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  104
  subtype2   10  118
  subtype3    1   55
     clus
vv    subtype1 subtype2 subtype3
  NO         1       10        1
  YES      104      118       55
D6V6, binary
          cls
clus         0   1
  subtype1  87   4
  subtype2 106   6
  subtype3  48   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   87    4
  subtype2  106    6
  subtype3   48    2
     clus
vv    subtype1 subtype2 subtype3
  NO        87      106       48
  YES        4        6        2
          vv
clus       M0 M1 MX
  subtype1 47  2 55
  subtype2 65  1 62
  subtype3 28  1 27
D6V7, multiclass
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1           13                       0   86
  subtype2           42                       5   74
  subtype3           12                       0   43
D6V8, multiclass
          vv
clus       N0 N1 N1A N1B NX
  subtype1 73  1   9   8 14
  subtype2 45 12  38  23 10
  subtype3 27  3  11  11  4
D6V9, multiclass
          vv
clus       R0 R1 R2 RX
  subtype1 85  5  0  7
  subtype2 99 10  0  9
  subtype3 45  3  1  4
D6V10, multiclass
D6V11, continuous
D6V12, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      57       19        22         4         2
  subtype2      74        8        30        15         1
  subtype3      32        7        10         7         0
D6V13, multiclass
D6V14, binary
          cls
clus        0  1
  subtype1 51 50
  subtype2 56 69
  subtype3 36 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51   50
  subtype2   56   69
  subtype3   36   18
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       51       56       36
  UNIFOCAL         50       69       18
D6V15, continuous

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  88   1
  subtype2 112   0
  subtype3 101   0
subtype1 subtype2 subtype3 
      89      112      101 
subtype1 subtype2 subtype3 
       1        0        0 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZC 
       15.75        11.70         7.63         8.25         8.68         6.02 
TCGA-BJ-A0ZE TCGA-BJ-A0ZF TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 
        7.79         6.90         7.56         2.79         0.43         7.73 
TCGA-BJ-A192 TCGA-BJ-A28V TCGA-DE-A2OL TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S 
        8.09         5.10         5.29         9.01         3.02         8.71 
TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 
       14.93         6.97         6.97         5.00         8.12         6.77 
TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VM 
       10.85         5.49        20.71        15.42         8.32        15.81 
TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-E3-A3E5 TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       40.27        12.00        14.04         8.05         7.13         9.34 
TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N 
       46.72        21.37         6.81         6.64         4.54         6.87 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CM TCGA-EM-A2CN 
        6.31        11.44         8.19         6.87        11.74        11.31 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV 
        6.02         2.96         6.54         7.17        10.49        11.61 
TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AP 
        7.20        11.41         7.36         6.61        13.05         5.29 
TCGA-EM-A3O8 TCGA-EM-A3OB TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N3 TCGA-ET-A2N5 
        0.49         2.33         0.33         0.49         6.51        38.86 
TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3BW TCGA-ET-A3DS TCGA-ET-A3DV 
        0.30         1.94        65.88         2.37         0.30        65.79 
TCGA-ET-A40P TCGA-FE-A236 TCGA-FE-A239 TCGA-FE-A3PD TCGA-FY-A2QD TCGA-FY-A3I5 
        3.22        65.88        65.92        62.89         1.25         1.64 
TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-H2-A2K9 
        0.99         0.59         2.17         0.76         0.95         4.77 
TCGA-H2-A3RH TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-KS-A41I TCGA-KS-A41L 
        4.87        12.89        13.64        15.95        65.88 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A28R TCGA-BJ-A290 
        5.98         6.48         0.72         5.00         4.87        20.58 
TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DJ-A13P 
        0.53        13.22         7.59        31.30         9.40        65.72 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13X TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A1QO 
       24.92        12.92         7.99         4.96         8.98         1.02 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU TCGA-DJ-A2PW 
        9.99         7.96        20.48        10.45        10.26         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK 
        5.03         9.44         9.90         9.57         9.99         8.25 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V7 
       12.49        15.78        23.70         7.40        17.75         9.83 
TCGA-DJ-A3VA TCGA-DJ-A3VE TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 
       11.93         4.41         3.06        31.07        50.76        40.18 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A438 
       46.72        20.88         0.26         1.48        66.15         6.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O 
       19.07         5.03        66.08         2.66         3.48         6.21 
TCGA-EM-A2CS TCGA-EM-A2OZ TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ 
        9.34         9.34         9.27        11.21        11.05         8.61 
TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R 
       35.77        29.69        19.36         2.47         4.44        20.42 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A39K TCGA-ET-A39M 
       19.04        12.26        14.76         1.41        65.95        65.88 
TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       43.04        46.45         7.79         5.82         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DT TCGA-ET-A3DW TCGA-ET-A40S 
        5.52         4.50        65.92         4.77        24.69         5.00 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       47.41        12.30        44.25        24.69        43.82        65.82 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FK-A3SG TCGA-FY-A3BL TCGA-FY-A3NN 
       62.70        65.82        61.41         0.92         1.15        66.12 
TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A3YR TCGA-FY-A40N TCGA-H2-A3RI 
        1.51         4.64         9.14         6.84         0.89         2.96 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-J8-A3NZ 
        2.20         2.89        35.18        30.87         3.25         2.24 
TCGA-J8-A3YE TCGA-J8-A3YH TCGA-KS-A41F TCGA-KS-A41J 
       27.81         5.72        65.82        15.68 

$subtype3
TCGA-BJ-A0ZB TCGA-BJ-A28T TCGA-BJ-A28X TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-CE-A27D 
        4.01         2.76        17.49         8.02        12.07         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
        0.20         0.23         7.07        10.98        65.85        18.05 
TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PV 
        7.99         0.99         5.95         1.94         9.60         7.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 
        8.78         8.42         9.34         9.21         8.61         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3UV 
       10.36        12.43        17.23         9.11        17.69        19.40 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V4 
       43.00        11.34        13.32        12.76        25.02        14.56 
TCGA-DJ-A3V6 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A3VJ 
       14.93         8.52         7.13        11.51         7.73        17.36 
TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 
        2.30         1.12         0.36        66.12         1.48         0.33 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
        0.23         0.16         0.72         0.53         0.16         0.23 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EM-A1CU TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CU 
        0.39         0.39         7.04        39.75         5.72         5.79 
TCGA-EM-A2OX TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-ET-A25L 
        2.89         6.28         6.38         0.33         6.81        14.79 
TCGA-ET-A25M TCGA-ET-A2N0 TCGA-ET-A39J TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN 
       12.33        34.49        11.90        13.35         0.66         1.68 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       24.72         1.28         1.84        50.50        44.91         2.14 
TCGA-ET-A3DU TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A3PB TCGA-FK-A3S3 
        4.54        51.45        65.92        39.95        65.88        46.06 
TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3TY 
       21.99        48.10         1.12         0.76         0.03        66.15 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3U2 
        4.14         6.54         4.54         6.77         3.48         2.63 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S 
        1.35        31.82        24.69        22.29         2.47 

subtype1 subtype2 subtype3 
    0.30     0.26     0.03 
subtype1 subtype2 subtype3 
   65.92    66.15    66.15 
subtype1 subtype2 subtype3 
    7.20     9.70     7.96 
[1] "0.3 - 65.9 (7.2)" "0.3 - 66.2 (9.7)" "0.0 - 66.2 (8.0)"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [25] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
 [37] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
 [43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [49] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [61] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [67] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [79] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [85] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[109] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[121] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[127] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[133] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[139] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[151] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[169] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[175] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[181] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
[187] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[193] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[199] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[205] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[211] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[217] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[223] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[229] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[235] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[241] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[247] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[253] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
[259] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
[265] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[271] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[277] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[283] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[289] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[295] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[301] "subtype2" "subtype1"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [25] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
 [37] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
 [43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [49] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [61] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [67] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [79] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [85] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[109] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[121] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[127] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[133] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[139] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[151] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[169] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[175] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[181] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
[187] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[193] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[199] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[205] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[211] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[217] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[223] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[229] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[235] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[241] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[247] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[253] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
[259] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
[265] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[271] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[277] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[283] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[289] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[295] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[301] "subtype2" "subtype1"
  [1] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
  [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [13] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [19] "subtype2" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
 [25] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
 [31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype3"
 [37] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
 [43] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
 [49] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
 [55] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
 [61] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
 [67] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype2"
 [73] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
 [79] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype2"
 [85] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
 [91] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [97] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[103] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[109] "subtype3" "subtype1" "subtype1" "subtype2" "subtype3" "subtype2"
[115] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[121] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[127] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[133] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[139] "subtype2" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
[145] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[151] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
[157] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[169] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype3"
[175] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[181] "subtype2" "subtype2" "subtype1" "subtype2" "subtype3" "subtype1"
[187] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[193] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[199] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[205] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[211] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[217] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[223] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[229] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[235] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[241] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[247] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[253] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype2"
[259] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
[265] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype3"
[271] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[277] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[283] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[289] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[295] "subtype3" "subtype3" "subtype2" "subtype3" "subtype2" "subtype1"
[301] "subtype2" "subtype1"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 65 24
  subtype2 81 31
  subtype3 80 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65   24
  subtype2   81   31
  subtype3   80   21
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       65       81       80
  MALE         24       31       21
          vv
clus       OTHER THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1    15                                            15
  subtype2     2                                            87
  subtype3     3                                            72
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     58
  subtype2                                                                     13
  subtype3                                                                      7
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   1
  subtype2                                                                  10
  subtype3                                                                  19
D7V4, multiclass
D7V5, binary
          cls
clus         0   1
  subtype1   3  86
  subtype2   8 104
  subtype3   3  98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   86
  subtype2    8  104
  subtype3    3   98
     clus
vv    subtype1 subtype2 subtype3
  NO         3        8        3
  YES       86      104       98
D7V6, binary
          cls
clus        0  1
  subtype1 78  3
  subtype2 91  6
  subtype3 85  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78    3
  subtype2   91    6
  subtype3   85    4
     clus
vv    subtype1 subtype2 subtype3
  NO        78       91       85
  YES        3        6        4
          vv
clus       M0 M1 MX
  subtype1 30  2 56
  subtype2 50  2 60
  subtype3 60  0 41
D7V7, multiclass
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1            7                       0   79
  subtype2           28                       1   76
  subtype3           33                       5   59
D7V8, multiclass
          vv
clus       N0 N1 N1A N1B NX
  subtype1 63  1   2   6 17
  subtype2 46 10  34  13  9
  subtype3 42  6  27  22  4
D7V9, multiclass
          vv
clus       R0 R1 R2 RX
  subtype1 71  6  0  8
  subtype2 88  7  1  7
  subtype3 81  8  0  4
D7V10, multiclass
D7V11, continuous
D7V12, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      49       19        15         3         2
  subtype2      69       10        23         9         1
  subtype3      53        6        28        14         0
D7V13, multiclass
D7V14, binary
          cls
clus        0  1
  subtype1 42 45
  subtype2 54 52
  subtype3 52 48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   45
  subtype2   54   52
  subtype3   52   48
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       42       54       52
  UNIFOCAL         45       52       48
D7V15, continuous

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 115   0
  subtype2 104   0
  subtype3  82   1
subtype1 subtype2 subtype3 
     115      104       83 
subtype1 subtype2 subtype3 
       0        0        1 
$subtype1
TCGA-BJ-A0ZB TCGA-BJ-A0ZG TCGA-BJ-A28T TCGA-BJ-A28X TCGA-BJ-A3PR TCGA-BJ-A3PT 
        4.01         7.56         2.76        17.49         8.02        12.07 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH 
        0.10         0.20         7.07        10.98        65.85         7.99 
TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PS TCGA-DJ-A2PT 
        0.99         1.02         5.95         9.99         1.94         9.60 
TCGA-DJ-A2PV TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 
        7.96         8.78         8.42         9.34         9.21         8.61 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UU 
        7.07        10.36        12.43        17.23         9.11        17.69 
TCGA-DJ-A3UV TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       19.40        43.00        11.34        13.32        12.76        25.02 
TCGA-DJ-A3V4 TCGA-DJ-A3V6 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VE 
       14.56        14.93         8.52         7.13        11.51         4.41 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
        7.73        17.36         2.30         1.12         0.36        66.12 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A419 
        1.48         0.33         0.23         0.16         0.72        66.15 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A44K TCGA-E8-A44M TCGA-EM-A1CU 
        0.53         0.16         0.23         0.39         0.39         7.04 
TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CU TCGA-EM-A2OX 
       39.75         2.66         3.48         5.72         5.79         2.89 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-ET-A25G TCGA-ET-A25L 
        6.28         6.38         0.33         6.81        35.77        14.79 
TCGA-ET-A25M TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39J TCGA-ET-A39M TCGA-ET-A39O 
       12.33        19.04        34.49        11.90        65.88        43.04 
TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       13.35         0.66         1.68        24.72         1.28         1.84 
TCGA-ET-A3DO TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-FE-A22Z 
       65.92        44.91         2.14         4.77         4.54        51.45 
TCGA-FE-A234 TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 
       43.82        65.92        65.88        21.99        48.10         1.12 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K 
        0.76         0.03         4.64        66.15         6.84         4.14 
TCGA-FY-A40L TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3U2 
        6.54         6.77         3.48         2.20        35.18         2.63 
TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG 
        3.25         2.24         1.35        31.82        24.69        22.29 
TCGA-J8-A42S 
        2.47 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A28R 
        5.98         6.48         8.25         0.72         5.00         4.87 
TCGA-BJ-A290 TCGA-CE-A13K TCGA-CE-A3ME TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       20.58         0.53         0.23        13.22         7.59        31.30 
TCGA-DE-A3KN TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13X TCGA-DJ-A1QF 
        9.40        65.72        24.92        12.92         7.99        18.05 
TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU 
        4.96         8.98         7.96        20.48        10.45        10.26 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2QC 
        7.69         5.03         9.44         9.90         9.57         9.99 
TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 
        8.25        12.49        15.78        23.70         7.40        17.75 
TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 
        9.83        11.93        40.27         3.06        31.07        50.76 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A438 
       40.18        46.72        20.88         0.26         1.48         6.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CV TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OZ 
       19.07         5.03        66.08         6.21         9.34         9.34 
TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-ET-A25J TCGA-ET-A25K 
        9.27        11.21        11.05         8.61        29.69        19.36 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N4 
        2.47         4.44        20.42        12.26        14.76         1.41 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BO TCGA-ET-A3BP 
       65.95         1.94        46.45         7.79         5.82         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DP TCGA-ET-A3DW 
        2.43         5.52         2.37         4.50        50.50        24.69 
TCGA-ET-A40S TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A235 
        5.00        47.41        12.30        44.25        24.69        65.82 
TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       65.88        39.95        62.70        65.82        61.41        62.89 
TCGA-FK-A3S3 TCGA-FK-A3SG TCGA-FY-A3BL TCGA-FY-A3NN TCGA-FY-A3ON TCGA-FY-A3RA 
       46.06         0.92         1.15        66.12         1.51         9.14 
TCGA-FY-A40N TCGA-H2-A3RI TCGA-H2-A422 TCGA-IM-A3ED TCGA-J8-A3YE TCGA-J8-A3YH 
        0.89         2.96         2.89        30.87        27.81         5.72 
TCGA-KS-A41F TCGA-KS-A41J 
       65.82        15.68 

$subtype3
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       15.75        11.70         7.63         8.68         6.02         7.79 
TCGA-BJ-A0ZF TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28V 
        6.90         2.79         0.43         7.73         8.09         5.10 
TCGA-DE-A2OL TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG 
        5.29         9.01         3.02         8.71        14.93         6.97 
TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP 
        6.97         5.00         8.12         6.77        10.85         5.49 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VM TCGA-E3-A3DZ TCGA-E3-A3E5 
       20.71        15.42         8.32        15.81        12.00        14.04 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22J 
        8.05         7.13         9.34        46.72        21.37         6.81 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
        6.64         4.54         6.87         6.31        11.44         8.19 
TCGA-EM-A2CL TCGA-EM-A2CM TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
        6.87        11.74        11.31         6.02         2.96         6.54 
TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 
        7.17        10.49        11.61         7.20        11.41         7.36 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AP TCGA-EM-A3O8 TCGA-EM-A3OB TCGA-ET-A25I 
        6.61        13.05         5.29         0.49         2.33         0.33 
TCGA-ET-A25P TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39N TCGA-ET-A3DS 
        0.49         6.51        38.86         0.30        65.88         0.30 
TCGA-ET-A3DV TCGA-ET-A40P TCGA-FE-A239 TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM 
       65.79         3.22        65.92         1.25         1.64         0.99 
TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-H2-A2K9 
        0.59         2.17         0.76         0.95         4.54         4.77 
TCGA-H2-A3RH TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-KS-A41I TCGA-KS-A41L 
        4.87        12.89        13.64        15.95        65.88 

subtype1 subtype2 subtype3 
    0.03     0.23     0.30 
subtype1 subtype2 subtype3 
   66.15    66.12    65.92 
subtype1 subtype2 subtype3 
   7.560    9.945    7.130 
[1] "0.0 - 66.2 (7.6)" "0.2 - 66.1 (9.9)" "0.3 - 65.9 (7.1)"
  [1] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
  [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
 [13] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [25] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [43] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [49] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [61] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [67] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [73] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [79] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [85] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [97] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[103] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[109] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[115] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[121] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[127] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[133] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[139] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[145] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[151] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
[157] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[163] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
[169] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[175] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[181] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
[187] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[193] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[199] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype3"
[205] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[211] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[217] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[223] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[229] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[235] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[241] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[247] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[253] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[259] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[265] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[271] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[277] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[283] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[289] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[295] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[301] "subtype2" "subtype3"
  [1] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
  [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
 [13] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [25] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [43] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [49] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [61] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [67] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [73] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [79] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [85] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [97] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[103] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[109] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[115] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[121] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[127] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[133] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[139] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[145] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[151] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
[157] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[163] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
[169] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[175] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[181] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
[187] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[193] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[199] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype3"
[205] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[211] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[217] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[223] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[229] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[235] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[241] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[247] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[253] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[259] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[265] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[271] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[277] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[283] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[289] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[295] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[301] "subtype2" "subtype3"
  [1] "subtype3" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
  [7] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
 [13] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [19] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [25] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
 [37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
 [43] "subtype2" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
 [49] "subtype2" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
 [55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
 [61] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [67] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [73] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
 [79] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [85] "subtype3" "subtype1" "subtype2" "subtype3" "subtype3" "subtype1"
 [91] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [97] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[103] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[109] "subtype1" "subtype3" "subtype2" "subtype2" "subtype1" "subtype2"
[115] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[121] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[127] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[133] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[139] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[145] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
[151] "subtype3" "subtype1" "subtype3" "subtype2" "subtype1" "subtype3"
[157] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[163] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
[169] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype1"
[175] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype2"
[181] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
[187] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[193] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[199] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype3"
[205] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype3"
[211] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
[217] "subtype2" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[223] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[229] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[235] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[241] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[247] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[253] "subtype2" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[259] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype2"
[265] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype1"
[271] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[277] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype2"
[283] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[289] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype2"
[295] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
[301] "subtype2" "subtype3"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 88 27
  subtype2 77 27
  subtype3 61 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   88   27
  subtype2   77   27
  subtype3   61   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       88       77       61
  MALE         27       27       22
          vv
clus       OTHER THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1     4                                            81
  subtype2     1                                            81
  subtype3    15                                            12
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      7
  subtype2                                                                     15
  subtype3                                                                     56
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  23
  subtype2                                                                   7
  subtype3                                                                   0
D8V4, multiclass
D8V5, binary
          cls
clus         0   1
  subtype1   3 112
  subtype2  10  94
  subtype3   1  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  112
  subtype2   10   94
  subtype3    1   82
     clus
vv    subtype1 subtype2 subtype3
  NO         3       10        1
  YES      112       94       82
D8V6, binary
          cls
clus        0  1
  subtype1 98  5
  subtype2 84  5
  subtype3 72  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   98    5
  subtype2   84    5
  subtype3   72    3
     clus
vv    subtype1 subtype2 subtype3
  NO        98       84       72
  YES        5        5        3
          vv
clus       M0 M1 MX
  subtype1 65  0 50
  subtype2 46  2 56
  subtype3 29  2 51
D8V7, multiclass
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1           37                       5   69
  subtype2           25                       1   71
  subtype3            6                       0   74
D8V8, multiclass
          vv
clus       N0 N1 N1A N1B NX
  subtype1 47  8  32  21  7
  subtype2 44  9  29  14  8
  subtype3 60  0   2   6 15
D8V9, multiclass
          vv
clus       R0 R1 R2 RX
  subtype1 92  9  0  6
  subtype2 80  8  1  6
  subtype3 68  4  0  7
D8V10, multiclass
D8V11, continuous
D8V12, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      62        5        34        14         0
  subtype2      65       11        18         9         1
  subtype3      44       19        14         3         2
D8V13, multiclass
D8V14, binary
          cls
clus        0  1
  subtype1 54 59
  subtype2 54 44
  subtype3 40 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54   59
  subtype2   54   44
  subtype3   40   42
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       54       54       40
  UNIFOCAL         59       44       42
D8V15, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
                     "HISTOLOGICAL.TYPE" 
                                      V5 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V6 
                     "RADIATIONEXPOSURE" 
                                      V7 
                    "DISTANT.METASTASIS" 
                                      V8 
              "EXTRATHYROIDAL.EXTENSION" 
                                      V9 
                 "LYMPH.NODE.METASTASIS" 
                                     V10 
             "COMPLETENESS.OF.RESECTION" 
                                     V11 
                 "NUMBER.OF.LYMPH.NODES" 
                                     V12 
                       "TUMOR.STAGECODE" 
                                     V13 
                 "NEOPLASM.DISEASESTAGE" 
                                     V14 
                         "MULTIFOCALITY" 
                                     V15 
                            "TUMOR.SIZE" 
> q(save="no")
