[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTTHCA-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THCA-TP/10006333/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/10667977/THCA-TP.mergedcluster.txt"

nPatients in clinical file=490, in cluster file=503, common to both=490
[1]  10 490
[1] "CN_CNMF"
[1] 3
  1   2   3 
 33 377  76 
  1   2   3 
 33 377  76 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
271 151  68 
  1   2   3 
271 151  68 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
61 79 80 
 1  2  3 
61 79 80 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
47 28 33 28 48 27  9 
 1  2  3  4  5  6  7 
47 28 33 28 48 27  9 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
154  52 115 165 
  1   2   3   4 
154  52 115 165 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
127  97  72 113  77 
  1   2   3   4   5 
127  97  72 113  77 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
150 170 167 
  1   2   3 
150 170 167 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
127 201 159 
  1   2   3 
127 201 159 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
163 166 158 
  1   2   3 
163 166 158 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4 
124 185 102  76 
  1   2   3   4 
124 185 102  76 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "RADIATIONEXPOSURE"                     
[17] "EXTRATHYROIDAL.EXTENSION"              
[18] "COMPLETENESS.OF.RESECTION"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "MULTIFOCALITY"                         
[21] "TUMOR.SIZE"                            
[22] "RACE"                                  
[23] "ETHNICITY"                             
[24] "BATCHNUMBER"                           

Input Data has 24 rows and 490 columns.

[1] "Batch" "24"   
[1] "Last Follow UP"
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
         754          419          554          497          448          251 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
         574          122          352          509          230          460 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
         538          710          630          626          147          246 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
         148          640           85          155          344          533 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
          37          627          696          559          504          623 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
         577          214          487          424          471          709 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
         567          175          197            1          105          193 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
         238          188          154          273          150          182 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
          16            3            6            7            3            2 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
           3           12            3          615          469         1109 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
         182          482          185          148          916          352 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A13M TCGA-DJ-A13O 
         529          764          130           98          287          224 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
        4194           92          265          771          408          362 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
         444          243          332         3042          563          212 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
         243          455          219           44          270           31 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
         181          307          243          162          624          318 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
          46          292          312          238          234          168 
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          305          459          944          380 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
         957          499          595         1105          998          470 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
         538         1308          345          650          388          761 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
         615          931          443          584          299          647 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
         623          363          697          639          577          236 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
         253          528          524          840          363          328 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
         334          371          287          284           95          103 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
         491         1670          655           71          945          367 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
        2019         1223         1922          922          427           35 
TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
         678           NA          596          414          434          420 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 
         428          434           92           NA          439          447 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
         429          455          234          629          419          413 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
          NA           NA         4731           NA         4831           NA 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
          NA           NA         4780         1154           NA         2461 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
         127         1789           44         2260         1381         1018 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
        3296         1196           43          918         3128         1989 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H1 
        3773         1532         1133         4494         3076           NA 
TCGA-EL-A3H2 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
          NA         1176         1604         3862         3989         3305 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
          NA           NA           NA          370         4484         3976 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
        3941          988         3556         2988         1256         2901 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
          NA         2035         2519         2353         2402          958 
TCGA-EL-A3ZL TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
        1531         1441         1597         1385         1465          215 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
        1358         1393          587         1398         1154          578 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
         596          594         1022          874         1251         1149 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
         911          405          361          265          817          553 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
         636          376          549          602          592         1649 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
        1734         1645          448          441          479          318 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
         442          324          357          339          433          500 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
         544          401          715          184           91          374 
TCGA-EM-A2CR TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
         415          462          319          400          674          421 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
         600          535          367          535          531          526 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
         444          531          577          477          430          597 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
         407          254          500          510          850          723 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
         511          639          367          532          529          492 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
         457          441          339          223          381          281 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
         423          238          350          499          475          411 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
         389         2149          514          274          147          262 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
         255          298          153         1152          387           29 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
        1444         1466          903          984          450          375 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
         450          824          559          622         1644          672 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
         373          489          888          601           81         1771 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
         418         2160         2205         1988         2582         2998 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
        1856         1786         1737         1676         1799          859 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
         178          127           74          169          752         1165 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
        1285           72          137         2458         1730         1821 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
        1323            9          547          770         4026          752 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
          98          218          146          153           65          122 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
          59         2243         1816          961         1346          751 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
        2075         3130         2031         2474         1215           NA 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
        2489         3235         2590         2606         2396         1401 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
         124           27          670           28         1463         2773 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NN 
          38           35           34           50           30           NA 
TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
         491           46           23            1          142          504 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
         550            9           23           30          209          126 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 
         200          138           27           NA           41           35 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
         381          517          659          379           91          610 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
         566         1488         1442          312          514          298 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
         293           90          263           68         1313          827 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
          41          968          847          751          678          175 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
          75           79            6         3680          486          477 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
        2637          183          378          205          376          531 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
        1964          447          623           18         1228           34 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
          22          506          440          265 
Variable 1:'AGE':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=394,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONEXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'EXTRATHYROIDAL.EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR.SIZE':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'BATCH.NUMBER':	nDistinctValues=19,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RADIATIONEXPOSURE"                     
[10] "EXTRATHYROIDAL.EXTENSION"              
[11] "COMPLETENESS.OF.RESECTION"             
[12] "NUMBER.OF.LYMPH.NODES"                 
[13] "MULTIFOCALITY"                         
[14] "TUMOR.SIZE"                            
[15] "RACE"                                  
[16] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 490 columns, 1 survival variables, and 16 non-survival variables.
AGE, nv=73, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
140 165 162  21 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
140 165 162  21 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
140 165 162  21 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
140 165 162  21 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
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
EXTRATHYROIDAL.EXTENSION, nv=4, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=30, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR.SIZE, nv=70, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1  29   3
  subtype2 364  10
  subtype3  75   1
subtype1 subtype2 subtype3 
      32      374       76 
subtype1 subtype2 subtype3 
       3       10        1 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A290 TCGA-BJ-A2N9 TCGA-BJ-A45E 
       24.79        20.58         8.09        20.61        20.48         0.03 
TCGA-DE-A4MB TCGA-DJ-A2PV TCGA-DJ-A2Q0 TCGA-E8-A432 TCGA-EL-A3GP TCGA-EL-A3MX 
       11.57         7.82         8.12        14.43         1.41        57.63 
TCGA-EL-A3T9 TCGA-EL-A3ZO TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
        5.72        47.38         8.71        54.21        57.01        54.08 
TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O3 TCGA-EM-A3O9 
       10.65         6.05        17.59        17.46        14.50         9.24 
TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39M TCGA-ET-A39N TCGA-FE-A231 TCGA-FE-A239 
       13.51        12.26        84.89        98.56        31.59        33.63 
TCGA-FY-A3I5 TCGA-FY-A3NM 
        1.64         0.99 

$subtype2
TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
       13.78        16.34         8.25        18.87         4.01        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R 
       16.73         7.56        17.69        20.71         4.83         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 
       22.88        18.38        16.57        18.97        16.01        13.94 
TCGA-BJ-A3PR TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       15.48        18.64         5.75         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 
        0.20         0.23         0.10         0.07         0.10         0.10 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA 
       15.42        36.46         5.98        15.85         4.87        30.12 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
       17.39        25.12         7.36       137.88         3.02         8.71 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       13.41        11.90        14.60         7.99        10.92       100.01 
TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO 
       18.51         7.99        14.96         7.20         1.45         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33        20.52        10.45 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
        9.60        10.26         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        9.34         6.77         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR 
        7.07        10.36        10.03        31.04        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        15.45        17.69        43.00        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       12.76        25.02        20.22        30.61        14.56        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
        9.83        21.27        20.48        11.93        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL 
       18.97         7.76         8.32        17.36        17.23        11.93 
TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.78        12.20         9.44         9.34         3.12         3.39 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 
       16.14        54.90        21.53         2.33        31.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       40.21        63.19        30.31         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.70        14.96         7.69        20.68        13.78        13.58 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR 
       58.82        33.47       108.36        39.32        30.18       102.84 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H1 
       65.39       124.04        50.37       147.75       101.13        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       33.50        38.66        52.73       126.97       131.15       108.66 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB 
      116.91        98.24        41.29        95.38        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       77.36        78.97        31.50        52.50        45.53         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       44.65        19.30        45.96        19.00        19.59        19.53 
TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT 
       33.60        41.13        29.95        13.32        11.87        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A22I 
       20.91        12.36        18.05        19.79        19.46        14.73 
TCGA-EM-A22J TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       14.50        11.74        14.24        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        12.07        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        21.01 
TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 
       12.07        17.39        16.18        15.02        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A4FF 
       12.53        13.91         7.82        11.51        16.41        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV 
       16.90         9.01         4.83         8.61         9.80        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M 
        0.95        47.47        48.20        29.69        32.35        12.33 
TCGA-ET-A25N TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       14.79        18.38        20.45        54.05        22.09        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       29.19        19.76        58.22        13.74        71.01        72.49 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        5.85         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        56.88        59.87        43.50 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R 
       17.98        25.32       132.36        24.72         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 
        5.03         4.01         1.94        73.74        59.70        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A23A 
       24.69        68.22       102.90        66.77        39.95        81.83 
TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
      106.36        85.68        78.77        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.12         1.51         0.76         4.67        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
        0.30         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
        1.35        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 
       18.61        48.92        47.41        10.26         9.80         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF 
        8.65         2.24        27.19         1.35        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J 
       22.29         2.47         2.60         0.20       120.99        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC 
       86.70         6.02        12.43         6.74        17.46        14.70 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       20.48         0.59        40.37         1.12         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       14.47         8.71 

$subtype3
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A2P4 TCGA-BJ-A3PT 
       18.21        14.73        15.12        23.34         7.04        23.31 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A4M8 TCGA-DJ-A13M 
        6.48         3.45         0.39        20.22         6.08         9.44 
TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q7 TCGA-DJ-A2QA 
       25.35         6.97         8.88         1.51         9.57        12.43 
TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3VM 
       10.85        15.09        12.49        31.46        16.41        27.62 
TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E3-A3E5 TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 
       10.98        12.07        14.04        14.10        31.66         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR 
       74.30        45.40        37.25        32.48        50.33        48.16 
TCGA-EL-A4JV TCGA-EL-A4JZ TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EM-A1CS TCGA-EM-A22K 
       45.80        37.94        28.73        37.78        26.86        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A3AP TCGA-EM-A3FO 
       10.45        14.53        11.15        16.44         8.35        17.49 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25L 
       15.62        12.79         8.38         5.03        37.87        14.79 
TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P 
       27.09         2.66        65.36         4.18         0.30         3.22 
TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA 
        2.14        81.34        85.15         0.03         0.76         0.99 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD 
        1.15        12.53        16.90         9.63        43.17        31.82 
TCGA-J8-A3YH TCGA-KS-A41I TCGA-KS-A4I7 TCGA-KS-A4IB 
        5.75        15.98        12.36        64.57 

subtype1 subtype2 subtype3 
    0.03     0.07     0.03 
subtype1 subtype2 subtype3 
   98.56   158.83    85.15 
subtype1 subtype2 subtype3 
  14.465   16.425   14.630 
[1] "0.0 - 98.6 (14.5)"  "0.1 - 158.8 (16.4)" "0.0 - 85.2 (14.6)" 
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1       9       10        10        1         2         1
  subtype2     220       33        84        0        34         4
  subtype3      46        7        13        1         8         1
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          9      220       46
  STAGE II        10       33        7
  STAGE III       10       84       13
  STAGE IV         1        0        1
  STAGE IVA        2       34        8
  STAGE IVC        1        4        1
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1   5  13  13   2
  subtype2 109 121 129  16
  subtype3  25  29  19   3
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        5      109       25
  T2       13      121       29
  T3       13      129       19
  T4        2       16        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus         0   1
  subtype1  18   8
  subtype2 164 178
  subtype3  38  33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    8
  subtype2  164  178
  subtype3   38   33
   clus
vv  subtype1 subtype2 subtype3
  0       18      164       38
  1        8      178       33
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1  11   1  21
  subtype2 216   6 154
  subtype3  40   2  34
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       11      216       40
  M1        1        6        2
  MX       21      154       34
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1  21  12
  subtype2 280  97
  subtype3  56  20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   12
  subtype2  280   97
  subtype3   56   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       21      280       56
  MALE         12       97       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              0                                            22
  subtype2              8                                           271
  subtype3              1                                            52
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     10
  subtype2                                                                     67
  subtype3                                                                     20
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   1
  subtype2                                                                  31
  subtype3                                                                   3
D1V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                22
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               271
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       67
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          31
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                52
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       20
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus         0   1
  subtype1   2  31
  subtype2  11 366
  subtype3   1  75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   31
  subtype2   11  366
  subtype3    1   75
     clus
vv    subtype1 subtype2 subtype3
  NO         2       11        1
  YES       31      366       75
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
          cls
clus         0   1
  subtype1  29   1
  subtype2 311  16
  subtype3  69   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    1
  subtype2  311   16
  subtype3   69    0
     clus
vv    subtype1 subtype2 subtype3
  NO        29      311       69
  YES        1       16        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1            7                       0   24                   1
  subtype2          106                      15  243                   0
  subtype3           15                       1   56                   0
D1V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                   7      106       15
  MODERATE/ADVANCED (T4A)        0       15        1
  NONE                          24      243       56
  VERY ADVANCED (T4B)            1        0        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  23   4   0   4
  subtype2 293  39   3  18
  subtype3  57   6   1   7
D1V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       23      293       57
  R1        4       39        6
  R2        0        3        1
  RX        4       18        7
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
D1V14, binary
          cls
clus         0   1
  subtype1  12  21
  subtype2 168 201
  subtype3  39  35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   21
  subtype2  168  201
  subtype3   39   35
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       12      168       39
  UNIFOCAL         21      201       35
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         1
  subtype2                                1    39                        16
  subtype3                                0     9                         3
          vv
clus       WHITE
  subtype1    21
  subtype2   251
  subtype3    46
D1V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   1       39        9
  BLACK OR AFRICAN AMERICAN               1       16        3
  WHITE                                  21      251       46
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V17, binary
          cls
clus         0   1
  subtype1   1  21
  subtype2  31 269
  subtype3   6  51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   21
  subtype2   31  269
  subtype3    6   51
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1       31        6
  NOT HISPANIC OR LATINO       21      269       51
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1 264   7
  subtype2 146   3
  subtype3  62   4
subtype1 subtype2 subtype3 
     271      149       66 
subtype1 subtype2 subtype3 
       7        3        4 
$subtype1
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A18Z TCGA-BJ-A28R 
       14.73         8.25         4.01        15.12        20.71         4.87 
TCGA-BJ-A290 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45H TCGA-BJ-A45I 
       20.61        18.97        16.01        18.64         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A3MD TCGA-CE-A482 
        5.06         4.93         5.98         0.53         0.20         0.07 
TCGA-CE-A483 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DE-A4MA 
        0.10        20.22        15.42        36.46        15.85        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A13P 
       11.57        17.39        25.12         4.27         3.22       137.88 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       25.35        13.41        11.90         7.99        10.92       100.01 
TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       18.51         7.99        14.96         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU TCGA-DJ-A2PV 
       10.09         7.99        20.52        10.45        10.26         7.82 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q4 TCGA-DJ-A2Q6 
        7.69         5.52         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        10.03        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       12.49        31.46        19.56        17.69        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VJ TCGA-DJ-A4UL TCGA-DJ-A4UQ 
       11.93        22.92        18.97        17.36        11.93        10.78 
TCGA-DJ-A4UW TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
        9.44         3.12         3.39        16.14        54.90        21.53 
TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       31.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A3X7 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A436 
       19.59        14.27         3.02        14.43        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        20.68        13.78        31.66        26.73       155.54 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CU TCGA-EL-A3CX TCGA-EL-A3D0 
      158.83         7.66        45.53       157.15        80.91         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
       74.30       108.36         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H5 
      124.04        50.37       147.75       101.13        38.66        52.73 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      126.97       131.15       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB 
       12.16       129.57       116.91        41.29        95.38        82.82 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZT 
       31.50        50.33        47.38        52.50        45.53        44.65 
TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4K7 
       19.30        37.94        19.00        19.59        33.60        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2CU 
       20.91        12.36        14.73        11.74        15.19        13.15 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P3 TCGA-EM-A3AK TCGA-EM-A3AN 
       19.73        12.07        17.59        14.60        15.68        19.63 
TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO 
       13.38        16.44        27.95        23.77        21.01        17.49 
TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM 
        7.33        16.41        15.62        12.79        70.65         4.83 
TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25K 
        8.61         9.80        12.72        47.47        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX 
       14.79        12.33        14.79        27.09        20.45        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K 
       22.09        12.26        16.08         2.66        71.01        72.49 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       61.02        58.72        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW 
        4.18         2.43         5.56        24.72        38.30         2.37 
TCGA-ET-A3BX TCGA-ET-A3DP TCGA-ET-A3DR TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R 
        4.50        56.88        43.50        24.72         7.17         4.80 
TCGA-ET-A40T TCGA-FE-A22Z TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
        2.14        73.74        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A3PA TCGA-FE-A3PB 
      102.90        66.77        81.34        39.95       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG 
       85.68        78.77        46.06         4.08        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA 
       48.10        91.17         1.15         1.51         4.67        18.08 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-H2-A3RI 
        6.87         4.14         6.58         1.35         1.15         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       20.05        18.61        47.41        10.26        16.90         9.80 
TCGA-IM-A420 TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YF TCGA-J8-A3YG 
        2.96         2.24        27.19         1.35        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J 
        5.75         2.47         2.60         0.20       120.99        15.68 
TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
        6.02         6.74        12.36        17.46        64.57        14.70 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
        0.59        40.37         1.12         0.72        16.64        14.47 
TCGA-MK-A4N9 
        8.71 

$subtype2
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        18.21        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S 
        7.56        23.34        20.58         4.83         8.09        21.04 
TCGA-BJ-A28V TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 
        5.10        22.88        18.38        16.57        20.48         7.04 
TCGA-BJ-A3F0 TCGA-BJ-A3PT TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       13.94        23.31         5.75         6.48         3.45         6.35 
TCGA-BJ-A45K TCGA-CE-A3ME TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M 
        8.98         0.23         0.39         5.98         4.87         9.44 
TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP 
        8.71        14.60         6.97         7.20         1.45         5.33 
TCGA-DJ-A2PS TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3UR 
        1.51         8.12         6.77        10.85        16.41        36.33 
TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3VG TCGA-DJ-A3VL 
       15.45        11.34        21.37        12.76         8.32        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A416 
       27.62        10.98        12.07        13.61        13.81        14.07 
TCGA-E8-A434 TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW 
       14.10        58.82        45.40        33.47        39.32        37.25 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T0 TCGA-EL-A3T2 TCGA-EL-A3TA TCGA-EL-A3ZG 
       49.32        33.50       130.72        32.48        66.90        77.36 
TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KI 
       78.97        48.16        45.80        19.53        28.73         8.71 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.50        15.75        10.45        10.65        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CQ TCGA-EM-A2CR 
       17.88        13.18        23.51         6.05        12.30        13.64 
TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI 
       10.49        22.16        13.84        17.59        17.29        17.46 
TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP 
       14.14         8.35        16.77        16.80        12.07        17.39 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.02        11.15        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4FU 
       11.51        13.51        16.90         9.01         5.03        37.87 
TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 
        0.95        48.20        18.38        29.19        19.76        58.22 
TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P 
       13.74        65.36        98.56         0.30       132.36         3.22 
TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I4 TCGA-FY-A3I5 
        1.94        33.63         0.89         1.25         1.12         1.64 
TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R7 TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA 
        0.99        16.14         0.03        16.57         0.76         0.99 
TCGA-FY-A40M TCGA-FY-A40N TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 
        4.54         0.89        21.67        12.46         9.63        43.17 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4I3 
       31.82        27.85        15.98        86.70        12.43 

$subtype3
TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       16.34        17.69         2.79        11.31        17.52         1.22 
TCGA-BJ-A3PR TCGA-BJ-A45E TCGA-CE-A27D TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 
       15.48         0.03         0.10         0.10         0.10         6.08 
TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A2PT TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 
        7.36         3.02         9.60         9.34         9.21         9.90 
TCGA-DJ-A2Q9 TCGA-DJ-A3US TCGA-DJ-A3UW TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A4UT 
       10.36        32.81        43.00        21.01         7.76        12.20 
TCGA-DJ-A4V0 TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A414 TCGA-E8-A44M 
        9.34         2.33         1.15        22.29        14.27        13.58 
TCGA-EL-A3CO TCGA-EL-A3CT TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3N3 
       97.74        60.95        37.94        57.01         4.18       147.42 
TCGA-EL-A3T6 TCGA-EL-A3T9 TCGA-EL-A3ZS TCGA-EL-A4JX TCGA-EM-A22M TCGA-EM-A22P 
       98.24         5.72         7.07        45.96        14.53        11.15 
TCGA-EM-A2CP TCGA-EM-A2P1 TCGA-EM-A3AJ TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A4FO 
        2.99        17.46        18.97        16.18        14.50         8.38 
TCGA-ET-A39M TCGA-ET-A39R TCGA-ET-A3BV TCGA-ET-A3DO TCGA-ET-A3DQ TCGA-ET-A3DT 
       84.89        57.11        42.25        80.81        59.87        17.98 
TCGA-ET-A3DU TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A230 TCGA-FE-A23A TCGA-FY-A3R6 
       25.32         5.03         4.01        59.70        81.83         0.76 
TCGA-FY-A3TY TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3EB TCGA-IM-A4EB TCGA-KS-A4ID 
        0.30        12.53        17.00        48.92         8.65        20.48 

subtype1 subtype2 subtype3 
    0.07     0.03     0.03 
subtype1 subtype2 subtype3 
  158.83   132.36   147.42 
subtype1 subtype2 subtype3 
  17.390   14.140   13.925 
[1] "0.1 - 158.8 (17.4)" "0.0 - 132.4 (14.1)" "0.0 - 147.4 (13.9)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1     145       19        67        0        35         4
  subtype2      88       30        26        1         3         2
  subtype3      44        2        15        1         6         0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        145       88       44
  STAGE II        19       30        2
  STAGE III       67       26       15
  STAGE IV         0        1        1
  STAGE IVA       35        3        6
  STAGE IVC        4        2        0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  63  88 101  18
  subtype2  54  57  39   1
  subtype3  23  20  22   2
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       63       54       23
  T2       88       57       20
  T3      101       39       22
  T4       18        1        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus         0   1
  subtype1  94 156
  subtype2 100  27
  subtype3  29  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94  156
  subtype2  100   27
  subtype3   29   36
   clus
vv  subtype1 subtype2 subtype3
  0       94      100       29
  1      156       27       36
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1 159   6 106
  subtype2  72   3  75
  subtype3  39   0  29
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      159       72       39
  M1        6        3        0
  MX      106       75       29
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus         0   1
  subtype1 199  72
  subtype2 110  41
  subtype3  51  17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  199   72
  subtype2  110   41
  subtype3   51   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      199      110       51
  MALE         72       41       17
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              5                                           220
  subtype2              2                                            72
  subtype3              2                                            55
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     17
  subtype2                                                                     77
  subtype3                                                                      5
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  29
  subtype2                                                                   0
  subtype3                                                                   6
D2V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               220
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       17
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          29
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                72
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       77
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                55
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus         0   1
  subtype1  11 260
  subtype2   1 150
  subtype3   2  66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11  260
  subtype2    1  150
  subtype3    2   66
     clus
vv    subtype1 subtype2 subtype3
  NO        11        1        2
  YES      260      150       66
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
          cls
clus         0   1
  subtype1 233   8
  subtype2 122   6
  subtype3  57   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  233    8
  subtype2  122    6
  subtype3   57    3
     clus
vv    subtype1 subtype2 subtype3
  NO       233      122       57
  YES        8        6        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           93                      15  157                   0
  subtype2           21                       0  121                   0
  subtype3           15                       1   48                   1
D2V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  93       21       15
  MODERATE/ADVANCED (T4A)       15        0        1
  NONE                         157      121       48
  VERY ADVANCED (T4B)            0        0        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 204  34   4  18
  subtype2 121   9   0   7
  subtype3  51   7   0   4
D2V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      204      121       51
  R1       34        9        7
  R2        4        0        0
  RX       18        7        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, continuous
D2V14, binary
          cls
clus         0   1
  subtype1 125 141
  subtype2  68  80
  subtype3  29  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  125  141
  subtype2   68   80
  subtype3   29   37
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL      125       68       29
  UNIFOCAL        141       80       37
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    29                        15
  subtype2                                0    13                         6
  subtype3                                0     7                         1
          vv
clus       WHITE
  subtype1   186
  subtype2    82
  subtype3    51
D2V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                  29       13        7
  BLACK OR AFRICAN AMERICAN              15        6        1
  WHITE                                 186       82       51
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V17, binary
          cls
clus         0   1
  subtype1  24 201
  subtype2   7  93
  subtype3   7  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24  201
  subtype2    7   93
  subtype3    7   50
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           24        7        7
  NOT HISPANIC OR LATINO      201       93       50
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 57  4
  subtype2 75  4
  subtype3 74  5
subtype1 subtype2 subtype3 
      61       79       79 
subtype1 subtype2 subtype3 
       4        4        5 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0ZA TCGA-BJ-A0ZC 
       24.79        13.78        18.21        16.34        18.87        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A2P4 
       16.73         7.56        17.69        23.34        20.58         7.04 
TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QM 
       15.85         9.44        14.60         7.99        18.51         1.45 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q2 TCGA-DJ-A2Q6 
       10.09         7.99         7.82         8.42         6.77         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-E3-A3DZ TCGA-EL-A3CL 
        9.57        10.36        12.43        10.03        12.07        31.66 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CU TCGA-EL-A3CW TCGA-EL-A3CY 
      155.54        97.74       158.83       157.15        57.01         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GV TCGA-EL-A3H1 TCGA-EM-A1CW 
       58.82        45.40        33.47        50.37        49.32        18.05 
TCGA-EM-A1YD TCGA-EM-A22L TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CQ 
       57.01        10.45        16.44        17.88        13.18        12.30 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AP 
       13.15        22.16        18.97        14.14        19.63         8.35 
TCGA-EM-A3FL TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A3BP TCGA-ET-A3DP TCGA-FY-A2QD 
       16.80        58.22        13.74         4.18        56.88         1.25 
TCGA-J8-A3O0 
       43.17 

$subtype2
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A290 
       14.73         8.25         4.01         8.09         4.87        20.61 
TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-CE-A3ME TCGA-DE-A0Y2 
       18.38        20.48        18.97        16.01         0.23        15.42 
TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QG 
        7.36         3.02         8.71        10.92       100.01         6.97 
TCGA-DJ-A1QO TCGA-DJ-A2PP TCGA-DJ-A2PY TCGA-DJ-A2Q0 TCGA-DJ-A2Q8 TCGA-DJ-A2QB 
        1.02         5.33         8.78         8.12         7.07        10.85 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A2EA 
       21.53        31.07        40.21        30.31        14.04        22.29 
TCGA-EL-A3CM TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CV TCGA-EL-A3D6 TCGA-EL-A3GS 
       26.73        45.53        60.95        37.94       108.36        65.39 
TCGA-EL-A3GU TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW 
      124.04       101.13        38.66        52.73       126.97       108.66 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EM-A1CT TCGA-EM-A1YA TCGA-EM-A1YB 
       52.50        12.16       147.42        18.18        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22O TCGA-EM-A2CO TCGA-EM-A2OY 
       54.21        14.73        14.50        11.74         6.05        17.59 
TCGA-EM-A2P1 TCGA-EM-A3FP TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25O 
       17.46        17.39        47.47        14.79        12.33        27.09 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39P TCGA-ET-A39T TCGA-ET-A3BT TCGA-ET-A3DO 
       22.09        16.08        58.72        59.15        24.72        80.81 
TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A234 
       24.72        73.74        59.70        31.59        44.25        68.22 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FY-A3BL TCGA-IM-A3EB TCGA-J8-A3NZ 
       66.77        81.34        81.83         1.15        48.92         2.24 
TCGA-J8-A3O1 
       27.19 

$subtype3
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       20.71         4.83        21.04         2.79         5.10        11.31 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A3F0 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        1.22        22.88        13.94         0.53         0.10         0.20 
TCGA-DE-A2OL TCGA-DJ-A13V TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QN TCGA-DJ-A2PQ 
        5.98        11.90        14.96         7.20         8.88        20.52 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 
       10.45         1.51        10.26         7.69         9.34         9.44 
TCGA-DJ-A2Q5 TCGA-DO-A1JZ TCGA-E3-A3E0 TCGA-EL-A3CR TCGA-EL-A3CX TCGA-EL-A3D0 
        9.90        54.90        66.38         7.66        80.91         1.45 
TCGA-EL-A3D1 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GW 
       74.30        39.32         1.41        30.18       102.84        37.25 
TCGA-EL-A3GX TCGA-EL-A3H2 TCGA-EL-A3H8 TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EM-A1CU 
      147.75        33.50       131.15        57.63        17.52        20.91 
TCGA-EM-A1CV TCGA-EM-A1YE TCGA-EM-A22M TCGA-EM-A22Q TCGA-EM-A2CN TCGA-EM-A2CP 
       12.36        54.08        14.53        14.24        23.51         2.99 
TCGA-EM-A2CR TCGA-EM-A2CS TCGA-EM-A3AI TCGA-EM-A3AO TCGA-EM-A3FJ TCGA-EM-A3FN 
       13.64        15.19        17.46        13.38        27.95        12.07 
TCGA-EM-A3FO TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39L 
       17.49        12.26        29.19         2.66        71.01        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39R TCGA-ET-A3BN TCGA-ET-A3BS TCGA-ET-A3BU 
       84.89        98.56        57.11        28.24         5.56        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DV 
       42.25         2.37         4.50         0.30        17.98       132.36 
TCGA-FE-A233 TCGA-FE-A235 TCGA-FE-A239 TCGA-FY-A3ON TCGA-GE-A2C6 TCGA-H2-A2K9 
       24.69       102.90        33.63         1.51        12.53        21.67 
TCGA-IM-A3ED 
       47.41 

subtype1 subtype2 subtype3 
    1.25     0.23     0.10 
subtype1 subtype2 subtype3 
  158.83   147.42   147.75 
subtype1 subtype2 subtype3 
   16.34    20.61    15.19 
[1] "1.2 - 158.8 (16.3)" "0.2 - 147.4 (20.6)" "0.1 - 147.8 (15.2)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      31       11        14         2         1
  subtype2      31       13        21        14         0
  subtype3      53        9        10         5         3
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         31       31       53
  STAGE II        11       13        9
  STAGE III       14       21       10
  STAGE IVA        2       14        5
  STAGE IVC        1        0        3
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 22 23 15  0
  subtype2 13 25 33  8
  subtype3 16 35 26  3
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       22       13       16
  T2       23       25       35
  T3       15       33       26
  T4        0        8        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus        0  1
  subtype1 34 18
  subtype2 29 41
  subtype3 34 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   18
  subtype2   29   41
  subtype3   34   35
   clus
vv  subtype1 subtype2 subtype3
  0       34       29       34
  1       18       41       35
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 38  1 21
  subtype2 43  1 35
  subtype3 35  3 42
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       38       43       35
  M1        1        1        3
  MX       21       35       42
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 43 18
  subtype2 57 22
  subtype3 52 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   18
  subtype2   57   22
  subtype3   52   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       43       57       52
  MALE         18       22       28
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              0                                            35
  subtype2              1                                            55
  subtype3              1                                            66
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     25
  subtype2                                                                     14
  subtype3                                                                     13
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   1
  subtype2                                                                   9
  subtype3                                                                   0
D3V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                35
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       25
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                55
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       14
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           9
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                66
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       13
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
          cls
clus        0  1
  subtype1  0 61
  subtype2  9 70
  subtype3  4 76
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   61
  subtype2    9   70
  subtype3    4   76
     clus
vv    subtype1 subtype2 subtype3
  NO         0        9        4
  YES       61       70       76
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
          cls
clus        0  1
  subtype1 52  3
  subtype2 67  4
  subtype3 63  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    3
  subtype2   67    4
  subtype3   63    4
     clus
vv    subtype1 subtype2 subtype3
  NO        52       67       63
  YES        3        4        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1           13                       0   47
  subtype2           28                       8   41
  subtype3           15                       2   58
D3V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  13       28       15
  MODERATE/ADVANCED (T4A)        0        8        2
  NONE                          47       41       58
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 48  6  1  5
  subtype2 58 13  0  4
  subtype3 60  4  1  5
D3V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       48       58       60
  R1        6       13        4
  R2        1        0        1
  RX        5        4        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, continuous
D3V14, binary
          cls
clus        0  1
  subtype1 35 23
  subtype2 27 50
  subtype3 39 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   23
  subtype2   27   50
  subtype3   39   39
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       35       27       39
  UNIFOCAL         23       50       39
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         7    34
  subtype2     3                         4    59
  subtype3     8                         2    50
D3V16, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        3        8
  BLACK OR AFRICAN AMERICAN        7        4        2
  WHITE                           34       59       50
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V17, binary
          cls
clus        0  1
  subtype1  1 45
  subtype2  8 58
  subtype3  7 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   45
  subtype2    8   58
  subtype3    7   59
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        8        7
  NOT HISPANIC OR LATINO       45       58       59
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 43  4
  subtype2 27  1
  subtype3 33  0
  subtype4 26  2
  subtype5 46  1
  subtype6 26  1
  subtype7  5  4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      47       28       33       28       47       27        9 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       4        1        0        2        1        1        4 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZG 
       24.79        13.78        18.21        18.87        11.57         7.56 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A28V TCGA-BJ-A2N9 TCGA-DE-A2OL 
       17.69        23.34        20.58         5.10        20.48         5.98 
TCGA-DJ-A13M TCGA-DJ-A13W TCGA-DJ-A1QL TCGA-DJ-A2PO TCGA-DJ-A2Q2 TCGA-E3-A3DZ 
        9.44        14.60         7.20         7.99         6.77        12.07 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CU TCGA-EL-A3CW TCGA-EL-A3CZ TCGA-EL-A3D4 
       97.74       158.83       157.15        57.01        58.82        45.40 
TCGA-EL-A3D5 TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EM-A1CW TCGA-EM-A1YD 
       33.47        37.25        49.32        33.50        18.05        57.01 
TCGA-EM-A1YE TCGA-EM-A22L TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CQ 
       54.08        10.45        16.44        17.88        13.18        12.30 
TCGA-EM-A2CR TCGA-EM-A2OV TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FL 
       13.64        22.16        18.97        14.14         8.35        16.80 
TCGA-ET-A39I TCGA-ET-A3BP TCGA-ET-A3DP TCGA-ET-A3DV TCGA-FY-A2QD 
       13.74         4.18        56.88       132.36         1.25 

$subtype2
TCGA-BJ-A0Z3 TCGA-DE-A3KN TCGA-DJ-A13O TCGA-DJ-A13X TCGA-DJ-A1QM TCGA-DJ-A2PN 
       16.34        15.85         7.36         7.99         1.45        10.09 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       20.52         1.51         7.82         8.42         8.61         9.57 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-EL-A3CL TCGA-EL-A3CV TCGA-EL-A3GQ 
       10.36        12.43        10.03        31.66        37.94        30.18 
TCGA-EM-A1CT TCGA-EM-A2CU TCGA-EM-A3AN TCGA-EM-A3FJ TCGA-ET-A25M TCGA-ET-A2MZ 
       18.18        13.15        19.63        27.95        12.33        12.26 
TCGA-ET-A39P TCGA-FE-A232 TCGA-FE-A236 TCGA-J8-A3O0 
       58.72        44.25        66.77        43.17 

$subtype3
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A290 TCGA-BJ-A3EZ TCGA-CE-A3ME 
       14.73         8.25         4.01        20.61        16.01         0.23 
TCGA-DE-A0Y2 TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QO TCGA-DJ-A2PY TCGA-DJ-A2Q8 
       15.42        10.92       100.01         1.02         8.78         7.07 
TCGA-DO-A1K0 TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-EL-A3D6 TCGA-EL-A3GS TCGA-EL-A3GU 
       21.53        40.21        30.31       108.36        65.39       124.04 
TCGA-EL-A3GY TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EM-A22O 
      101.13        52.73       126.97       108.66        12.16        11.74 
TCGA-EM-A2P1 TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A3DO TCGA-ET-A3DW TCGA-FE-A230 
       17.46        47.47        14.79        80.81        24.72        59.70 
TCGA-FE-A234 TCGA-FE-A23A TCGA-J8-A3NZ 
       68.22        81.83         2.24 

$subtype4
TCGA-BJ-A0ZE TCGA-BJ-A28S TCGA-BJ-A28W TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2P4 
       16.73        21.04        11.31         1.22        22.88         7.04 
TCGA-BJ-A3F0 TCGA-EL-A3CN TCGA-EL-A3CR TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3GO 
       13.94       155.54         7.66         4.18         1.45        39.32 
TCGA-EM-A22Q TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A3AI TCGA-EM-A3FN TCGA-EM-A3FP 
       14.24        23.51         2.99        17.46        12.07        17.39 
TCGA-ET-A2N1 TCGA-ET-A2N5 TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39R TCGA-ET-A3BS 
       29.19        58.22        65.36        98.56        57.11         5.56 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-FE-A239 TCGA-H2-A2K9 
        0.30        17.98        33.63        21.67 

$subtype5
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28T TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
       20.71         4.83         2.79         0.53         0.10         0.20 
TCGA-DJ-A13V TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PR TCGA-DJ-A2PU 
       11.90        18.51        14.96         8.88        10.45        10.26 
TCGA-DJ-A2PW TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DO-A1JZ TCGA-E3-A3E0 
        7.69         9.34         9.44         9.90        54.90        66.38 
TCGA-E8-A2EA TCGA-EL-A3CX TCGA-EL-A3D1 TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GV 
       22.29        80.91        74.30         1.41       102.84        50.37 
TCGA-EL-A3GX TCGA-EL-A3H8 TCGA-EL-A3MX TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22M 
      147.75       131.15        57.63        20.91        12.36        14.53 
TCGA-EM-A2CS TCGA-EM-A3AO TCGA-EM-A3FO TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39M 
       15.19        13.38        17.49         2.66        71.01        84.89 
TCGA-ET-A3BN TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-FE-A233 
       28.24        38.30        42.25         2.37         4.50        24.69 
TCGA-FE-A235 TCGA-FY-A3ON TCGA-GE-A2C6 TCGA-IM-A3EB TCGA-IM-A3ED 
      102.90         1.51        12.53        48.92        47.41 

$subtype6
TCGA-BJ-A192 TCGA-BJ-A2N7 TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A2PP 
        8.09        18.38         3.02         8.71         6.97         5.33 
TCGA-DJ-A2Q0 TCGA-DJ-A2QB TCGA-E3-A3DY TCGA-EL-A3MZ TCGA-EM-A1YA TCGA-EM-A1YB 
        8.12        10.85        31.07        52.50        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A2CO TCGA-EM-A2OY TCGA-ET-A25O 
       54.21        14.73        14.50         6.05        17.59        27.09 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39T TCGA-ET-A3BT TCGA-FE-A22Z TCGA-FE-A231 
       22.09        16.08        59.15        24.72        73.74        31.59 
TCGA-FE-A237 TCGA-FY-A3BL TCGA-J8-A3O1 
       81.34         1.15        27.19 

$subtype7
TCGA-BJ-A28R TCGA-BJ-A2NA TCGA-E3-A3E5 TCGA-EL-A3CM TCGA-EL-A3CS TCGA-EL-A3CT 
        4.87        18.97        14.04        26.73        45.53        60.95 
TCGA-EL-A3H4 TCGA-EL-A3MY TCGA-EL-A3N3 
       38.66        17.52       147.42 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    1.25     1.45     0.23     0.30     0.10     1.15     4.87 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  158.83    66.77   126.97   155.54   147.75    81.34   147.42 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  17.880   12.790   21.530   17.425   15.190   18.380   26.730 
[1] "1.2 - 158.8 (17.9)" "1.4 - 66.8 (12.8)"  "0.2 - 127.0 (21.5)"
[4] "0.3 - 155.5 (17.4)" "0.1 - 147.8 (15.2)" "1.1 - 81.3 (18.4)" 
[7] "4.9 - 147.4 (26.7)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
  subtype1      26       11         6         1         1
  subtype2      16        3         7         2         0
  subtype3      13        4        11         5         0
  subtype4      16        4         6         1         1
  subtype5      34        3         6         4         1
  subtype6       9        7         7         4         0
  subtype7       1        1         2         4         1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I         26       16       13       16       34        9        1
  STAGE II        11        3        4        4        3        7        1
  STAGE III        6        7       11        6        6        7        2
  STAGE IVA        1        2        5        1        4        4        4
  STAGE IVC        1        0        0        1        1        0        1
[1] 5 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 16 22  9  0
  subtype2 11  9  8  0
  subtype3  3 11 17  2
  subtype4  4 10 12  1
  subtype5 10 21 16  1
  subtype6  6 10  9  2
  subtype7  1  0  3  5
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1       16       11        3        4       10        6        1
  T2       22        9       11       10       21       10        0
  T3        9        8       17       12       16        9        3
  T4        0        0        2        1        1        2        5
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1 28 11
  subtype2 13 13
  subtype3 10 22
  subtype4 17  8
  subtype5 15 26
  subtype6 11 10
  subtype7  3  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   11
  subtype2   13   13
  subtype3   10   22
  subtype4   17    8
  subtype5   15   26
  subtype6   11   10
  subtype7    3    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       28       13       10       17       15       11        3
  1       11       13       22        8       26       10        4
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 21  1 24
  subtype2 19  0  9
  subtype3 21  1 11
  subtype4 12  1 15
  subtype5 25  1 22
  subtype6 11  0 16
  subtype7  7  1  1
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  M0       21       19       21       12       25       11        7
  M1        1        0        1        1        1        0        1
  MX       24        9       11       15       22       16        1
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 31 16
  subtype2 18 10
  subtype3 25  8
  subtype4 20  8
  subtype5 32 16
  subtype6 20  7
  subtype7  6  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   16
  subtype2   18   10
  subtype3   25    8
  subtype4   20    8
  subtype5   32   16
  subtype6   20    7
  subtype7    6    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       31       18       25       20       32       20        6
  MALE         16       10        8        8       16        7        3
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              0                                            22
  subtype2              0                                            22
  subtype3              0                                            25
  subtype4              0                                            21
  subtype5              1                                            45
  subtype6              1                                            12
  subtype7              0                                             9
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     25
  subtype2                                                                      5
  subtype3                                                                      0
  subtype4                                                                      7
  subtype5                                                                      2
  subtype6                                                                     13
  subtype7                                                                      0
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   0
  subtype2                                                                   1
  subtype3                                                                   8
  subtype4                                                                   0
  subtype5                                                                   0
  subtype6                                                                   1
  subtype7                                                                   0
D4V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                22
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       25
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                22
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                25
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           8
                                                                        clus
vv                                                                       subtype4
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                21
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype5
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                45
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype6
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                12
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       13
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype7
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                 9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
          cls
clus        0  1
  subtype1  0 47
  subtype2  2 26
  subtype3  4 29
  subtype4  1 27
  subtype5  3 45
  subtype6  3 24
  subtype7  0  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   47
  subtype2    2   26
  subtype3    4   29
  subtype4    1   27
  subtype5    3   45
  subtype6    3   24
  subtype7    0    9
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         0        2        4        1        3        3        0
  YES       47       26       29       27       45       24        9
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
          cls
clus        0  1
  subtype1 39  3
  subtype2 26  0
  subtype3 29  0
  subtype4 21  2
  subtype5 38  2
  subtype6 23  3
  subtype7  6  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    3
  subtype2   26    0
  subtype3   29    0
  subtype4   21    2
  subtype5   38    2
  subtype6   23    3
  subtype7    6    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        39       26       29       21       38       23        6
  YES        3        0        0        2        2        3        1
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  subtype1            4                       0   42
  subtype2            9                       0   19
  subtype3           15                       3   14
  subtype4            6                       1   17
  subtype5           13                       0   34
  subtype6            6                       2   19
  subtype7            3                       4    1
D4V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  MINIMAL (T3)                   4        9       15        6       13        6
  MODERATE/ADVANCED (T4A)        0        0        3        1        0        2
  NONE                          42       19       14       17       34       19
                         clus
vv                        subtype7
  MINIMAL (T3)                   3
  MODERATE/ADVANCED (T4A)        4
  NONE                           1
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 37  5  0  3
  subtype2 22  3  0  2
  subtype3 24  7  0  0
  subtype4 18  2  2  1
  subtype5 38  3  0  3
  subtype6 23  1  0  3
  subtype7  4  2  0  2
D4V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       37       22       24       18       38       23        4
  R1        5        3        7        2        3        1        2
  R2        0        0        0        2        0        0        0
  RX        3        2        0        1        3        3        2
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
D4V14, binary
          cls
clus        0  1
  subtype1 28 16
  subtype2 12 16
  subtype3 12 20
  subtype4 12 16
  subtype5 25 21
  subtype6 10 16
  subtype7  2  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   16
  subtype2   12   16
  subtype3   12   20
  subtype4   12   16
  subtype5   25   21
  subtype6   10   16
  subtype7    2    7
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  MULTIFOCAL       28       12       12       12       25       10        2
  UNIFOCAL         16       16       20       16       21       16        7
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         6    24
  subtype2     2                         1    18
  subtype3     2                         0    28
  subtype4     2                         1    18
  subtype5     6                         2    31
  subtype6     1                         2    16
  subtype7     0                         1     8
D4V16, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        2        2        2        6
  BLACK OR AFRICAN AMERICAN        6        1        0        1        2
  WHITE                           24       18       28       18       31
                           clus
vv                          subtype6 subtype7
  ASIAN                            1        0
  BLACK OR AFRICAN AMERICAN        2        1
  WHITE                           16        8
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V17, binary
          cls
clus        0  1
  subtype1  2 31
  subtype2  1 23
  subtype3  3 27
  subtype4  2 20
  subtype5  5 36
  subtype6  2 17
  subtype7  1  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   31
  subtype2    1   23
  subtype3    3   27
  subtype4    2   20
  subtype5    5   36
  subtype6    2   17
  subtype7    1    8
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            2        1        3        2        5        2
  NOT HISPANIC OR LATINO       31       23       27       20       36       17
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO        8
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 149   4
  subtype2  50   1
  subtype3 112   2
  subtype4 157   7
subtype1 subtype2 subtype3 subtype4 
     153       51      114      164 
subtype1 subtype2 subtype3 subtype4 
       4        1        2        7 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        18.21        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S 
        7.56        23.34        20.58         4.83         8.09        21.04 
TCGA-BJ-A28V TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 
        5.10        22.88        18.38        16.57        20.48         7.04 
TCGA-BJ-A3F0 TCGA-BJ-A3PT TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       13.94        23.31         5.75         6.48         3.45         6.35 
TCGA-BJ-A45K TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O 
        8.98         0.39         5.98         4.87         9.44         7.36 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM 
        3.02         8.71        14.60         6.97         7.20         1.45 
TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UP 
        5.33         8.12         6.77        12.43        10.85        16.41 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UZ TCGA-DJ-A3V4 TCGA-DJ-A3VG TCGA-DJ-A3VL 
       32.81        15.45        12.76        14.56         8.32        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-DJ-A4V0 TCGA-E3-A3DZ TCGA-E8-A415 TCGA-E8-A416 
       27.62        10.98         9.34        12.07        13.81        14.07 
TCGA-E8-A434 TCGA-EL-A3CO TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 
       14.10        97.74        80.91        58.82        45.40        33.47 
TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T0 TCGA-EL-A3T2 
       39.32        37.25        49.32        33.50       130.72        32.48 
TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KD 
       78.97        48.16        45.80        19.53        28.73        29.95 
TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
        8.71        18.05        19.79        19.46        54.21        57.01 
TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q 
       54.08        14.50        15.75        10.45        10.65        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY 
       12.30        13.64        10.49        22.16        13.84        17.59 
TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3AR 
       17.29        17.46        18.97        14.14         8.35        16.77 
TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 
       16.80        12.07        17.39        15.02        11.15        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH 
        9.24        13.91         7.82        11.51        13.51        16.90 
TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P 
        9.01         5.03        37.87         0.95        48.20        18.38 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39S 
       19.76        58.22        13.74        65.36        98.56        55.10 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ 
       59.87        43.50         0.30       132.36         3.22         1.94 
TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP 
       33.63         0.89         1.25         1.64         0.99        16.14 
TCGA-FY-A3R7 TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A40N 
        0.03        16.57         0.76         0.99         4.54         0.89 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YE 
       21.67        12.46         9.63        43.17        31.82        27.85 
TCGA-J8-A4HY TCGA-KS-A41I TCGA-KS-A41L 
        0.20        15.98        86.70 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       16.34        17.69         2.79        11.31        17.52         1.22 
TCGA-BJ-A3PR TCGA-BJ-A45E TCGA-CE-A27D TCGA-CE-A481 TCGA-DE-A4M8 TCGA-DJ-A2PX 
       15.48         0.03         0.10         0.10         6.08         5.52 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q9 TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3VD TCGA-DJ-A4UT 
        9.21        10.36        43.00        11.34        21.01        12.20 
TCGA-DO-A2HM TCGA-E8-A2EA TCGA-E8-A414 TCGA-E8-A417 TCGA-E8-A44M TCGA-EL-A3CU 
        2.33        22.29        14.27        14.27        13.58       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3GP TCGA-EL-A3TA TCGA-EL-A3ZP 
       37.94        57.01         4.18         1.41        66.90        52.50 
TCGA-EL-A3ZS TCGA-EL-A4JZ TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2P1 TCGA-EM-A3FQ 
        7.07        37.94        14.53        11.15        17.46        16.18 
TCGA-EM-A3O3 TCGA-EM-A4FO TCGA-ET-A39R TCGA-ET-A3BO TCGA-ET-A3DT TCGA-ET-A3DU 
       14.50         8.38        57.11         5.85        17.98        25.32 
TCGA-ET-A40R TCGA-ET-A40S TCGA-FE-A3PB TCGA-FY-A3R6 TCGA-FY-A3TY TCGA-GE-A2C6 
        4.80         5.03        85.15         0.76         0.30        12.53 
TCGA-H2-A26U TCGA-J8-A3O2 TCGA-KS-A4ID 
       17.00         1.35        20.48 

$subtype3
TCGA-BJ-A0Z5 TCGA-BJ-A290 TCGA-BJ-A45H TCGA-BJ-A45J TCGA-BJ-A4O9 TCGA-CE-A13K 
       14.73        20.61         7.82         5.06         5.98         0.53 
TCGA-CE-A3MD TCGA-CE-A482 TCGA-DE-A0XZ TCGA-DE-A3KN TCGA-DJ-A13P TCGA-DJ-A13T 
        0.20         0.07        20.22        15.85       137.88        25.35 
TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PO 
       11.90         7.99        18.51        14.96         8.88         7.99 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2Q5 
       20.52        10.45         1.51        10.26         7.82         9.90 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO 
        8.61         9.57        10.03        15.09        12.49        31.46 
TCGA-DJ-A3UR TCGA-DJ-A3UU TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       36.33        17.69        20.22        30.61        20.48        11.93 
TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4UW TCGA-DO-A1JZ TCGA-E3-A3DY TCGA-E3-A3E0 
       18.97        11.93         9.44        54.90        31.07        66.38 
TCGA-E3-A3E2 TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CP 
       63.19        14.04        14.43        20.68        31.66       158.83 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GQ TCGA-EL-A3GV TCGA-EL-A3MW TCGA-EL-A3MX 
        1.45        74.30        30.18        50.37       108.66        57.63 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZL TCGA-EL-A3ZQ 
       41.29        95.38        82.82        77.36        50.33        45.53 
TCGA-EL-A4K0 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CV 
       19.00        41.13        37.78        11.87        26.86        12.36 
TCGA-EM-A2CS TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO 
       15.19        13.15        19.73        15.68        19.63        13.38 
TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3O7 TCGA-EM-A3SX TCGA-EM-A4FV TCGA-ET-A25K 
       16.44        27.95         7.33        15.62        12.72        32.35 
TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39M 
       27.09        12.26         2.66        71.01        72.49        84.89 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BW TCGA-ET-A3DP TCGA-ET-A40T 
        4.18         2.43         5.56         2.37        56.88         2.14 
TCGA-FE-A235 TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      102.90       106.36        85.68        78.77        46.06         4.08 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A40K TCGA-H2-A3RI TCGA-J8-A3YH 
        0.92        48.10        91.17         4.14         2.99         5.75 
TCGA-J8-A42S TCGA-KS-A41F TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4IB 
        2.47       120.99         6.02         6.74        12.36        64.57 
TCGA-KS-A4IC TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 
       14.70         0.59        40.37         1.12        14.47         8.71 

$subtype4
TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A18Z TCGA-BJ-A28R TCGA-BJ-A2NA 
        8.25         4.01        15.12        20.71         4.87        18.97 
TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A3ME TCGA-CE-A483 
       16.01        18.64         6.18         4.93         0.23         0.10 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
        0.10        15.42        36.46        30.12        11.57        17.39 
TCGA-DE-A4MD TCGA-DJ-A13U TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QO 
       25.12        13.41        10.92       100.01         7.99         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PT TCGA-DJ-A2PW TCGA-DJ-A2PY TCGA-DJ-A2PZ 
        5.95        10.09         9.60         7.69         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UY TCGA-DJ-A3V0 
        9.34         9.44        31.04        19.56        21.37        25.02 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3VB TCGA-DJ-A3VF TCGA-DJ-A3VJ 
       19.20         9.83        21.27        22.92         7.76        17.36 
TCGA-DJ-A4UQ TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1K0 TCGA-E3-A3E1 
       10.78         3.12         3.39        16.14        21.53        40.21 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A418 TCGA-E8-A433 
       30.31         1.15        19.59        13.61         3.02        14.70 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CR 
       14.96         7.69        13.78        26.73       155.54         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3D6 TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       45.53        60.95       108.36       102.84        65.39       124.04 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
      147.75       101.13        38.66        52.73       126.97       131.15 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T1 TCGA-EL-A3T3 
       17.52        52.50        12.16       147.42       129.57       116.91 
TCGA-EL-A3T6 TCGA-EL-A3T9 TCGA-EL-A3ZK TCGA-EL-A3ZO TCGA-EL-A3ZT TCGA-EL-A4JW 
       98.24         5.72        31.50        47.38        44.65        19.30 
TCGA-EL-A4JX TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4KG TCGA-EM-A1CT TCGA-EM-A1CU 
       45.96        19.59        33.60        13.32        18.18        20.91 
TCGA-EM-A22I TCGA-EM-A22O TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P3 TCGA-EM-A3FK 
       14.73        11.74        12.07        17.59        14.60        23.77 
TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3SU TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM 
       21.01        17.49        16.41        12.79        70.65         4.83 
TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25L TCGA-ET-A25M 
        8.61         9.80        47.47        29.69        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39O 
       14.79        20.45        54.05        22.09        16.08        61.02 
TCGA-ET-A39P TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       58.72        59.15        28.24        24.72        38.30        42.25 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A4KN TCGA-FE-A22Z 
        4.50        80.81        24.72         7.17         4.01        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A236 
       59.70        31.59        44.25        24.69        68.22        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FK-A3SE TCGA-FY-A3BL TCGA-FY-A3I4 
       81.34        39.95        81.83        22.03         1.15         1.12 
TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A3YR TCGA-FY-A40L TCGA-FY-A4B3 
        1.51         4.67        18.08         6.87         6.58         1.35 
TCGA-FY-A4B4 TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        1.15        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 
       16.90         9.80         2.96         8.65         2.24        27.19 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I3 TCGA-KS-A4I9 
       24.69        22.29         2.60        15.68        12.43        17.46 
TCGA-L6-A4EU TCGA-MK-A4N6 
        0.72        16.64 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.03     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 
  132.36   157.15   158.83   155.54 
subtype1 subtype2 subtype3 subtype4 
  14.500   13.580   15.650   17.835 
[1] "0.0 - 132.4 (14.5)" "0.0 - 157.2 (13.6)" "0.1 - 158.8 (15.6)"
[4] "0.1 - 155.5 (17.8)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      90       29        27        1         4         2
  subtype2      36        1        12        0         3         0
  subtype3      66       14        22        0        10         2
  subtype4      83        7        45        1        27         2
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         90       36       66       83
  STAGE II        29        1       14        7
  STAGE III       27       12       22       45
  STAGE IV         1        0        0        1
  STAGE IVA        4        3       10       27
  STAGE IVC        2        0        2        2
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 55 56 41  2
  subtype2 22 14 14  1
  subtype3 33 48 30  4
  subtype4 29 45 76 14
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       55       22       33       29
  T2       56       14       48       45
  T3       41       14       30       76
  T4        2        1        4       14
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus         0   1
  subtype1 102  28
  subtype2  20  32
  subtype3  48  58
  subtype4  51 100
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102   28
  subtype2   20   32
  subtype3   48   58
  subtype4   51  100
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      102       20       48       51
  1       28       32       58      100
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 71  3 79
  subtype2 34  0 18
  subtype3 70  3 42
  subtype4 92  3 70
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       71       34       70       92
  M1        3        0        3        3
  MX       79       18       42       70
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus         0   1
  subtype1 111  43
  subtype2  39  13
  subtype3  87  28
  subtype4 119  46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  111   43
  subtype2   39   13
  subtype3   87   28
  subtype4  119   46
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      111       39       87      119
  MALE         43       13       28       46
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              2                                            70
  subtype2              1                                            44
  subtype3              2                                            98
  subtype4              4                                           132
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     81
  subtype2                                                                      3
  subtype3                                                                     12
  subtype4                                                                      3
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   1
  subtype2                                                                   4
  subtype3                                                                   3
  subtype4                                                                  26
D5V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                70
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       81
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                44
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           4
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                98
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       12
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           3
                                                                        clus
vv                                                                       subtype4
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               132
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          26
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
          cls
clus         0   1
  subtype1   1 153
  subtype2   0  52
  subtype3   2 113
  subtype4  11 154
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  153
  subtype2    0   52
  subtype3    2  113
  subtype4   11  154
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        2       11
  YES      153       52      113      154
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
          cls
clus         0   1
  subtype1 128   6
  subtype2  41   2
  subtype3  97   4
  subtype4 142   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  128    6
  subtype2   41    2
  subtype3   97    4
  subtype4  142    5
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       128       41       97      142
  YES        6        2        4        5
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           22                       1  123                   0
  subtype2           12                       1   36                   0
  subtype3           28                       1   83                   0
  subtype4           66                      13   81                   1
D5V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  MINIMAL (T3)                  22       12       28       66
  MODERATE/ADVANCED (T4A)        1        1        1       13
  NONE                         123       36       83       81
  VERY ADVANCED (T4B)            0        0        0        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 123  10   0   7
  subtype2  36   5   0   5
  subtype3  89   9   2   8
  subtype4 125  25   2   9
D5V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      123       36       89      125
  R1       10        5        9       25
  R2        0        0        2        2
  RX        7        5        8        9
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, continuous
D5V14, binary
          cls
clus        0  1
  subtype1 72 79
  subtype2 22 28
  subtype3 58 54
  subtype4 67 96
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72   79
  subtype2   22   28
  subtype3   58   54
  subtype4   67   96
            clus
vv           subtype1 subtype2 subtype3 subtype4
  MULTIFOCAL       72       22       58       67
  UNIFOCAL         79       28       54       96
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    10                         6
  subtype2                                0     6                         1
  subtype3                                0    16                         5
  subtype4                                1    16                         8
          vv
clus       WHITE
  subtype1    88
  subtype2    38
  subtype3    73
  subtype4   120
D5V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                  10        6       16       16
  BLACK OR AFRICAN AMERICAN               6        1        5        8
  WHITE                                  88       38       73      120
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V17, binary
          cls
clus         0   1
  subtype1   9  94
  subtype2   3  41
  subtype3   3  87
  subtype4  23 118
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   94
  subtype2    3   41
  subtype3    3   87
  subtype4   23  118
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            9        3        3       23
  NOT HISPANIC OR LATINO       94       41       87      118
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1 123   3
  subtype2  95   2
  subtype3  69   2
  subtype4 105   6
  subtype5  76   1
subtype1 subtype2 subtype3 subtype4 subtype5 
     126       97       71      111       77 
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        2        2        6        1 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        18.21        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S 
        7.56        23.34        20.58         4.83         8.09        21.04 
TCGA-BJ-A28V TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2P4 TCGA-BJ-A3F0 
        5.10        22.88        18.38        16.57         7.04        13.94 
TCGA-BJ-A3PT TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45K 
       23.31         5.75         6.48         3.45         6.35         8.98 
TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13S TCGA-DJ-A13W 
        0.39         5.98         4.87         9.44         8.71        14.60 
TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB 
        6.97         7.20         5.33         8.12         6.77        10.85 
TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ 
       16.41        15.45         8.32        27.62        10.98        12.07 
TCGA-E8-A416 TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW 
       14.07        80.91        58.82        33.47        39.32        37.25 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV 
       49.32        33.50        32.48        78.97        48.16        45.80 
TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       19.53        28.73         8.71        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        57.01        54.08        14.50        15.75        10.45 
TCGA-EM-A22N TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       10.65        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW 
        6.05        12.30        13.64        10.49        22.16        13.84 
TCGA-EM-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP 
       17.59        17.29        17.46        18.97        14.14         8.35 
TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 
       16.80        12.07        15.02        11.15        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK 
       13.91         7.82        11.51        13.51        16.90         9.01 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25P TCGA-ET-A2N3 TCGA-ET-A2N5 
        5.03        37.87         0.95        18.38        19.76        58.22 
TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P 
       13.74        65.36        98.56         0.30       132.36         3.22 
TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM 
        1.94        33.63         0.89         1.25         1.64         0.99 
TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-H2-A2K9 
       16.14        16.57         0.76         0.99         4.54        21.67 
TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A4HY TCGA-KS-A41I TCGA-KS-A41L 
       12.46         9.63        43.17         0.20        15.98        86.70 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0ZJ TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28Z TCGA-BJ-A2N9 
       16.34        17.69         2.79        11.31         1.22        20.48 
TCGA-BJ-A45E TCGA-BJ-A45H TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A481 
        0.03         7.82         0.53         0.10         0.20         0.10 
TCGA-CE-A482 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DJ-A13O 
        0.07         0.10        20.22        15.85         6.08         7.36 
TCGA-DJ-A13R TCGA-DJ-A13X TCGA-DJ-A1QM TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PV 
        3.02         7.99         1.45        10.45         1.51         7.82 
TCGA-DJ-A2PX TCGA-DJ-A2Q5 TCGA-DJ-A2QA TCGA-DJ-A3US TCGA-DJ-A3UU TCGA-DJ-A3UX 
        5.52         9.90        12.43        32.81        17.69        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3VL 
       21.37        12.76        20.22        30.61        14.56        17.23 
TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-E3-A3E0 
       10.78        12.20         9.44         9.34         3.39        66.38 
TCGA-E3-A3E2 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A432 TCGA-E8-A434 
       63.19        13.61        14.27        13.81        14.43        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44M TCGA-EL-A3CO TCGA-EL-A3CW 
       14.96         7.69        20.68        13.58        97.74        57.01 
TCGA-EL-A3D4 TCGA-EL-A3GQ TCGA-EL-A3T0 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZQ 
       45.40        30.18       130.72        66.90        82.82        45.53 
TCGA-EL-A3ZS TCGA-EL-A4KD TCGA-EM-A22M TCGA-EM-A2CP TCGA-EM-A2CU TCGA-EM-A3AN 
        7.07        29.95        14.53         2.99        13.15        19.63 
TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FP TCGA-EM-A4FO TCGA-EM-A4FV 
       13.38        16.44        16.77        17.39         8.38        12.72 
TCGA-ET-A25I TCGA-ET-A39M TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A3BS TCGA-ET-A3DQ 
       48.20        84.89        57.11        55.10         5.56        59.87 
TCGA-ET-A3DT TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-FE-A232 TCGA-FE-A3PA 
       17.98         4.80         5.03         2.14        44.25       106.36 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SG TCGA-FK-A4UB TCGA-FY-A3R6 TCGA-FY-A3R7 
       78.77        46.06         0.92        91.17         0.76         0.03 
TCGA-FY-A3TY TCGA-FY-A40N TCGA-IM-A3ED TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A42S 
        0.30         0.89        47.41         1.35        31.82         2.47 
TCGA-KS-A4ID 
       20.48 

$subtype3
TCGA-BJ-A0Z5 TCGA-BJ-A290 TCGA-BJ-A45J TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13V 
       14.73        20.61         5.06       137.88        25.35        11.90 
TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PQ TCGA-DJ-A2PU TCGA-DJ-A2PW 
       18.51        14.96         8.88        20.52        10.26         7.69 
TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR 
        9.57        10.03        15.09        12.49        31.46        36.33 
TCGA-DJ-A3V9 TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DO-A1JZ TCGA-E3-A3E5 TCGA-EL-A3CL 
       20.48        18.97        11.93        54.90        14.04        31.66 
TCGA-EL-A3CP TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GV TCGA-EL-A3MW TCGA-EL-A3MX 
      158.83         1.45        74.30        50.37       108.66        57.63 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3ZL TCGA-EL-A4K0 TCGA-EL-A4K7 TCGA-EL-A4K9 
       41.29        95.38        50.33        19.00        41.13        37.78 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CV TCGA-EM-A2CS TCGA-EM-A2OX TCGA-EM-A3AK 
       11.87        26.86        12.36        15.19        19.73        15.68 
TCGA-EM-A3FJ TCGA-EM-A3FO TCGA-EM-A3O7 TCGA-EM-A3SX TCGA-ET-A25K TCGA-ET-A25O 
       27.95        17.49         7.33        15.62        32.35        27.09 
TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A3BP TCGA-ET-A3BQ 
       12.26         2.66        71.01        72.49         4.18         2.43 
TCGA-ET-A3BW TCGA-ET-A3DP TCGA-FE-A235 TCGA-FK-A3SB TCGA-FK-A3SH TCGA-FY-A40K 
        2.37        56.88       102.90         4.08        48.10         4.14 
TCGA-J8-A3YH TCGA-KS-A41F TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4IB 
        5.75       120.99         6.02         6.74        12.36        64.57 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 
        0.59        40.37         1.12        14.47         8.71 

$subtype4
TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28R TCGA-BJ-A28X TCGA-BJ-A2NA 
        8.25         4.01        20.71         4.87        17.52        18.97 
TCGA-BJ-A3PR TCGA-BJ-A3PU TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-DE-A4MA TCGA-DE-A4MB 
       15.48        18.64         6.18         4.93        30.12        11.57 
TCGA-DE-A4MC TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A2PT TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       17.39       100.01         7.99         9.60         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 TCGA-DJ-A2Q9 TCGA-DJ-A3UQ TCGA-DJ-A3UW 
        9.34         9.21         8.61        10.36        19.56        43.00 
TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A4V5 
       25.02        19.20        22.92        21.01         7.76        16.14 
TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A433 TCGA-E8-A44K 
        2.33         1.15        22.29        19.59        14.70        13.78 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CR TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
       26.73       155.54         7.66        60.95       157.15        37.94 
TCGA-EL-A3CY TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3H7 
        4.18       108.36         1.41       124.04        52.73       126.97 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T1 TCGA-EL-A3T6 
       17.52        52.50        12.16       147.42       129.57        98.24 
TCGA-EL-A3T9 TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K1 
        5.72        47.38        52.50        45.96        37.94        19.59 
TCGA-EL-A4K4 TCGA-EL-A4KG TCGA-EM-A22I TCGA-EM-A22P TCGA-EM-A2P1 TCGA-EM-A2P3 
       33.60        13.32        14.73        11.15        17.46        14.60 
TCGA-EM-A3FM TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A3SU TCGA-EM-A3SZ TCGA-EM-A4FF 
       21.01        16.18        14.50        16.41        12.79        70.65 
TCGA-EM-A4FM TCGA-EM-A4FQ TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25L TCGA-ET-A25M 
        4.83         9.80        47.47        29.69        14.79        12.33 
TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A3BO 
       20.45        22.09        16.08        61.02        58.72         5.85 
TCGA-ET-A3BT TCGA-ET-A3BV TCGA-ET-A3DO TCGA-ET-A3DU TCGA-ET-A3DW TCGA-ET-A40Q 
       24.72        42.25        80.81        25.32        24.72         7.17 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A234 TCGA-FE-A237 TCGA-FE-A23A 
        4.01        73.74        59.70        68.22        81.34        81.83 
TCGA-FE-A3PB TCGA-FY-A3R8 TCGA-FY-A3YR TCGA-FY-A40L TCGA-GE-A2C6 TCGA-H2-A26U 
       85.15         4.67         6.87         6.58        12.53        17.00 
TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A420 TCGA-IM-A4EB 
       20.05        48.92        10.26        16.90         2.96         8.65 
TCGA-J8-A3YF TCGA-L6-A4EU TCGA-MK-A4N6 
       24.69         0.72        16.64 

$subtype5
TCGA-BJ-A0ZH TCGA-BJ-A3EZ TCGA-BJ-A4O9 TCGA-CE-A3ME TCGA-CE-A483 TCGA-DE-A0Y2 
       15.12        16.01         5.98         0.23         0.10        15.42 
TCGA-DE-A0Y3 TCGA-DE-A4MD TCGA-DJ-A13U TCGA-DJ-A1QD TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       36.46        25.12        13.41        10.92         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2Q4 TCGA-DJ-A3UM TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       10.09         7.99         9.44        31.04         9.83        21.27 
TCGA-DJ-A3VA TCGA-DJ-A3VJ TCGA-DJ-A4V2 TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E1 
       11.93        17.36         3.12        21.53        31.07        40.21 
TCGA-E3-A3E3 TCGA-E8-A417 TCGA-E8-A418 TCGA-EL-A3CS TCGA-EL-A3GR TCGA-EL-A3GS 
       30.31        14.27         3.02        45.53       102.84        65.39 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3T3 TCGA-EL-A3ZG 
      147.75       101.13        38.66       131.15       116.91        77.36 
TCGA-EL-A3ZK TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A22O 
       31.50        44.65        19.30        18.18        20.91        11.74 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A3FK TCGA-EM-A4FN TCGA-ET-A25N TCGA-ET-A2MX 
       12.07        17.59        23.77         8.61        14.79        54.05 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BU TCGA-ET-A3BX TCGA-ET-A3DR TCGA-FE-A231 
       59.15        28.24        38.30         4.50        43.50        31.59 
TCGA-FE-A233 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A3PC TCGA-FK-A3SE TCGA-FY-A3BL 
       24.69        66.77        39.95        85.68        22.03         1.15 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3RA TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-H2-A3RI 
        1.12         1.51        18.08         1.35         1.15         2.99 
TCGA-H2-A422 TCGA-IM-A41Y TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A3YG 
       18.61         9.80         2.24        27.19        27.85        22.29 
TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I3 TCGA-KS-A4I9 TCGA-KS-A4IC 
        2.60        15.68        12.43        17.46        14.70 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.20     0.03     0.59     0.72     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
  132.36   130.72   158.83   157.15   147.75 
subtype1 subtype2 subtype3 subtype4 subtype5 
  14.105   13.610   17.490   17.520   18.080 
[1] "0.2 - 132.4 (14.1)" "0.0 - 130.7 (13.6)" "0.6 - 158.8 (17.5)"
[4] "0.7 - 157.2 (17.5)" "0.1 - 147.8 (18.1)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      73       28        19        1         3         2
  subtype2      62        7        21        0         7         0
  subtype3      40        8        14        0         7         2
  subtype4      50        2        41        1        18         1
  subtype5      50        6        11        0         9         1
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         73       62       40       50       50
  STAGE II        28        7        8        2        6
  STAGE III       19       21       14       41       11
  STAGE IV         1        0        0        1        0
  STAGE IVA        3        7        7       18        9
  STAGE IVC        2        0        2        1        1
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 43 51 31  2
  subtype2 38 32 25  1
  subtype3 19 32 18  3
  subtype4 21 22 59 10
  subtype5 18 26 28  5
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       43       38       19       21       18
  T2       51       32       32       22       26
  T3       31       25       18       59       28
  T4        2        1        3       10        5
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1 86 17
  subtype2 50 44
  subtype3 31 33
  subtype4 29 77
  subtype5 25 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   86   17
  subtype2   50   44
  subtype3   31   33
  subtype4   29   77
  subtype5   25   47
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       86       50       31       29       25
  1       17       44       33       77       47
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 53  3 70
  subtype2 63  1 33
  subtype3 44  2 26
  subtype4 60  1 52
  subtype5 47  2 28
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       53       63       44       60       47
  M1        3        1        2        1        2
  MX       70       33       26       52       28
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 92 35
  subtype2 71 26
  subtype3 55 17
  subtype4 87 26
  subtype5 51 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92   35
  subtype2   71   26
  subtype3   55   17
  subtype4   87   26
  subtype5   51   26
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       92       71       55       87       51
  MALE         35       26       17       26       26
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              2                                            53
  subtype2              1                                            74
  subtype3              0                                            65
  subtype4              2                                            84
  subtype5              4                                            68
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     72
  subtype2                                                                     19
  subtype3                                                                      5
  subtype4                                                                      2
  subtype5                                                                      1
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   0
  subtype2                                                                   3
  subtype3                                                                   2
  subtype4                                                                  25
  subtype5                                                                   4
D6V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                53
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       72
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                74
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       19
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           3
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                65
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           2
                                                                        clus
vv                                                                       subtype4
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                84
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          25
                                                                        clus
vv                                                                       subtype5
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                68
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus         0   1
  subtype1   1 126
  subtype2   1  96
  subtype3   2  70
  subtype4   5 108
  subtype5   5  72
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  126
  subtype2    1   96
  subtype3    2   70
  subtype4    5  108
  subtype5    5   72
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         1        1        2        5        5
  YES      126       96       70      108       72
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
          cls
clus         0   1
  subtype1 104   5
  subtype2  77   5
  subtype3  63   1
  subtype4 102   4
  subtype5  62   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  104    5
  subtype2   77    5
  subtype3   63    1
  subtype4  102    4
  subtype5   62    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO       104       77       63      102       62
  YES        5        5        1        4        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           13                       1  105                   0
  subtype2           24                       0   70                   0
  subtype3           14                       1   54                   0
  subtype4           56                      10   44                   1
  subtype5           21                       4   50                   0
D6V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5
  MINIMAL (T3)                  13       24       14       56       21
  MODERATE/ADVANCED (T4A)        1        0        1       10        4
  NONE                         105       70       54       44       50
  VERY ADVANCED (T4B)            0        0        0        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 99  8  0  7
  subtype2 78  7  1  5
  subtype3 56  5  1  6
  subtype4 77 23  2  7
  subtype5 63  6  0  4
D6V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       99       78       56       77       63
  R1        8        7        5       23        6
  R2        0        1        1        2        0
  RX        7        5        6        7        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, continuous
D6V14, binary
          cls
clus        0  1
  subtype1 59 65
  subtype2 46 48
  subtype3 39 31
  subtype4 44 69
  subtype5 31 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   65
  subtype2   46   48
  subtype3   39   31
  subtype4   44   69
  subtype5   31   44
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  MULTIFOCAL       59       46       39       44       31
  UNIFOCAL         65       48       31       69       44
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     6                         5
  subtype2                                0    20                         2
  subtype3                                0     7                         4
  subtype4                                1     5                         7
  subtype5                                0    10                         2
          vv
clus       WHITE
  subtype1    69
  subtype2    62
  subtype3    47
  subtype4    86
  subtype5    55
D6V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                   6       20        7        5       10
  BLACK OR AFRICAN AMERICAN               5        2        4        7        2
  WHITE                                  69       62       47       86       55
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V17, binary
          cls
clus        0  1
  subtype1  9 72
  subtype2  2 80
  subtype3  3 50
  subtype4 16 83
  subtype5  8 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   72
  subtype2    2   80
  subtype3    3   50
  subtype4   16   83
  subtype5    8   55
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            9        2        3       16        8
  NOT HISPANIC OR LATINO       72       80       50       83       55
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 146   3
  subtype2 166   2
  subtype3 157   9
subtype1 subtype2 subtype3 
     149      168      166 
subtype1 subtype2 subtype3 
       3        2        9 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        18.21        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
        7.56        17.69        23.34        20.58         4.83         8.09 
TCGA-BJ-A28S TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       21.04         5.10        11.31        18.38        16.57        20.48 
TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
        7.04        13.94         5.75         6.48         3.45         6.35 
TCGA-BJ-A45K TCGA-CE-A3ME TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DE-A4MD 
        8.98         0.23         0.39         5.98         4.87        25.12 
TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QG 
        9.44         3.02         8.71        14.60         7.99         6.97 
TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP 
        7.20         5.33         8.12         6.77        10.85        16.41 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR 
       32.81        15.45         8.32        17.23        27.62        10.98 
TCGA-DJ-A4V0 TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E5 TCGA-EL-A3CX 
        9.34        54.90        12.07        66.38        14.04        80.91 
TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GS TCGA-EL-A3GW TCGA-EL-A3H1 
       58.82        33.47        39.32        65.39        37.25        49.32 
TCGA-EL-A3H2 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 
       33.50        32.48        78.97        48.16        45.80        19.53 
TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       28.73         8.71        18.05        19.79        19.46        54.21 
TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q 
       54.08        14.50        15.75        10.45        10.65        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY 
       12.30        13.64        10.49        22.16        13.84        17.59 
TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FL 
       17.29        17.46        18.97        14.14         8.35        16.80 
TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 
       12.07        17.39        15.02        11.15        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK 
       13.91         7.82        11.51        13.51        16.90         9.01 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2MX 
        5.03        37.87         0.95        48.20        18.38        54.05 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3BQ 
       19.76        58.22        13.74        65.36        98.56         2.43 
TCGA-ET-A3BW TCGA-ET-A3DP TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A40R 
        2.37        56.88         0.30       132.36         3.22         4.80 
TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A236 TCGA-FE-A239 TCGA-FE-A3PD TCGA-FK-A3S3 
        1.94        59.70        66.77        33.63        78.77        46.06 
TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R9 
        0.89         1.25         1.64         0.99        16.14        16.57 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 
        0.76         0.99        21.67        12.46         9.63        43.17 
TCGA-J8-A3O1 TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4IB TCGA-KS-A4ID 
       27.19        15.98        86.70        64.57        20.48 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A28R TCGA-BJ-A28Z TCGA-BJ-A290 
       16.34        14.73        15.12         4.87         1.22        20.61 
TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O9 
       18.97        16.01        18.64         6.18         5.06         5.98 
TCGA-CE-A13K TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.53         0.07         0.10        20.22        15.42        36.46 
TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U 
       15.85        30.12        17.39       137.88        25.35        13.41 
TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU 
       14.96         8.88         7.99        20.52        10.45        10.26 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2QC 
        7.69         5.52         9.44         9.90         9.57        10.03 
TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       15.09        12.49        31.46        36.33        20.22        30.61 
TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4V2 
        9.83        11.93        22.92        18.97        11.93         3.12 
TCGA-DJ-A4V5 TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A417 
       16.14        21.53        31.07        63.19        30.31        14.27 
TCGA-E8-A418 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CT TCGA-EL-A3D6 TCGA-EL-A3GV 
        3.02        20.68        31.66        60.95       108.36        50.37 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3N2 
      147.75       101.13        38.66       131.15       108.66        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      147.42       129.57       116.91        98.24        41.29        95.38 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JX TCGA-EL-A4K7 
       82.82        77.36        45.53        44.65        45.96        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OZ 
       12.36        14.73        14.53        11.74        15.19        12.07 
TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK 
       15.68        19.63        13.38        16.44        27.95        23.77 
TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       21.01        17.49         7.33        16.41        15.62        12.79 
TCGA-EM-A4FF TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25G TCGA-ET-A25J 
       70.65         8.61         9.80        12.72        47.47        29.69 
TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       32.35        14.79        27.09        20.45        22.09        12.26 
TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A39K TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39R 
       29.19         2.66        72.49        84.89        61.02        57.11 
TCGA-ET-A39T TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BS TCGA-ET-A3BX TCGA-ET-A3DO 
       59.15         5.85         4.18         5.56         4.50        80.81 
TCGA-ET-A3DW TCGA-ET-A40S TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       24.72         5.03        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FK-A3SB TCGA-FK-A3SG 
      102.90        81.83       106.36        85.68         4.08         0.92 
TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A40N 
       91.17         1.15         1.51         4.67        18.08         0.89 
TCGA-FY-A4B4 TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
        1.15         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A420 TCGA-J8-A3NZ TCGA-J8-A3YE TCGA-J8-A3YH 
       16.90         9.80         2.96         2.24        27.85         5.75 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 
        0.20       120.99        15.68         6.02         6.74        12.36 
TCGA-KS-A4I9 TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 
       17.46         0.59        40.37         1.12        14.47         8.71 

$subtype3
TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28X TCGA-BJ-A291 
        8.25         4.01        20.71         2.79        17.52        22.88 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H TCGA-BJ-A4O8 TCGA-CE-A27D 
       15.48        23.31         0.03         7.82         4.93         0.10 
TCGA-CE-A3MD TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DE-A4MB TCGA-DJ-A13O 
        0.20         0.10         0.10         6.08        11.57         7.36 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QO 
       10.92       100.01        18.51         7.99         1.45         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PV TCGA-DJ-A2PY 
        5.95        10.09         1.51         9.60         7.82         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        8.42         9.34         9.21         8.61         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       12.43        31.04        19.56        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 
       21.37        12.76        25.02        14.56        19.20        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A4UQ TCGA-DJ-A4UT 
       20.48        21.01         7.76        17.36        10.78        12.20 
TCGA-DJ-A4UW TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E3-A3E1 TCGA-E8-A242 TCGA-E8-A2EA 
        9.44         3.39         2.33        40.21         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A432 
       19.59        13.61        14.27        13.81        14.07        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
       14.70        14.10        14.96         7.69        13.78        13.58 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D1 
      157.15        37.94        57.01         4.18         1.45        74.30 
TCGA-EL-A3D4 TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3H5 
       45.40         1.41        30.18       102.84       124.04        52.73 
TCGA-EL-A3H7 TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3T0 TCGA-EL-A3T9 
      126.97        57.63        17.52        52.50       130.72         5.72 
TCGA-EL-A3TA TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS 
       66.90        31.50        50.33        47.38        52.50         7.07 
TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EM-A1CU 
       19.30        37.94        19.00        19.59        33.60        20.91 
TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A2P0 TCGA-EM-A2P1 
       57.01        11.15        13.15        19.73        17.59        17.46 
TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A4FM TCGA-EM-A4FO 
       14.60        16.77        16.18        14.50         4.83         8.38 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A2N0 TCGA-ET-A39J TCGA-ET-A39P TCGA-ET-A39S 
       14.79        12.33        16.08        71.01        58.72        55.10 
TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3DQ TCGA-ET-A3DR 
       28.24        24.72        38.30        42.25        59.87        43.50 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z 
       17.98        25.32         7.17         2.14         4.01        73.74 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A3PB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 
       81.34        39.95        85.15        22.03        48.10         1.12 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.76         0.03         0.30         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3U2 TCGA-IM-A4EB 
        4.54         1.35        12.53        17.00        10.26         8.65 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW 
        1.35        31.82        24.69        22.29         2.47         2.60 
TCGA-KS-A4I3 TCGA-KS-A4IC TCGA-L6-A4EU TCGA-MK-A4N6 
       12.43        14.70         0.72        16.64 

subtype1 subtype2 subtype3 
    0.23     0.07     0.03 
subtype1 subtype2 subtype3 
  132.36   147.75   158.83 
subtype1 subtype2 subtype3 
  15.020   17.145   14.700 
[1] "0.2 - 132.4 (15.0)" "0.1 - 147.8 (17.1)" "0.0 - 158.8 (14.7)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      93       29        20        1         4         2
  subtype2      99       17        35        0        17         2
  subtype3      83        5        52        1        23         2
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         93       99       83
  STAGE II        29       17        5
  STAGE III       20       35       52
  STAGE IV         1        0        1
  STAGE IVA        4       17       23
  STAGE IVC        2        2        2
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 43 68 37  2
  subtype2 44 61 58  7
  subtype3 53 35 65 12
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       43       44       53
  T2       68       61       35
  T3       37       58       65
  T4        2        7       12
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus         0   1
  subtype1  96  27
  subtype2  67  90
  subtype3  59 101
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96   27
  subtype2   67   90
  subtype3   59  101
   clus
vv  subtype1 subtype2 subtype3
  0       96       67       59
  1       27       90      101
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1  64   3  82
  subtype2  92   4  74
  subtype3 111   2  54
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       64       92      111
  M1        3        4        2
  MX       82       74       54
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1 108  42
  subtype2 125  45
  subtype3 124  43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  108   42
  subtype2  125   45
  subtype3  124   43
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      108      125      124
  MALE         42       45       43
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              2                                            66
  subtype2              3                                           146
  subtype3              4                                           132
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     82
  subtype2                                                                      9
  subtype3                                                                      8
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   0
  subtype2                                                                  12
  subtype3                                                                  23
D7V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                66
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       82
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               146
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          12
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               132
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          23
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus         0   1
  subtype1   4 146
  subtype2   7 163
  subtype3   3 164
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  146
  subtype2    7  163
  subtype3    3  164
     clus
vv    subtype1 subtype2 subtype3
  NO         4        7        3
  YES      146      163      164
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
          cls
clus         0   1
  subtype1 126   5
  subtype2 142   6
  subtype3 141   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  126    5
  subtype2  142    6
  subtype3  141    6
     clus
vv    subtype1 subtype2 subtype3
  NO       126      142      141
  YES        5        6        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           15                       0  128                   0
  subtype2           53                       5  107                   0
  subtype3           59                      11   90                   1
D7V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  15       53       59
  MODERATE/ADVANCED (T4A)        0        5       11
  NONE                         128      107       90
  VERY ADVANCED (T4B)            0        0        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 119  10   0   9
  subtype2 135  15   2   8
  subtype3 120  24   2  12
D7V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      119      135      120
  R1       10       15       24
  R2        0        2        2
  RX        9        8       12
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, continuous
D7V14, binary
          cls
clus        0  1
  subtype1 64 81
  subtype2 76 90
  subtype3 79 87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64   81
  subtype2   76   90
  subtype3   79   87
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       64       76       79
  UNIFOCAL         81       90       87
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     8                         8
  subtype2                                1    16                         7
  subtype3                                0    25                         5
          vv
clus       WHITE
  subtype1    85
  subtype2   114
  subtype3   120
D7V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   8       16       25
  BLACK OR AFRICAN AMERICAN               8        7        5
  WHITE                                  85      114      120
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V17, binary
          cls
clus         0   1
  subtype1  10  91
  subtype2  17 118
  subtype3  11 132
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   91
  subtype2   17  118
  subtype3   11  132
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           10       17       11
  NOT HISPANIC OR LATINO       91      118      132
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 123   3
  subtype2 198   1
  subtype3 148  10
subtype1 subtype2 subtype3 
     126      199      158 
subtype1 subtype2 subtype3 
       3        1       10 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        18.21        18.87        11.57        16.73 
TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A28S TCGA-BJ-A28V TCGA-BJ-A291 
       23.34        20.58         4.83        21.04         5.10        22.88 
TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-BJ-A45C 
       18.38        16.57        20.48         7.04        13.94         5.75 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45K TCGA-CE-A484 TCGA-DE-A2OL 
        6.48         3.45         6.35         8.98         0.39         5.98 
TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG 
        4.87         9.44         3.02         8.71        14.60         6.97 
TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP 
        7.20         5.33         8.12         6.77        10.85        16.41 
TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ 
       15.45         8.32        17.23        27.62        10.98        12.07 
TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 
       58.82        45.40        33.47        39.32        37.25        49.32 
TCGA-EL-A3H2 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 
       33.50        32.48        78.97        48.16        45.80        19.53 
TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       28.73         8.71        18.05        19.79        19.46        54.21 
TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q 
       54.08        14.50        15.75        10.45        10.65        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY 
       12.30        13.64        10.49        22.16        13.84        17.59 
TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FL 
       17.29        17.46        18.97        14.14         8.35        16.80 
TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 
       12.07        17.39        15.02        11.15        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK 
       13.91         7.82        11.51        13.51        16.90         9.01 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N3 
        5.03        37.87         0.95        48.20        18.38        19.76 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P 
       58.22        13.74        98.56         0.30       132.36         3.22 
TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM 
        1.94        33.63         0.89         1.25         1.64         0.99 
TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-H2-A2K9 TCGA-H2-A3RH 
       16.14        16.57         0.76         0.99        21.67        12.46 
TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4ID 
        9.63        43.17        27.19        15.98        86.70        20.48 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A192 
       16.34        14.73         8.25        15.12        17.69         8.09 
TCGA-BJ-A28R TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J 
        4.87         1.22        20.61        16.01        18.64         5.06 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A483 
        5.98         0.53         0.20         0.23         0.07         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC 
       20.22        15.42        36.46        15.85        30.12        17.39 
TCGA-DE-A4MD TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13X TCGA-DJ-A1QF 
       25.12       137.88        25.35        13.41         7.99        18.51 
TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       14.96         8.88        10.09         7.99        20.52        10.45 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       10.26         7.82         7.69         5.52         9.44         9.90 
TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR 
        9.57        10.03        15.09        12.49        31.46        36.33 
TCGA-DJ-A3US TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       32.81        20.22        30.61         9.83        11.93        22.92 
TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       18.97        11.93         3.12        16.14        54.90        21.53 
TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A417 
       31.07        66.38        63.19        30.31        14.04        14.27 
TCGA-E8-A418 TCGA-E8-A438 TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CX TCGA-EL-A3D6 
        3.02        20.68        13.58        31.66        80.91       108.36 
TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H8 
       65.39        50.37       147.75       101.13        38.66       131.15 
TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      108.66        12.16       116.91        98.24        41.29        95.38 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JX TCGA-EL-A4K7 
       82.82        77.36        45.53        44.65        45.96        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       37.78        29.95        11.87        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2CU 
       12.36        14.73        14.53        11.74        15.19        13.15 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO 
       19.73        12.07        17.59        15.68        19.63        13.38 
TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3FQ 
       16.44        27.95        23.77        21.01        17.49        16.18 
TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FN TCGA-EM-A4FQ 
        7.33        16.41        15.62        12.79         8.61         9.80 
TCGA-EM-A4FV TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A2MX 
       12.72        29.69        32.35        14.79        27.09        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K 
       22.09        12.26        29.19         2.66        71.01        72.49 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BO 
       65.36        84.89        61.02        57.11        59.15         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
        4.18         2.43         5.56        38.30         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DW TCGA-ET-A40R 
       80.81        56.88        17.98        25.32        24.72         4.80 
TCGA-ET-A40S TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
        5.03        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC 
      102.90        66.77        39.95        81.83       106.36        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
       78.77        46.06         4.08         0.92        48.10        91.17 
TCGA-FY-A3BL TCGA-FY-A3ON TCGA-FY-A3RA TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B4 
        1.15         1.51        18.08         4.54         0.89         1.15 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U3 
        2.99        20.05        18.61        48.92        47.41        16.90 
TCGA-IM-A41Y TCGA-J8-A3NZ TCGA-J8-A3YE TCGA-J8-A3YH TCGA-J8-A4HW TCGA-J8-A4HY 
        9.80         2.24        27.85         5.75         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
      120.99        15.68         6.02        12.43         6.74        12.36 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N7 
       17.46        64.57         0.59        40.37         1.12        14.47 
TCGA-MK-A4N9 
        8.71 

$subtype3
TCGA-BJ-A0ZB TCGA-BJ-A0ZG TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X 
        4.01         7.56        20.71         2.79        11.31        17.52 
TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H TCGA-BJ-A45I 
       18.97        15.48        23.31         0.03         7.82         6.18 
TCGA-BJ-A4O8 TCGA-CE-A27D TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DE-A4MB 
        4.93         0.10         0.10         0.10         6.08        11.57 
TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QO 
        7.36        10.92       100.01         7.99         1.45         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
        5.95         1.51         9.60         8.78         8.42         9.34 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3UM 
        9.21         8.61         7.07        10.36        12.43        31.04 
TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       19.56        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD 
       25.02        14.56        19.20        21.27        20.48        21.01 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
        7.76        17.36        10.78        12.20         9.44         9.34 
TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E3-A3E1 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
        3.39         2.33        40.21         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A432 TCGA-E8-A433 
       13.61        14.27        13.81        14.07        14.43        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-EL-A3CM TCGA-EL-A3CN 
       14.10        14.96         7.69        13.78        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GP 
       37.94        57.01         4.18         1.45        74.30         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MX 
       30.18       102.84       124.04        52.73       126.97        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T9 
       17.52        52.50       147.42       130.72       129.57         5.72 
TCGA-EL-A3TA TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS 
       66.90        31.50        50.33        47.38        52.50         7.07 
TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4KG 
       19.30        37.94        19.00        19.59        33.60        13.32 
TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3O3 
       57.01        11.15        17.46        14.60        16.77        14.50 
TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FO TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M 
       70.65         4.83         8.38        47.47        14.79        12.33 
TCGA-ET-A25R TCGA-ET-A2N0 TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT 
       20.45        16.08        58.72        55.10        28.24        24.72 
TCGA-ET-A3BV TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN 
       42.25        59.87        43.50         7.17         2.14         4.01 
TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SE TCGA-FY-A3I4 TCGA-FY-A3R6 
       73.74        81.34        85.15        22.03         1.12         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.03         4.67         0.30         6.87         4.14         6.58 
TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3U2 TCGA-IM-A420 TCGA-IM-A4EB 
        1.35        12.53        17.00        10.26         2.96         8.65 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-KS-A4IC 
        1.35        31.82        24.69        22.29         2.47        14.70 
TCGA-L6-A4EU TCGA-MK-A4N6 
        0.72        16.64 

subtype1 subtype2 subtype3 
    0.30     0.07     0.03 
subtype1 subtype2 subtype3 
  132.36   147.75   158.83 
subtype1 subtype2 subtype3 
   14.55    17.49    14.58 
[1] "0.3 - 132.4 (14.6)" "0.1 - 147.8 (17.5)" "0.0 - 158.8 (14.6)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      74       28        18        1         3         2
  subtype2     125       19        36        0        19         2
  subtype3      76        4        53        1        22         2
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         74      125       76
  STAGE II        28       19        4
  STAGE III       18       36       53
  STAGE IV         1        0        1
  STAGE IVA        3       19       22
  STAGE IVC        2        2        2
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 42 53 31  1
  subtype2 50 80 64  7
  subtype3 48 31 65 13
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       42       50       48
  T2       53       80       31
  T3       31       64       65
  T4        1        7       13
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus         0   1
  subtype1  86  18
  subtype2  77 109
  subtype3  59  91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   86   18
  subtype2   77  109
  subtype3   59   91
   clus
vv  subtype1 subtype2 subtype3
  0       86       77       59
  1       18      109       91
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1  54   3  69
  subtype2 103   4  94
  subtype3 110   2  47
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       54      103      110
  M1        3        4        2
  MX       69       94       47
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  90  37
  subtype2 146  55
  subtype3 121  38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   90   37
  subtype2  146   55
  subtype3  121   38
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       90      146      121
  MALE         37       55       38
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              2                                            49
  subtype2              4                                           172
  subtype3              3                                           123
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     76
  subtype2                                                                     15
  subtype3                                                                      8
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   0
  subtype2                                                                  10
  subtype3                                                                  25
D8V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                49
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       76
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               172
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       15
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          10
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               123
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          25
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus         0   1
  subtype1   1 126
  subtype2  11 190
  subtype3   2 157
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  126
  subtype2   11  190
  subtype3    2  157
     clus
vv    subtype1 subtype2 subtype3
  NO         1       11        2
  YES      126      190      157
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
          cls
clus         0   1
  subtype1 105   5
  subtype2 171   6
  subtype3 133   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  105    5
  subtype2  171    6
  subtype3  133    6
     clus
vv    subtype1 subtype2 subtype3
  NO       105      171      133
  YES        5        6        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           13                       0  107                   0
  subtype2           51                       4  140                   0
  subtype3           63                      12   78                   1
D8V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  13       51       63
  MODERATE/ADVANCED (T4A)        0        4       12
  NONE                         107      140       78
  VERY ADVANCED (T4B)            0        0        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 101   9   0   5
  subtype2 161  17   1  11
  subtype3 112  23   3  13
D8V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      101      161      112
  R1        9       17       23
  R2        0        1        3
  RX        5       11       13
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, continuous
D8V14, binary
          cls
clus         0   1
  subtype1  60  65
  subtype2  90 105
  subtype3  69  88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60   65
  subtype2   90  105
  subtype3   69   88
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       60       90       69
  UNIFOCAL         65      105       88
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     5                         6
  subtype2                                1    21                         9
  subtype3                                0    23                         5
          vv
clus       WHITE
  subtype1    69
  subtype2   132
  subtype3   118
D8V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   5       21       23
  BLACK OR AFRICAN AMERICAN               6        9        5
  WHITE                                  69      132      118
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V17, binary
          cls
clus         0   1
  subtype1   8  72
  subtype2  18 139
  subtype3  12 130
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   72
  subtype2   18  139
  subtype3   12  130
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8       18       12
  NOT HISPANIC OR LATINO       72      139      130
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 159   3
  subtype2 163   1
  subtype3 147  10
subtype1 subtype2 subtype3 
     162      164      157 
subtype1 subtype2 subtype3 
       3        1       10 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZA TCGA-BJ-A0ZC 
       24.79        13.78        18.21        14.73        18.87        11.57 
TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 
       16.73         7.56        17.69        23.34        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28S TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A2N7 TCGA-BJ-A2N8 
        8.09        21.04         5.10        11.31        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F 
       20.48         7.04        13.94         5.75         6.48         3.45 
TCGA-BJ-A45G TCGA-BJ-A45K TCGA-CE-A484 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 
        6.35         8.98         0.39         5.98        15.85         4.87 
TCGA-DE-A4MD TCGA-DJ-A13M TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       25.12         9.44       137.88         3.02         8.71        25.35 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 
       14.60         7.99         6.97         7.20         5.33         8.12 
TCGA-DJ-A2Q2 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3US TCGA-DJ-A3UT 
        6.77        12.43        10.85        16.41        32.81        15.45 
TCGA-DJ-A3UZ TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-DO-A1JZ 
       12.76         8.32        17.23        27.62        10.98        54.90 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E5 TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D4 
       12.07        66.38        14.04        80.91        58.82        45.40 
TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3H1 
       33.47        39.32        65.39        50.37        37.25        49.32 
TCGA-EL-A3H2 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 
       33.50        32.48        78.97        48.16        45.80        19.53 
TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CV TCGA-EM-A1CW 
       28.73        29.95         8.71        26.86        12.36        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.21        54.08        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.45        10.65        11.74        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR 
       13.18        23.51         6.05         2.99        12.30        13.64 
TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P0 TCGA-EM-A2P2 
       10.49        22.16        13.84        17.59        17.59        17.29 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FL TCGA-EM-A3FN 
       17.46        18.97        14.14         8.35        16.80        12.07 
TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       17.39        15.02        11.15        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK 
        7.82        11.51        15.62        13.51        16.90         9.01 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2MZ 
        5.03        37.87         0.95        48.20        18.38        12.26 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L 
       29.19        19.76         2.66        58.22        13.74        65.36 
TCGA-ET-A39N TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BW TCGA-ET-A3DP TCGA-ET-A3DR 
       98.56         4.18         2.43         2.37        56.88        43.50 
TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A40R TCGA-ET-A4KQ TCGA-FE-A236 
        0.30       132.36         3.22         4.80         1.94        66.77 
TCGA-FE-A239 TCGA-FK-A3S3 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM 
       33.63        46.06         0.89         1.25         1.64         0.99 
TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-H2-A2K9 TCGA-H2-A3RH 
       16.14        16.57         0.76         0.99        21.67        12.46 
TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4IB 
        9.63        43.17        27.19        15.98        86.70        64.57 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZH TCGA-BJ-A28R TCGA-BJ-A28Z TCGA-BJ-A290 
       16.34         8.25        15.12         4.87         1.22        20.61 
TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A3ME 
       16.01        18.64         5.06         5.98         0.53         0.23 
TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A4MA 
        0.07         0.10        20.22        15.42        36.46        30.12 
TCGA-DE-A4MC TCGA-DJ-A13U TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A2PO 
       17.39        13.41        14.96         8.88         1.02         7.99 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 
       20.52        10.45        10.26         7.69         5.52         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO 
        9.90         9.57        10.03        15.09        12.49        31.46 
TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V7 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       36.33        20.22        30.61         9.83        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DJ-A4V5 TCGA-DO-A1K0 
       22.92        18.97        11.93         3.12        16.14        21.53 
TCGA-E3-A3DY TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A438 
       31.07        63.19        30.31        14.27         3.02        20.68 
TCGA-EL-A3CL TCGA-EL-A3CN TCGA-EL-A3D6 TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 
       31.66       155.54       108.36       147.75       101.13        38.66 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 
      131.15       108.66        12.16       129.57       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZQ TCGA-EL-A3ZT 
       41.29        95.38        82.82        77.36        45.53        44.65 
TCGA-EL-A4JX TCGA-EL-A4K1 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KG TCGA-EL-A4KH 
       45.96        19.59        41.13        37.78        13.32        11.87 
TCGA-EM-A1CT TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A2CS TCGA-EM-A2OZ TCGA-EM-A3AK 
       18.18        14.73        14.53        15.19        12.07        15.68 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM 
       19.63        13.38        16.44        27.95        23.77        21.01 
TCGA-EM-A3FO TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FN 
       17.49         7.33        16.41        12.79        70.65         8.61 
TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N 
        9.80        12.72        47.47        29.69        32.35        14.79 
TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A39K TCGA-ET-A39M 
       27.09        20.45        54.05        22.09        72.49        84.89 
TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BO TCGA-ET-A3BS TCGA-ET-A3BX 
       61.02        57.11        59.15         5.85         5.56         4.50 
TCGA-ET-A3DO TCGA-ET-A3DT TCGA-ET-A3DW TCGA-ET-A40S TCGA-FE-A230 TCGA-FE-A231 
       80.81        17.98        24.72         5.03        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A238 TCGA-FE-A23A 
       44.25        24.69        68.22       102.90        39.95        81.83 
TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3SG TCGA-FK-A4UB TCGA-FY-A3BL 
      106.36        85.68        78.77         0.92        91.17         1.15 
TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A3YR TCGA-FY-A40N TCGA-FY-A4B4 
        1.51         4.67        18.08         6.87         0.89         1.15 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U3 
        2.99        20.05        18.61        48.92        47.41        16.90 
TCGA-IM-A41Y TCGA-IM-A420 TCGA-J8-A3NZ TCGA-J8-A3YE TCGA-J8-A3YH TCGA-J8-A4HY 
        9.80         2.96         2.24        27.85         5.75         0.20 
TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
      120.99        15.68         6.02        12.43         6.74        12.36 
TCGA-KS-A4I9 TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 
       17.46        20.48         0.59        40.37         1.12        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       14.47         8.71 

$subtype3
TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28X TCGA-BJ-A291 TCGA-BJ-A2NA 
        4.01        20.71         2.79        17.52        22.88        18.97 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A4O8 
       15.48        23.31         0.03         7.82         6.18         4.93 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DE-A4MB 
        0.10         0.20         0.10         0.10         6.08        11.57 
TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QM 
        7.36        10.92       100.01        18.51         7.99         1.45 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PV TCGA-DJ-A2PY 
        5.95        10.09         1.51         9.60         7.82         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        8.42         9.34         9.21         8.61         7.07        10.36 
TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       31.04        19.56        17.69        43.00        11.34        21.37 
TCGA-DJ-A3V0 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3VD TCGA-DJ-A3VF 
       25.02        14.56        19.20        21.27        21.01         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 
       17.36        10.78        12.20         9.44         9.34         3.39 
TCGA-DO-A2HM TCGA-E3-A3E1 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
        2.33        40.21         1.15        22.29        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.27        13.81        14.07        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CO 
       14.96         7.69        13.78        13.58        26.73        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GP TCGA-EL-A3GQ 
       57.01         4.18         1.45        74.30         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MX TCGA-EL-A3MY 
      102.84       124.04        52.73       126.97        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3ZK 
       52.50       147.42       130.72         5.72        66.90        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A4JW TCGA-EL-A4JZ 
       50.33        47.38        52.50         7.07        19.30        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K4 TCGA-EM-A1CU TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CU 
       19.00        33.60        20.91        57.01        11.15        13.15 
TCGA-EM-A2OX TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3FQ TCGA-EM-A3O3 
       19.73        17.46        14.60        16.77        16.18        14.50 
TCGA-EM-A4FM TCGA-EM-A4FO TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A2N0 TCGA-ET-A39J 
        4.83         8.38        14.79        12.33        16.08        71.01 
TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       58.72        55.10        28.24        24.72        38.30        42.25 
TCGA-ET-A3DQ TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z 
       59.87        25.32         7.17         2.14         4.01        73.74 
TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 
       81.34        85.15         4.08        22.03        48.10         1.12 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3TY TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76         0.03         0.30         4.14         6.58         4.54 
TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3U2 TCGA-IM-A4EB TCGA-J8-A3O2 
        1.35        12.53        17.00        10.26         8.65         1.35 
TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW TCGA-KS-A4IC 
       31.82        24.69        22.29         2.47         2.60        14.70 
TCGA-L6-A4EU 
        0.72 

subtype1 subtype2 subtype3 
    0.30     0.07     0.03 
subtype1 subtype2 subtype3 
  137.88   155.54   158.83 
subtype1 subtype2 subtype3 
  15.235   17.475   14.600 
[1] "0.3 - 137.9 (15.2)" "0.1 - 155.5 (17.5)" "0.0 - 158.8 (14.6)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      97       28        27        1         7         2
  subtype2      99       18        32        0        15         2
  subtype3      79        5        48        1        22         2
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         97       99       79
  STAGE II        28       18        5
  STAGE III       27       32       48
  STAGE IV         1        0        1
  STAGE IVA        7       15       22
  STAGE IVC        2        2        2
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 46 68 46  3
  subtype2 42 63 56  5
  subtype3 52 33 58 13
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       46       42       52
  T2       68       63       33
  T3       46       56       58
  T4        3        5       13
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
          cls
clus         0   1
  subtype1 101  35
  subtype2  65  89
  subtype3  56  94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  101   35
  subtype2   65   89
  subtype3   56   94
   clus
vv  subtype1 subtype2 subtype3
  0      101       65       56
  1       35       89       94
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1  70   3  89
  subtype2  90   4  72
  subtype3 107   2  49
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       70       90      107
  M1        3        4        2
  MX       89       72       49
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1 116  47
  subtype2 122  44
  subtype3 119  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  116   47
  subtype2  122   44
  subtype3  119   39
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      116      122      119
  MALE         47       44       39
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              2                                            79
  subtype2              3                                           140
  subtype3              4                                           125
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     82
  subtype2                                                                     10
  subtype3                                                                      7
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   0
  subtype2                                                                  13
  subtype3                                                                  22
D9V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                79
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       82
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               140
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          13
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               125
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          22
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
          cls
clus         0   1
  subtype1   3 160
  subtype2   9 157
  subtype3   2 156
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  160
  subtype2    9  157
  subtype3    2  156
     clus
vv    subtype1 subtype2 subtype3
  NO         3        9        2
  YES      160      157      156
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
          cls
clus         0   1
  subtype1 136   7
  subtype2 141   5
  subtype3 132   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  136    7
  subtype2  141    5
  subtype3  132    5
     clus
vv    subtype1 subtype2 subtype3
  NO       136      141      132
  YES        7        5        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           23                       1  131                   0
  subtype2           49                       3  108                   0
  subtype3           55                      12   86                   1
D9V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  23       49       55
  MODERATE/ADVANCED (T4A)        1        3       12
  NONE                         131      108       86
  VERY ADVANCED (T4B)            0        0        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 126  12   0  11
  subtype2 136  14   2   6
  subtype3 112  23   2  12
D9V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      126      136      112
  R1       12       14       23
  R2        0        2        2
  RX       11        6       12
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
D9V14, binary
          cls
clus        0  1
  subtype1 77 80
  subtype2 69 94
  subtype3 73 84
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77   80
  subtype2   69   94
  subtype3   73   84
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       77       69       73
  UNIFOCAL         80       94       84
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     8                         9
  subtype2                                1    16                         7
  subtype3                                0    25                         4
          vv
clus       WHITE
  subtype1    91
  subtype2   115
  subtype3   113
D9V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   8       16       25
  BLACK OR AFRICAN AMERICAN               9        7        4
  WHITE                                  91      115      113
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V17, binary
          cls
clus         0   1
  subtype1  11  97
  subtype2  17 118
  subtype3  10 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   97
  subtype2   17  118
  subtype3   10  126
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           11       17       10
  NOT HISPANIC OR LATINO       97      118      126
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 120   3
  subtype2 183   1
  subtype3  99   3
  subtype4  67   7
subtype1 subtype2 subtype3 subtype4 
     123      184      102       74 
subtype1 subtype2 subtype3 subtype4 
       3        1        3        7 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        18.21        18.87        11.57        16.73 
TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28S TCGA-BJ-A28V 
       23.34        20.58         4.83         8.09        21.04         5.10 
TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3F0 TCGA-BJ-A45C 
       18.38        16.57        20.48         7.04        13.94         5.75 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45K TCGA-CE-A484 TCGA-DE-A2OL 
        6.48         3.45         6.35         8.98         0.39         5.98 
TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG 
        4.87         9.44         3.02         8.71        14.60         6.97 
TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB TCGA-DJ-A3UP 
        7.20         5.33         8.12         6.77        10.85        16.41 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ 
       32.81        15.45         8.32        27.62        10.98        12.07 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 
       80.91        58.82        33.47        39.32        37.25        49.32 
TCGA-EL-A3H2 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 
       33.50        32.48        78.97        48.16        45.80        19.53 
TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       28.73         8.71        18.05        19.79        19.46        54.21 
TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q 
       54.08        14.50        15.75        10.45        10.65        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY 
       12.30        13.64        10.49        22.16        13.84        17.59 
TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FL TCGA-EM-A3FN 
       17.29        17.46        14.14         8.35        16.80        12.07 
TCGA-EM-A3FP TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       17.39        15.02        11.15        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SY TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FR 
        7.82        11.51        13.51        16.90         9.01         5.03 
TCGA-EM-A4FU TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A25P TCGA-ET-A2N3 TCGA-ET-A2N5 
       37.87         0.95        48.20        18.38        19.76        58.22 
TCGA-ET-A39I TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ 
       13.74        98.56         0.30       132.36         3.22         1.94 
TCGA-FE-A239 TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R9 
       33.63         1.25         1.64         0.99        16.14        16.57 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 
        0.76         0.99         4.54        12.46         9.63        43.17 
TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4ID 
       15.98        86.70        20.48 

$subtype2
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A28R 
       16.34        14.73         8.25        15.12        17.69         4.87 
TCGA-BJ-A290 TCGA-BJ-A3PU TCGA-BJ-A45J TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A3MD 
       20.61        18.64         5.06         5.98         0.53         0.20 
TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.23         0.07         0.10        20.22        15.42        36.46 
TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DJ-A13P TCGA-DJ-A13T 
       15.85        30.12        17.39        25.12       137.88        25.35 
TCGA-DJ-A13U TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PN 
       13.41         7.99        18.51        14.96         8.88        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2PX 
        7.99        20.52        10.45        10.26         7.69         5.52 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
        9.44         9.90         9.57        10.03        15.09        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V7 TCGA-DJ-A3VA 
       31.46        36.33        20.22        30.61         9.83        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DJ-A4V5 
       22.92        18.97        17.23        11.93         3.12        16.14 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E3-A3E3 
       54.90        21.53        31.07        66.38        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3GS 
       14.04        14.27         3.02        20.68        31.66        65.39 
TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3MW 
       50.37       147.75       101.13        38.66       131.15       108.66 
TCGA-EL-A3N2 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
       12.16       129.57       116.91        98.24        41.29        95.38 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JX TCGA-EL-A4K7 
       82.82        77.36        45.53        44.65        45.96        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       37.78        29.95        11.87        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OZ TCGA-EM-A2P0 
       12.36        14.73        11.74        15.19        12.07        17.59 
TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3FK 
       15.68        19.63        13.38        16.44        27.95        23.77 
TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3FQ TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX 
       21.01        17.49        16.18         7.33        16.41        15.62 
TCGA-EM-A3SZ TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25J TCGA-ET-A25K 
       12.79         8.61         9.80        12.72        29.69        32.35 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N1 
       14.79        27.09        54.05        22.09        12.26        29.19 
TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
        2.66        71.01        72.49        65.36        84.89        61.02 
TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       57.11        59.15         5.85         4.18         2.43         5.56 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DP TCGA-ET-A3DT TCGA-ET-A3DW 
       38.30         2.37         4.50        56.88        17.98        24.72 
TCGA-ET-A40R TCGA-ET-A40S TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        4.80         5.03        59.70        31.59        44.25        24.69 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC 
      102.90        66.77        39.95        81.83       106.36        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A4UB TCGA-FY-A3BL 
       78.77        46.06         4.08         0.92        91.17         1.15 
TCGA-FY-A3ON TCGA-FY-A3RA TCGA-FY-A40N TCGA-FY-A4B4 TCGA-H2-A3RI TCGA-H2-A421 
        1.51        18.08         0.89         1.15         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-J8-A3NZ 
       18.61        48.92        47.41        16.90         9.80         2.24 
TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A3YH TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J 
       27.19        27.85         5.75         0.20       120.99        15.68 
TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP 
        6.02         6.74        12.36        17.46        64.57         0.59 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37         1.12        14.47         8.71 

$subtype3
TCGA-BJ-A0ZB TCGA-BJ-A0ZG TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A291 TCGA-BJ-A3EZ 
        4.01         7.56         2.79        11.31        22.88        16.01 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H TCGA-CE-A27D TCGA-CE-A481 
       15.48        23.31         0.03         7.82         0.10         0.10 
TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DJ-A13O TCGA-DJ-A1QM TCGA-DJ-A1QQ TCGA-DJ-A2PS 
        0.10         6.08         7.36         1.45         5.95         1.51 
TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q8 TCGA-DJ-A2QA TCGA-DJ-A3UM TCGA-DJ-A3UU 
        7.82         8.42         7.07        12.43        31.04        17.69 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V4 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       11.34        21.37        12.76        14.56        21.27        20.48 
TCGA-DJ-A3VJ TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 
       17.36        10.78        12.20         9.44         9.34         3.39 
TCGA-DO-A2HM TCGA-E3-A3E1 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
        2.33        40.21        13.61        14.27        13.81        14.07 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44M 
       14.43        14.70        14.10        14.96         7.69        13.58 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D0 
       97.74       158.83        37.94        57.01         4.18         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3MX 
       74.30        45.40         1.41        30.18       102.84        57.63 
TCGA-EL-A3T0 TCGA-EL-A3TA TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZP TCGA-EL-A3ZS 
      130.72        66.90        31.50        50.33        52.50         7.07 
TCGA-EL-A4JW TCGA-EL-A4K0 TCGA-EM-A1YD TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CU 
       19.30        19.00        57.01        14.53        11.15        13.15 
TCGA-EM-A2OX TCGA-EM-A3AJ TCGA-EM-A3AR TCGA-EM-A4FF TCGA-EM-A4FO TCGA-ET-A25R 
       19.73        18.97        16.77        70.65         8.38        20.45 
TCGA-ET-A2N0 TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A40T 
       16.08        55.10        28.24        59.87        43.50         2.14 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 TCGA-FY-A3R6 TCGA-FY-A3R7 
        0.89        22.03        48.10         1.12         0.76         0.03 
TCGA-FY-A3TY TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-J8-A3O2 
        0.30         4.14         1.35        12.53        21.67         1.35 
TCGA-J8-A3YD TCGA-J8-A42S TCGA-J8-A4HW TCGA-KS-A4I3 TCGA-KS-A4IC TCGA-MK-A4N6 
       31.82         2.47         2.60        12.43        14.70        16.64 

$subtype4
TCGA-BJ-A18Z TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A2NA TCGA-BJ-A45I TCGA-BJ-A4O8 
       20.71        17.52         1.22        18.97         6.18         4.93 
TCGA-DE-A4MB TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QO TCGA-DJ-A2PT 
       11.57        10.92       100.01         7.99         1.02         9.60 
TCGA-DJ-A2PY TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 TCGA-DJ-A2Q9 TCGA-DJ-A3UQ 
        8.78         9.34         9.21         8.61        10.36        19.56 
TCGA-DJ-A3UW TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-E8-A242 
       43.00        25.02        19.20        21.01         7.76         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A44K TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CR 
       22.29        19.59        13.78        26.73       155.54         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3D6 TCGA-EL-A3GU TCGA-EL-A3H5 
       45.53        60.95       157.15       108.36       124.04        52.73 
TCGA-EL-A3H7 TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T9 TCGA-EL-A3ZO 
      126.97        17.52        52.50       147.42         5.72        47.38 
TCGA-EL-A4JZ TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4KG TCGA-EM-A2P1 TCGA-EM-A2P3 
       37.94        19.59        33.60        13.32        17.46        14.60 
TCGA-EM-A3O3 TCGA-EM-A4FM TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A39P 
       14.50         4.83        47.47        14.79        12.33        58.72 
TCGA-ET-A3BT TCGA-ET-A3BV TCGA-ET-A3DO TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A4KN 
       24.72        42.25        80.81        25.32         7.17         4.01 
TCGA-FE-A22Z TCGA-FE-A234 TCGA-FE-A237 TCGA-FE-A3PB TCGA-FY-A3R8 TCGA-FY-A3YR 
       73.74        68.22        81.34        85.15         4.67         6.87 
TCGA-FY-A40L TCGA-H2-A26U TCGA-IM-A3U2 TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3YF 
        6.58        17.00        10.26         2.96         8.65        24.69 
TCGA-J8-A3YG TCGA-L6-A4EU 
       22.29         0.72 

subtype1 subtype2 subtype3 subtype4 
    0.30     0.07     0.03     0.72 
subtype1 subtype2 subtype3 subtype4 
  132.36   147.75   158.83   157.15 
subtype1 subtype2 subtype3 subtype4 
  14.140   17.640   14.085   18.245 
[1] "0.3 - 132.4 (14.1)" "0.1 - 147.8 (17.6)" "0.0 - 158.8 (14.1)"
[4] "0.7 - 157.2 (18.2)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      71       28        19        1         2         2
  subtype2     118       18        30        0        17         2
  subtype3      62        3        24        0        11         1
  subtype4      24        2        34        1        14         1
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         71      118       62       24
  STAGE II        28       18        3        2
  STAGE III       19       30       24       34
  STAGE IV         1        0        0        1
  STAGE IVA        2       17       11       14
  STAGE IVC        2        2        1        1
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 41 53 29  1
  subtype2 45 73 60  7
  subtype3 43 25 29  3
  subtype4 11 13 42 10
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       41       45       43       11
  T2       53       73       25       13
  T3       29       60       29       42
  T4        1        7        3       10
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1 86 14
  subtype2 73 99
  subtype3 45 52
  subtype4 18 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   86   14
  subtype2   73   99
  subtype3   45   52
  subtype4   18   53
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       86       73       45       18
  1       14       99       52       53
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 52  3 68
  subtype2 95  4 86
  subtype3 74  1 27
  subtype4 46  1 29
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       52       95       74       46
  M1        3        4        1        1
  MX       68       86       27       29
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1  91  33
  subtype2 133  52
  subtype3  69  33
  subtype4  64  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   91   33
  subtype2  133   52
  subtype3   69   33
  subtype4   64   12
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       91      133       69       64
  MALE         33       52       33       12
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              2                                            48
  subtype2              4                                           156
  subtype3              2                                            85
  subtype4              1                                            55
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     74
  subtype2                                                                     15
  subtype3                                                                      9
  subtype4                                                                      1
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   0
  subtype2                                                                  10
  subtype3                                                                   6
  subtype4                                                                  19
D10V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                48
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       74
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               156
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       15
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          10
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                85
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           6
                                                                        clus
vv                                                                       subtype4
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                55
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          19
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus         0   1
  subtype1   1 123
  subtype2  10 175
  subtype3   0 102
  subtype4   3  73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  123
  subtype2   10  175
  subtype3    0  102
  subtype4    3   73
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1       10        0        3
  YES      123      175      102       73
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
          cls
clus         0   1
  subtype1 103   5
  subtype2 156   6
  subtype3  84   2
  subtype4  66   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  103    5
  subtype2  156    6
  subtype3   84    2
  subtype4   66    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       103      156       84       66
  YES        5        6        2        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  subtype1           13                       0  106                   0
  subtype2           48                       4  128                   0
  subtype3           23                       3   68                   0
  subtype4           43                       9   23                   1
D10V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  MINIMAL (T3)                  13       48       23       43
  MODERATE/ADVANCED (T4A)        0        4        3        9
  NONE                         106      128       68       23
  VERY ADVANCED (T4B)            0        0        0        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 100   8   0   6
  subtype2 151  13   1  10
  subtype3  72  12   1   9
  subtype4  51  16   2   4
D10V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      100      151       72       51
  R1        8       13       12       16
  R2        0        1        1        2
  RX        6       10        9        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
D10V14, binary
          cls
clus        0  1
  subtype1 57 65
  subtype2 81 98
  subtype3 48 52
  subtype4 33 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   65
  subtype2   81   98
  subtype3   48   52
  subtype4   33   43
            clus
vv           subtype1 subtype2 subtype3 subtype4
  MULTIFOCAL       57       81       48       33
  UNIFOCAL         65       98       52       43
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     5                         5
  subtype2                                1    19                        10
  subtype3                                0    22                         3
  subtype4                                0     3                         2
          vv
clus       WHITE
  subtype1    68
  subtype2   120
  subtype3    65
  subtype4    66
D10V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   5       19       22        3
  BLACK OR AFRICAN AMERICAN               5       10        3        2
  WHITE                                  68      120       65       66
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V17, binary
          cls
clus         0   1
  subtype1   8  69
  subtype2  17 130
  subtype3   3  83
  subtype4  10  59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   69
  subtype2   17  130
  subtype3    3   83
  subtype4   10   59
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            8       17        3       10
  NOT HISPANIC OR LATINO       69      130       83       59
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
