[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/11541741/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/11590674/THCA-TP.mergedcluster.txt"

nPatients in clinical file=497, in cluster file=503, common to both=497
[1]  10 497
[1] "CN_CNMF"
[1] 3
  1   2   3 
 54 354  87 
  1   2   3 
 54 354  87 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
274 155  68 
  1   2   3 
274 155  68 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
61 79 82 
 1  2  3 
61 79 82 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
47 28 33 29 49 27  9 
 1  2  3  4  5  6  7 
47 28 33 29 49 27  9 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
165 156  57 117 
  1   2   3   4 
165 156  57 117 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
102 135  85  96  77 
  1   2   3   4   5 
102 135  85  96  77 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
179 151 166 
  1   2   3 
179 151 166 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
175 130 191 
  1   2   3 
175 130 191 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
158 164 144 
  1   2   3 
158 164 144 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
161 127 178 
  1   2   3 
161 127 178 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [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 497 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          919          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          346          325 
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          564          573          916          352 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
         913          764          130           98           84          525 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
         428         4194          103          265          771          408 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
         362          444          243          335         3042          563 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
         399          243          455          219           44          270 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
          31          181          307          243          162          258 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
         318           46          292          382          252          234 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
         168          267          256          247          284          206 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
         280          287          301          262          307          215 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
         315          378          330          483          459          944 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
         380          957          499          595         1105          998 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
         737          538         1308          345          650          388 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
         761          615          931          443          584          299 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
         647          623          363          697          639          577 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
         236          253          528          524          840          554 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
         328          334          430          447          542           95 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
         481          740         1670          655           71          945 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
         367         2019         1223         1922          922          427 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
          35          678           NA          596          414          434 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
         420          428          434           92           NA          439 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
         447          429          455          234          629          419 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
         413           NA           NA         4731           NA         4831 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
          NA           NA           NA         4780         1154           NA 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
        2461          127         1789           44         2260         1381 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
        1018         3296         1196           43          918         3128 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
        1989         3773         1532         1133         4494         3076 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
        4258           NA           NA         1319         1176         1604 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
        4228         3989         3305           NA           NA           NA 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
         370         4484         3976         3941          988         3556 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
        2988         1256         2901           NA         2035         2519 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
        2353         2402          958         1531         1614         1441 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
        1597         1385         1465          215         1358         1393 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
         587         1398         1154          944          596          928 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
        1022          874         1251         1149          911          405 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
         361          265          817          553          636          376 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
         549          602          592         1649         1734         1645 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
         448          441          479          318          442          324 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
         357          339          433          500          544          401 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CS 
         715          184           91          374          415          462 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
         319          400          674          421          600          535 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
         367          535          531          526          444          531 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
         577          477          430          597          407          254 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
         500          510          850          723          511          639 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
         367          532          529          492          457          441 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
         339          223          381          281          423          238 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
         350          499          475          411          389         2149 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
         514          274          147          262          255          298 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
         153         1152          387           29         1444         1466 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
         903          984          450          375          450          824 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
         559          897         1644          672          373          489 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
         888          601           81         1771          418         2160 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
        2434         1988         2582         2998         1856         1786 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
        1737         1676         1799          859          178          127 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
          74          169          752         1165         1285           72 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
         137         2458         2106         1821         1323            9 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
         547          770         4026          752           98          218 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
         146          153           65          122           59         2243 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
        1816          961         1346          751         2075         3130 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
        2031         2474         1215           NA         2489         3235 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
        2590         2606         2396         1401          124           27 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
         670           28         1463         2773           38           35 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NN TCGA-FY-A3NP TCGA-FY-A3ON 
         542           50           30           NA          491           46 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
          23            1          142          504          550            9 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
          23          519          209          126          200          138 
TCGA-FY-A40N TCGA-FY-A4B0 TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
          27           NA           41           35           51          381 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
         517          659          379           91          610          566 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
        1488         1442          312          514          298          293 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
          90          263          524         1313          827          342 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
         968          847          751          678          175           75 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
          79            6         4367          486          477         2637 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
         183          378          205          987         2658         2577 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
        1073         1011         1016         1228          664           22 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
         506          987          265          334          158 
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=409,	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=5,	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=26,	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 497 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 
141 167 165  21 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
141 167 165  21 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
141 167 165  21 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
141 167 165  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  50   3
  subtype2 341  10
  subtype3  86   1
subtype1 subtype2 subtype3 
      53      351       87 
subtype1 subtype2 subtype3 
       3       10        1 
$subtype1
TCGA-BJ-A0YZ TCGA-BJ-A0ZB TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A290 TCGA-BJ-A2N8 
       24.79         4.01        20.58         8.09        30.21        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DE-A4MB TCGA-DE-A4MD TCGA-DJ-A1QE TCGA-DJ-A2PU 
       20.48         0.03        11.57        25.12       100.01        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2Q0 TCGA-DO-A2HM TCGA-E8-A432 TCGA-EL-A3GP TCGA-EL-A3GU 
        8.28         8.12         2.33        14.43         1.41       124.04 
TCGA-EL-A3H5 TCGA-EL-A3MX TCGA-EL-A3T9 TCGA-EL-A3ZO TCGA-EL-A4JX TCGA-EL-A4K7 
       52.73        57.63         5.72        47.38        45.96        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       37.78         8.71        19.46        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-A3SU TCGA-EM-A3SY TCGA-ET-A25L TCGA-ET-A2MZ TCGA-ET-A39M TCGA-ET-A39N 
       16.41        13.51        14.79        12.26        84.89        98.56 
TCGA-ET-A3BV TCGA-ET-A40S TCGA-FE-A231 TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       42.25         5.03        31.59        33.63         1.64         0.99 
TCGA-FY-A3WA TCGA-IM-A3EB TCGA-IM-A3U2 TCGA-J8-A3YG TCGA-L6-A4EU 
       17.06        48.92        10.26        22.29         0.72 

$subtype2
TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZE TCGA-BJ-A0ZJ 
       13.78        16.34         8.25        18.87        16.73        17.69 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
       20.71         4.83         4.87        21.04         2.79         5.10 
TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2NA 
       11.31        17.52         1.22        22.88        18.38        18.97 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45G 
       16.01        13.94        15.48        18.64         5.75         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A4M9 
        0.10         0.10        15.42        36.46         5.98        18.84 
TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13O 
       30.12        30.02         4.27         3.22         2.76        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13X 
      137.88         3.39         8.71        13.41        11.90         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO 
       11.01        18.51        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         8.48        10.45 
TCGA-DJ-A2PT TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q2 
        9.60         7.69         5.52         8.78         8.42         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.21         9.44         9.90         8.61         7.07        10.36 
TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       15.88        31.04        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UT 
        8.32        17.36        17.23        18.21        10.78        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       21.53        31.07        66.38        40.21        63.19        30.31 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A437 TCGA-E8-A438 
       14.07        14.27         3.02        14.70         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.78        13.58        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D6 TCGA-EL-A3GQ TCGA-EL-A3GR 
       80.91         4.18        58.82       108.36        30.18       102.84 
TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       65.39        50.37       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       33.50        43.36        38.66       139.00       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-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       77.36        78.97        31.50        53.06        52.50        45.53 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
        7.07        44.65        19.30        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU 
       33.60        29.95        13.32        11.87        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22O 
       12.36        18.05        19.79        14.73        14.50        11.74 
TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       14.24        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OZ 
       15.19        10.49        13.15        22.16        13.84        12.07 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        17.29        14.60        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        19.63        13.38        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ 
       23.77        16.80        21.01        12.07        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.02        11.15         7.33        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       11.51        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
        9.80        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       32.35        12.33        14.79        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I 
       22.09        16.08        29.19        19.76        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       71.01        80.02        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       59.15        28.24         5.85         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       38.30         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q 
       43.50        17.98        25.32       132.36        24.72         7.17 
TCGA-ET-A40R TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 
        4.80         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-A3SH TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       22.03        48.10        91.17         1.15        17.82         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3YR 
        0.76         4.67        16.57        18.08         0.30         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A76V 
        4.14         6.58         4.54         0.89         1.35         1.68 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3ED TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 
       47.41         9.80         2.96         8.65        17.23        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       11.24        27.85        24.69         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
      143.57        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       87.39        35.28        33.24        33.40        40.37        21.83 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       16.64        32.45         8.71 

$subtype3
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZC TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A18Y 
       18.21        14.73        11.57         7.56        15.12        23.34 
TCGA-BJ-A2P4 TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ 
        7.04        23.31         6.48         3.45         0.39        20.22 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A13W TCGA-DJ-A1QG 
       15.85        18.54        17.26        25.35        14.60        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q1 TCGA-DJ-A2Q7 TCGA-DJ-A2QA 
        7.99         8.88         1.51         9.34        10.09        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-E8-A436 TCGA-EL-A3CL 
       10.98        12.07        14.04        14.10        14.96        31.66 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW 
        1.45        74.30        45.40        33.47        39.32        37.25 
TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4JZ TCGA-EL-A4K6 
       32.48        50.33        48.16        45.80        37.94        28.73 
TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ 
       26.86        15.75        10.45        14.53        11.15        16.44 
TCGA-EM-A2OX TCGA-EM-A3AP TCGA-EM-A3FO TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO 
       19.73         8.35        17.49        15.62        12.79         8.38 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L TCGA-ET-A3BP 
        5.03        37.87        27.09         2.66        65.36         4.18 
TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SG 
        0.30         3.22         2.14        81.34        85.15         0.92 
TCGA-FY-A2QD TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-IM-A3U3 
        1.25         0.03         0.76         1.15        12.53        16.90 
TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH TCGA-KS-A41I TCGA-KS-A4I7 
        9.63        43.17        31.82         5.75        15.98        32.45 
TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       84.72        10.98         5.19 

subtype1 subtype2 subtype3 
    0.03     0.10     0.03 
subtype1 subtype2 subtype3 
  124.04   158.83    85.15 
subtype1 subtype2 subtype3 
   17.06    17.29    14.73 
[1] "0.0 - 124.0 (17.1)" "0.1 - 158.8 (17.3)" "0.0 - 85.2 (14.7)" 
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      14       14        16        1         8         1
  subtype2     214       31        78        0        26         4
  subtype3      52        6        15        1        11         1
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         14      214       52
  STAGE II        14       31        6
  STAGE III       16       78       15
  STAGE IV         1        0        1
  STAGE IVA        8       26       11
  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   8  21  22   3
  subtype2 102 114 120  15
  subtype3  30  31  23   3
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        8      102       30
  T2       21      114       31
  T3       22      120       23
  T4        3       15        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  24  21
  subtype2 157 161
  subtype3  42  40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   21
  subtype2  157  161
  subtype3   42   40
   clus
vv  subtype1 subtype2 subtype3
  0       24      157       42
  1       21      161       40
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1  22   1  31
  subtype2 203   6 145
  subtype3  48   2  36
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       22      203       48
  M1        1        6        2
  MX       31      145       36
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1  36  18
  subtype2 264  90
  subtype3  64  23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   18
  subtype2  264   90
  subtype3   64   23
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       36      264       64
  MALE         18       90       23
[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                                            38
  subtype2              8                                           254
  subtype3              1                                            61
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     12
  subtype2                                                                     64
  subtype3                                                                     22
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                   4
  subtype2                                                                  28
  subtype3                                                                   3
D1V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                38
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       12
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           4
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               254
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       64
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          28
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                61
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       22
  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  52
  subtype2  11 343
  subtype3   1  86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   52
  subtype2   11  343
  subtype3    1   86
     clus
vv    subtype1 subtype2 subtype3
  NO         2       11        1
  YES       52      343       86
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
          cls
clus         0   1
  subtype1  47   3
  subtype2 295  12
  subtype3  75   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47    3
  subtype2  295   12
  subtype3   75    2
     clus
vv    subtype1 subtype2 subtype3
  NO        47      295       75
  YES        3       12        2
[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                       2   34                   1
  subtype2           98                      13  230                   0
  subtype3           17                       1   64                   0
D1V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  15       98       17
  MODERATE/ADVANCED (T4A)        2       13        1
  NONE                          34      230       64
  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  37   8   0   6
  subtype2 278  36   3  15
  subtype3  63   7   1   9
D1V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       37      278       63
  R1        8       36        7
  R2        0        3        1
  RX        6       15        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
D1V14, binary
          cls
clus         0   1
  subtype1  21  33
  subtype2 155 193
  subtype3  48  35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   33
  subtype2  155  193
  subtype3   48   35
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       21      155       48
  UNIFOCAL         33      193       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                         3
  subtype2                                1    38                        17
  subtype3                                0    10                         6
          vv
clus       WHITE
  subtype1    38
  subtype2   231
  subtype3    52
D1V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   1       38       10
  BLACK OR AFRICAN AMERICAN               3       17        6
  WHITE                                  38      231       52
[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   4  35
  subtype2  27 255
  subtype3   7  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   35
  subtype2   27  255
  subtype3    7   60
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4       27        7
  NOT HISPANIC OR LATINO       35      255       60
[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 267   7
  subtype2 150   3
  subtype3  62   4
subtype1 subtype2 subtype3 
     274      153       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 
       30.21        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        10.68 
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-DE-A7U5 
       11.57        30.02        25.12         4.27         3.22         2.76 
TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QD 
      137.88        25.35        13.41        11.90         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A1QO 
      100.01        18.51         7.99        14.96         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU 
        5.95        10.09         7.99         8.48        10.45        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q4 
        8.28         7.69         5.52         8.78         8.42         9.44 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-DJ-A3UK 
        8.61        10.09         7.07        12.43        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3V0 
       31.04        12.49        31.46        19.56        17.69        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VJ TCGA-DJ-A4UL 
       20.48        11.93        22.92        18.97        17.36        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UW TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       10.78        14.70         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       21.53        31.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A3X7 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 
       14.04        19.59        14.27         3.02        14.43        14.70 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-EL-A3CL TCGA-EL-A3CM 
       14.96         7.69        20.68        13.78        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CU TCGA-EL-A3CX 
      155.54       158.83         7.66        45.53       157.15        80.91 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
        1.45        74.30       108.36         1.41        30.18       102.84 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
       65.39       124.04        50.37       147.75       101.13       139.99 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        38.66        52.73       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T1 TCGA-EL-A3T3 
       57.63        17.52        52.50        12.16       129.57       116.91 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZO 
       41.29        95.38        82.82        31.50        50.33        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 
       52.50        45.53        44.65        19.30        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       19.59        33.60        41.13        37.78        29.95        13.32 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I 
       11.87        26.86        18.18        20.91        12.36        14.73 
TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       11.74        15.19        13.15        19.73        12.07        17.59 
TCGA-EM-A2P3 TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ 
       14.60        15.68        19.63        13.38        16.44        27.95 
TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX 
       23.77        21.01        17.49         7.33        16.41        15.62 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV 
       12.79        70.65         4.83         8.61         9.80        12.72 
TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       47.47        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       27.09        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39S 
        2.66        71.01        80.02        61.02        58.72        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DP TCGA-ET-A3DR 
       24.72        38.30         2.37         4.50        69.24        43.50 
TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-FE-A22Z TCGA-FE-A231 
       24.72         7.17         4.80         2.14        73.74        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
TCGA-FE-A238 TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       39.95       106.36        85.15        85.68        78.77        46.06 
TCGA-FK-A3SB TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A3BL 
        4.08        22.03         0.92        48.10        91.17         1.15 
TCGA-FY-A3ON TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        1.51         4.67        18.08         6.87         4.14         6.58 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED 
        1.35         1.15         2.99        20.05        18.61        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A420 TCGA-J8-A3NZ TCGA-J8-A3O1 
       10.26        16.90         9.80         2.96        17.23        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       11.24        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 
        0.20       143.57        15.68         6.02         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       87.39        84.72        35.28        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
        0.72        16.64        32.45         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        18.84        17.26 
TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP 
        8.71        14.60        13.12         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 
       24.23        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-A3ZN TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 
       78.97        53.06        48.16        45.80        30.51        28.73 
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-A2CQ 
       16.44        17.88        13.18        23.51         6.05        12.30 
TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 
       13.64        10.49        22.16        13.84        17.59        17.29 
TCGA-EM-A3AI TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FL TCGA-EM-A3FN 
       17.46        14.14         8.35        16.77        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-A2N1 TCGA-ET-A2N3 
       37.87         0.95        48.20        18.38        29.19        19.76 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV 
       58.22        13.74        65.36        98.56         0.30       132.36 
TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I4 
        3.22         1.94        33.63         0.89         1.25        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R7 TCGA-FY-A3R9 TCGA-FY-A3W9 
        1.64         0.99        16.14         0.03        16.57         0.76 
TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A76V TCGA-H2-A2K9 TCGA-H2-A3RH 
       17.06         4.54         0.89         1.68        21.67        12.46 
TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-KS-A41I TCGA-KS-A41L 
        9.63        43.17        31.82        27.85        15.98        86.70 
TCGA-KS-A4I3 TCGA-MK-A84Z TCGA-QD-A8IV 
       12.43        10.98         5.19 

$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        11.38         0.10        18.54 
TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A2PT TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 
       14.07         3.39         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        14.14 
TCGA-DJ-A4V0 TCGA-DO-A2HM TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A414 TCGA-E8-A44M 
       17.82         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        33.24 

subtype1 subtype2 subtype3 
    0.10     0.03     0.03 
subtype1 subtype2 subtype3 
  158.83   132.36   147.42 
subtype1 subtype2 subtype3 
  18.360   14.600   14.515 
[1] "0.1 - 158.8 (18.4)" "0.0 - 132.4 (14.6)" "0.0 - 147.4 (14.5)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1     148       19        67        0        35         4
  subtype2      89       31        27        1         4         2
  subtype3      44        2        15        1         6         0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        148       89       44
  STAGE II        19       31        2
  STAGE III       67       27       15
  STAGE IV         0        1        1
  STAGE IVA       35        4        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  64  89 101  18
  subtype2  54  58  42   1
  subtype3  23  20  22   2
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       64       54       23
  T2       89       58       20
  T3      101       42       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  96 157
  subtype2 100  29
  subtype3  29  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96  157
  subtype2  100   29
  subtype3   29   36
   clus
vv  subtype1 subtype2 subtype3
  0       96      100       29
  1      157       29       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 162   6 106
  subtype2  73   3  78
  subtype3  39   0  29
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      162       73       39
  M1        6        3        0
  MX      106       78       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 202  72
  subtype2 112  43
  subtype3  51  17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  202   72
  subtype2  112   43
  subtype3   51   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      202      112       51
  MALE         72       43       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                                           223
  subtype2              2                                            75
  subtype3              2                                            55
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                     17
  subtype2                                                                     78
  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                               223
  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                                75
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       78
  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  11 263
  subtype2   1 154
  subtype3   2  66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11  263
  subtype2    1  154
  subtype3    2   66
     clus
vv    subtype1 subtype2 subtype3
  NO        11        1        2
  YES      263      154       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 236   8
  subtype2 125   6
  subtype3  57   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  236    8
  subtype2  125    6
  subtype3   57    3
     clus
vv    subtype1 subtype2 subtype3
  NO       236      125       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           92                      15  160                   0
  subtype2           23                       0  122                   0
  subtype3           15                       1   48                   1
D2V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  92       23       15
  MODERATE/ADVANCED (T4A)       15        0        1
  NONE                         160      122       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 206  35   4  18
  subtype2 123   9   0   8
  subtype3  51   7   0   4
D2V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      206      123       51
  R1       35        9        7
  R2        4        0        0
  RX       18        8        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 125 144
  subtype2  71  81
  subtype3  29  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  125  144
  subtype2   71   81
  subtype3   29   37
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL      125       71       29
  UNIFOCAL        144       81       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                        16
  subtype2                                0    13                         9
  subtype3                                0     7                         1
          vv
clus       WHITE
  subtype1   188
  subtype2    83
  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              16        9        1
  WHITE                                 188       83       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  24 204
  subtype2   7  97
  subtype3   7  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24  204
  subtype2    7   97
  subtype3    7   50
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           24        7        7
  NOT HISPANIC OR LATINO      204       97       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 76  5
subtype1 subtype2 subtype3 
      61       79       81 
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        17.26        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         8.28         8.42         6.77         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-E3-A3DZ TCGA-EL-A3CL 
       10.09        10.36        12.43        15.88        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        69.24         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        30.21 
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 
       14.07         3.39         8.71        11.01       100.01        13.12 
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       139.00       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        17.23 
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         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 
       10.45         1.51        12.56         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-A3GZ TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H8 TCGA-EL-A3MX 
      147.75       139.99        33.50        43.36       131.15        57.63 
TCGA-EL-A3MY TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1YE TCGA-EM-A22M TCGA-EM-A22Q 
       17.52        20.91        12.36        54.08        14.53        14.24 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CR TCGA-EM-A2CS TCGA-EM-A3AI TCGA-EM-A3AO 
       23.51         2.99        13.64        15.19        17.46        13.38 
TCGA-EM-A3FJ TCGA-EM-A3FN TCGA-EM-A3FO TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N4 
       27.95        12.07        17.49        12.26        29.19         2.66 
TCGA-ET-A39J TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39R TCGA-ET-A3BN 
       71.01        65.36        84.89        98.56        57.11        28.24 
TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DS 
        5.56        38.30        42.25         2.37         4.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DV TCGA-FE-A233 TCGA-FE-A235 TCGA-FE-A239 TCGA-FY-A3ON 
       17.98       132.36        24.69       102.90        33.63         1.51 
TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-IM-A3ED 
       12.53        21.67        47.41 

subtype1 subtype2 subtype3 
    1.25     0.23     0.10 
subtype1 subtype2 subtype3 
  158.83   147.42   147.75 
subtype1 subtype2 subtype3 
   16.44    21.53    15.19 
[1] "1.2 - 158.8 (16.4)" "0.2 - 147.4 (21.5)" "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      55        9        10         5         3
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         31       31       55
  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 22 15  0
  subtype2 13 25 33  8
  subtype3 17 36 26  3
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       22       13       17
  T2       22       25       36
  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 35 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   18
  subtype2   29   41
  subtype3   35   36
   clus
vv  subtype1 subtype2 subtype3
  0       34       29       35
  1       18       41       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 38  1 21
  subtype2 43  1 35
  subtype3 37  3 42
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       38       43       37
  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 54 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   18
  subtype2   57   22
  subtype3   54   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       43       57       54
  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                                            68
          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                                68
  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 78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   61
  subtype2    9   70
  subtype3    4   78
     clus
vv    subtype1 subtype2 subtype3
  NO         0        9        4
  YES       61       70       78
[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 65  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    3
  subtype2   67    4
  subtype3   65    4
     clus
vv    subtype1 subtype2 subtype3
  NO        52       67       65
  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           12                       0   48
  subtype2           28                       8   41
  subtype3           15                       2   60
D3V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  12       28       15
  MODERATE/ADVANCED (T4A)        0        8        2
  NONE                          48       41       60
[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 62  4  1  5
D3V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       48       58       62
  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 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   23
  subtype2   27   50
  subtype3   39   41
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       35       27       39
  UNIFOCAL         23       50       41
[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    52
D3V16, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        3        8
  BLACK OR AFRICAN AMERICAN        7        4        2
  WHITE                           34       59       52
[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 61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   45
  subtype2    8   58
  subtype3    7   61
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        8        7
  NOT HISPANIC OR LATINO       45       58       61
[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 27  2
  subtype5 47  1
  subtype6 26  1
  subtype7  5  4
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      47       28       33       29       48       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 
       17.26        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        69.24       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        14.07         7.99         1.45        10.09 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PV TCGA-DJ-A2PZ TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        8.48         1.51         8.28         8.42         8.61        10.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-EL-A3CL TCGA-EL-A3CV TCGA-EL-A3GQ 
       10.36        12.43        15.88        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        30.21        16.01         0.23 
TCGA-DE-A0Y2 TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QO TCGA-DJ-A2PY TCGA-DJ-A2Q8 
       15.42        11.01       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       139.00       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        17.23 

$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-EL-A3H3 TCGA-EM-A22Q TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A3AI TCGA-EM-A3FN 
       43.36        14.24        23.51         2.99        17.46        12.07 
TCGA-EM-A3FP TCGA-ET-A2N1 TCGA-ET-A2N5 TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39R 
       17.39        29.19        58.22        65.36        98.56        57.11 
TCGA-ET-A3BS TCGA-ET-A3DS TCGA-ET-A3DT TCGA-FE-A239 TCGA-H2-A2K9 
        5.56         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        12.56 
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-A3GZ TCGA-EL-A3H8 TCGA-EL-A3MX TCGA-EM-A1CU TCGA-EM-A1CV 
      147.75       139.99       131.15        57.63        20.91        12.36 
TCGA-EM-A22M TCGA-EM-A2CS TCGA-EM-A3AO TCGA-EM-A3FO TCGA-ET-A2N4 TCGA-ET-A39J 
       14.53        15.19        13.38        17.49         2.66        71.01 
TCGA-ET-A39M TCGA-ET-A3BN TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
       84.89        28.24        38.30        42.25         2.37         4.50 
TCGA-FE-A233 TCGA-FE-A235 TCGA-FY-A3ON TCGA-GE-A2C6 TCGA-IM-A3EB TCGA-IM-A3ED 
       24.69       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         3.39         8.71        13.12         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   139.00   155.54   147.75    81.34   147.42 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   17.88    13.61    24.72    17.46    16.34    18.38    26.73 
[1] "1.2 - 158.8 (17.9)" "1.4 - 66.8 (13.6)"  "0.2 - 139.0 (24.7)"
[4] "0.3 - 155.5 (17.5)" "0.1 - 147.8 (16.3)" "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      17        4         6         1         1
  subtype5      35        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       17       35        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 11 12  1
  subtype5 11 20 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       11        6        1
  T2       22        9       11       11       20       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  9
  subtype5 16 26
  subtype6 11 10
  subtype7  3  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   11
  subtype2   13   13
  subtype3   10   22
  subtype4   17    9
  subtype5   16   26
  subtype6   11   10
  subtype7    3    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       28       13       10       17       16       11        3
  1       11       13       22        9       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 13  1 15
  subtype5 26  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       13       26       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 21  8
  subtype5 33 16
  subtype6 20  7
  subtype7  6  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   16
  subtype2   18   10
  subtype3   25    8
  subtype4   21    8
  subtype5   33   16
  subtype6   20    7
  subtype7    6    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       31       18       25       21       33       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                                            22
  subtype5              1                                            46
  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                                22
  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                                46
  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 28
  subtype5  3 46
  subtype6  3 24
  subtype7  0  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   47
  subtype2    2   26
  subtype3    4   29
  subtype4    1   28
  subtype5    3   46
  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       28       46       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 22  2
  subtype5 39  2
  subtype6 23  3
  subtype7  6  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    3
  subtype2   26    0
  subtype3   29    0
  subtype4   22    2
  subtype5   39    2
  subtype6   23    3
  subtype7    6    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        39       26       29       22       39       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   18
  subtype5           12                       0   36
  subtype6            6                       2   19
  subtype7            3                       4    1
D4V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  MINIMAL (T3)                   4        9       15        6       12        6
  MODERATE/ADVANCED (T4A)        0        0        3        1        0        2
  NONE                          42       19       14       18       36       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 19  2  2  1
  subtype5 39  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       19       39       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 17
  subtype5 25 22
  subtype6 10 16
  subtype7  2  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   16
  subtype2   12   16
  subtype3   12   20
  subtype4   12   17
  subtype5   25   22
  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       17       22       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    19
  subtype5     6                         2    32
  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       19       32
                           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 21
  subtype5  5 37
  subtype6  2 17
  subtype7  1  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   31
  subtype2    1   23
  subtype3    3   27
  subtype4    2   21
  subtype5    5   37
  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       21       37       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 157   7
  subtype2 152   3
  subtype3  54   2
  subtype4 114   2
subtype1 subtype2 subtype3 subtype4 
     164      155       56      116 
subtype1 subtype2 subtype3 subtype4 
       7        3        2        2 
$subtype1
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        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A7U5 TCGA-DJ-A13U TCGA-DJ-A1QD TCGA-DJ-A1QE 
       25.12         4.27         2.76        13.41        11.01       100.01 
TCGA-DJ-A1QH TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PT TCGA-DJ-A2PW 
        7.99         1.02         5.95        10.09         9.60         7.69 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q4 TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UY 
        8.78         8.42         9.44        31.04        19.56        21.37 
TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3VB TCGA-DJ-A3VF 
       25.02        19.20         9.83        21.27        22.92         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A4UQ TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1K0 
       17.36        10.78         3.12        15.81        24.33        21.53 
TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A3X7 TCGA-E8-A417 TCGA-E8-A418 
       40.21        30.31         1.15        19.59        14.27         3.02 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-EL-A3CM TCGA-EL-A3CN 
       14.70        14.96         7.69        13.78        26.73       155.54 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3D6 TCGA-EL-A3GR TCGA-EL-A3GS 
        7.66        45.53        60.95       108.36       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H7 TCGA-EL-A3H8 
      124.04       147.75       101.13        38.66       139.00       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        29.49        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        17.82 
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        17.23        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        87.39 
TCGA-L6-A4EU TCGA-MK-A4N6 
        0.72        16.64 

$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-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13R 
        8.98         0.39         5.98        18.84        17.26         3.39 
TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A2PP 
        8.71        14.60        13.12         7.20         1.45         5.33 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3US 
        8.12         6.77        12.43        10.85        16.41        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UZ TCGA-DJ-A3V4 TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM 
       24.23        12.76        14.56         8.32        17.23        27.62 
TCGA-DJ-A4UR TCGA-DJ-A4V0 TCGA-E3-A3DZ TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A434 
       10.98        17.82        12.07        13.81        14.07        14.10 
TCGA-EL-A3CX TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW 
       80.91        58.82        45.40        33.47        39.32        37.25 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T0 TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZN 
       49.32        33.50       130.72        32.48        78.97        53.06 
TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KI 
       48.16        45.80        30.51        28.73        29.95         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-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2P2 
       13.64        10.49        22.16        13.84        17.59        17.29 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FL 
       17.46        18.97        14.14         8.35        16.77        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-A39L TCGA-ET-A39N TCGA-ET-A39S TCGA-ET-A3DQ 
       58.22        13.74        65.36        98.56        55.10        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 
       43.50         0.30       132.36         3.22         1.94        33.63 
TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R7 
        0.89         1.25         1.64         0.99        16.14         0.03 
TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A76V 
       16.57         0.76        17.06         4.54         0.89         1.68 
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 TCGA-MK-A84Z TCGA-QD-A8IV 
        0.20        15.98        86.70        10.98         5.19 

$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-DE-A4M8 TCGA-DJ-A13O 
       15.48         0.03         0.10        11.38        18.54        14.07 
TCGA-DJ-A2PX TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q9 TCGA-DJ-A3UW TCGA-DJ-A3UX 
        5.52         9.34         9.21        10.36        43.00        11.34 
TCGA-DJ-A3VD TCGA-DJ-A4UT TCGA-DO-A2HM TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A414 
       21.01        14.14         2.33        22.29        13.61        14.27 
TCGA-E8-A44M TCGA-EL-A3CO TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY 
       13.58        97.74       157.15        37.94        57.01         4.18 
TCGA-EL-A3GP TCGA-EL-A3H3 TCGA-EL-A3H5 TCGA-EL-A3TA TCGA-EL-A3ZP TCGA-EL-A3ZS 
        1.41        43.36        52.73        66.90        52.50         7.07 
TCGA-EL-A4JZ TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2P1 TCGA-EM-A3FQ TCGA-EM-A3O3 
       37.94        14.53        11.15        17.46        16.18        14.50 
TCGA-EM-A4FO TCGA-ET-A39R TCGA-ET-A3BO TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40R 
        8.38        57.11         5.85        17.98        25.32         4.80 
TCGA-ET-A40S TCGA-FE-A3PB TCGA-FY-A3R6 TCGA-FY-A3TY TCGA-GE-A2C6 TCGA-H2-A26U 
        5.03        85.15         0.76         0.30        12.53        17.00 
TCGA-J8-A3O2 TCGA-KS-A4ID 
       11.24        33.24 

$subtype4
TCGA-BJ-A0Z5 TCGA-BJ-A290 TCGA-BJ-A45H TCGA-BJ-A45J TCGA-BJ-A4O9 TCGA-CE-A13K 
       14.73        30.21         7.82         5.06         5.98         0.53 
TCGA-CE-A3MD TCGA-CE-A482 TCGA-DE-A0XZ TCGA-DE-A3KN TCGA-DE-A69K TCGA-DJ-A13P 
        0.20        10.68        20.22        15.85         3.22       137.88 
TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN 
       25.35        11.90         7.99        18.51        14.96         8.88 
TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PV 
        7.99         8.48        10.45         1.51        12.56         8.28 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
        9.90         8.61        10.09        15.88        15.09        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3UU TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V9 
       31.46        36.33        17.69        20.22        30.61        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4UW TCGA-DO-A1JZ TCGA-E3-A3DY 
       11.93        18.97        18.21        14.70        54.90        31.07 
TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A438 TCGA-EL-A3CL 
       66.38        63.19        14.04        14.43        20.68        31.66 
TCGA-EL-A3CP TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GQ TCGA-EL-A3GV TCGA-EL-A3GZ 
      158.83         1.45        74.30        30.18        50.37       139.99 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZG 
      108.66        57.63        41.29        95.38        82.82        77.36 
TCGA-EL-A3ZL TCGA-EL-A3ZQ TCGA-EL-A4K0 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KH 
       50.33        45.53        31.04        41.13        37.78        11.87 
TCGA-EM-A1CS TCGA-EM-A1CV TCGA-EM-A2CS TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A3AK 
       26.86        12.36        15.19        13.15        19.73        15.68 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3FJ TCGA-EM-A3O7 TCGA-EM-A3SX 
       19.63        13.38        16.44        27.95         7.33        15.62 
TCGA-EM-A4FV TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J 
       12.72        32.35        27.09        12.26         2.66        71.01 
TCGA-ET-A39K TCGA-ET-A39M TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BW 
       80.02        84.89         4.18         2.43         5.56         2.37 
TCGA-ET-A3DP TCGA-ET-A40T TCGA-FE-A235 TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       69.24         2.14       102.90       106.36        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A40K 
       46.06         4.08         0.92        48.10        91.17         4.14 
TCGA-H2-A3RI TCGA-J8-A3YH TCGA-J8-A42S TCGA-KS-A41F TCGA-KS-A4I1 TCGA-KS-A4I5 
        2.99         5.75         2.47       143.57         6.02         6.74 
TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       32.45        84.72        35.28        33.40        40.37        21.83 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.03     0.03     0.20 
subtype1 subtype2 subtype3 subtype4 
  155.54   132.36   157.15   158.83 
subtype1 subtype2 subtype3 subtype4 
  18.395   15.020   14.205   18.360 
[1] "0.1 - 155.5 (18.4)" "0.0 - 132.4 (15.0)" "0.0 - 157.2 (14.2)"
[4] "0.2 - 158.8 (18.4)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      84        7        45        1        26         2
  subtype2      90       30        27        1         5         2
  subtype3      39        1        13        0         4         0
  subtype4      67       14        23        0        10         2
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         84       90       39       67
  STAGE II         7       30        1       14
  STAGE III       45       27       13       23
  STAGE IV         1        1        0        0
  STAGE IVA       26        5        4       10
  STAGE IVC        2        2        0        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 27 48 76 13
  subtype2 54 57 43  2
  subtype3 25 14 15  2
  subtype4 34 47 31  4
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       27       54       25       34
  T2       48       57       14       47
  T3       76       43       15       31
  T4       13        2        2        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"
D5V5, binary
          cls
clus         0   1
  subtype1  51  99
  subtype2 101  29
  subtype3  22  35
  subtype4  50  58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51   99
  subtype2  101   29
  subtype3   22   35
  subtype4   50   58
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       51      101       22       50
  1       99       29       35       58
[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 92  3 70
  subtype2 70  3 82
  subtype3 39  0 18
  subtype4 72  3 42
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       92       70       39       72
  M1        3        3        0        3
  MX       70       82       18       42
[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 119  46
  subtype2 113  43
  subtype3  42  15
  subtype4  89  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  119   46
  subtype2  113   43
  subtype3   42   15
  subtype4   89   28
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      119      113       42       89
  MALE         46       43       15       28
[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              4                                           132
  subtype2              2                                            71
  subtype3              1                                            49
  subtype4              2                                           100
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      3
  subtype2                                                                     82
  subtype3                                                                      3
  subtype4                                                                     12
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  26
  subtype2                                                                   1
  subtype3                                                                   4
  subtype4                                                                   3
D5V8, multiclass
                                                                        clus
vv                                                                       subtype1
  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
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                71
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       82
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           1
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                49
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           4
                                                                        clus
vv                                                                       subtype4
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               100
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       12
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
          cls
clus         0   1
  subtype1  11 154
  subtype2   1 155
  subtype3   0  57
  subtype4   2 115
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11  154
  subtype2    1  155
  subtype3    0   57
  subtype4    2  115
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        11        1        0        2
  YES      154      155       57      115
[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 141   5
  subtype2 129   6
  subtype3  47   2
  subtype4  99   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  141    5
  subtype2  129    6
  subtype3   47    2
  subtype4   99    4
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       141      129       47       99
  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           66                      12   81                   1
  subtype2           23                       1  123                   0
  subtype3           13                       2   39                   0
  subtype4           28                       1   85                   0
D5V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4
  MINIMAL (T3)                  66       23       13       28
  MODERATE/ADVANCED (T4A)       12        1        2        1
  NONE                          81      123       39       85
  VERY ADVANCED (T4B)            1        0        0        0
[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 125  25   2   9
  subtype2 124   9   0   8
  subtype3  39   7   0   5
  subtype4  90  10   2   8
D5V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      125      124       39       90
  R1       25        9        7       10
  R2        2        0        0        2
  RX        9        8        5        8
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, continuous
D5V14, binary
          cls
clus        0  1
  subtype1 66 97
  subtype2 74 79
  subtype3 25 30
  subtype4 59 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66   97
  subtype2   74   79
  subtype3   25   30
  subtype4   59   55
            clus
vv           subtype1 subtype2 subtype3 subtype4
  MULTIFOCAL       66       74       25       59
  UNIFOCAL         97       79       30       55
[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                                1    16                        10
  subtype2                                0    10                         9
  subtype3                                0     6                         1
  subtype4                                0    16                         6
          vv
clus       WHITE
  subtype1   118
  subtype2    87
  subtype3    43
  subtype4    74
D5V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                  16       10        6       16
  BLACK OR AFRICAN AMERICAN              10        9        1        6
  WHITE                                 118       87       43       74
[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  23 118
  subtype2   9  96
  subtype3   3  46
  subtype4   3  89
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23  118
  subtype2    9   96
  subtype3    3   46
  subtype4    3   89
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           23        9        3        3
  NOT HISPANIC OR LATINO      118       96       46       89
[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  95   5
  subtype2 130   4
  subtype3  84   1
  subtype4  93   2
  subtype5  75   2
subtype1 subtype2 subtype3 subtype4 subtype5 
     100      134       85       95       77 
subtype1 subtype2 subtype3 subtype4 subtype5 
       5        4        1        2        2 
$subtype1
TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28R TCGA-BJ-A3PU TCGA-BJ-A45I 
        8.25         4.01        20.71         4.87        18.64         6.18 
TCGA-BJ-A4O8 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A7U5 
        4.93        30.12        11.57        30.02         4.27         2.76 
TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A2PT TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
      100.01         7.99         9.60         8.78         8.42         9.34 
TCGA-DJ-A2Q6 TCGA-DJ-A3UQ TCGA-DJ-A3V0 TCGA-DJ-A3V5 TCGA-DJ-A3VB TCGA-DJ-A3VF 
        8.61        19.56        25.02        19.20        22.92         7.76 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A433 TCGA-E8-A44K TCGA-EL-A3CM 
        1.15        22.29        19.59        14.70        13.78        26.73 
TCGA-EL-A3CN TCGA-EL-A3CR TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3D6 TCGA-EL-A3GP 
      155.54         7.66       157.15        37.94       108.36         1.41 
TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      124.04        52.73       139.00        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T1 TCGA-EL-A3T6 TCGA-EL-A3T9 TCGA-EL-A3ZO TCGA-EL-A4JX 
      147.42       129.57        98.24         5.72        47.38        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EL-A4KG TCGA-EM-A22I TCGA-EM-A2P3 
       37.94        19.59        33.60        13.32        14.73        14.60 
TCGA-EM-A3FM TCGA-EM-A3O3 TCGA-EM-A3SU TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FM 
       21.01        14.50        16.41        12.79        70.65         4.83 
TCGA-EM-A4FQ TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25R 
        9.80        47.47        29.69        14.79        12.33        29.49 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A3BO TCGA-ET-A3BT 
       22.09        16.08        61.02        58.72         5.85        24.72 
TCGA-ET-A3BV TCGA-ET-A3DO TCGA-ET-A3DU TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A4KN 
       42.25        80.81        25.32        24.72         7.17         4.01 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A234 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB 
       73.74        59.70        68.22        81.34        81.83        85.15 
TCGA-FY-A3R8 TCGA-FY-A3YR TCGA-FY-A40L TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A421 
        4.67         6.87         6.58        12.53        17.00        20.05 
TCGA-IM-A3EB TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       48.92        10.26        16.90         2.96         8.65        17.23 
TCGA-J8-A3YF TCGA-KS-A4I9 TCGA-L6-A4EU TCGA-MK-A4N6 
       24.69        87.39         0.72        16.64 

$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-A484 TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13S 
        8.98         0.39         5.98        18.84        17.26         8.71 
TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 
       14.60        13.12         7.20         5.33         8.12         6.77 
TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM 
       10.85        16.41        24.23         8.32        17.23        27.62 
TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E8-A416 TCGA-EL-A3CO TCGA-EL-A3CX TCGA-EL-A3CZ 
       10.98        12.07        14.07        97.74        80.91        58.82 
TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3T2 
       33.47        39.32        37.25        49.32        33.50        32.48 
TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KI 
       78.97        48.16        45.80        30.51        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-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP 
       18.97        14.14         8.35        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-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I 
        0.95        48.20        18.38        19.76        58.22        13.74 
TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ 
       65.36        98.56         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-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A76V TCGA-H2-A2K9 
       16.57         0.76        17.06         4.54         1.68        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 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

$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-BJ-A45H TCGA-CE-A27D TCGA-CE-A485 TCGA-DE-A0XZ 
       15.48         0.03         7.82         0.10         0.10        20.22 
TCGA-DE-A4M8 TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A1QM TCGA-DJ-A2PR TCGA-DJ-A2PS 
       18.54        14.07         3.39         1.45        10.45         1.51 
TCGA-DJ-A2PX TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3US 
        5.52         9.21         9.90        10.36        12.43        32.81 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V2 
       17.69        43.00        11.34        21.37        12.76        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3VD TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.61        14.56        21.01        10.78        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A2HM TCGA-E3-A3E2 TCGA-E8-A413 
       17.82        15.81        24.33         2.33        63.19        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44M 
       14.27        13.81        14.10        14.96         7.69        13.58 
TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D4 TCGA-EL-A3H3 TCGA-EL-A3T0 TCGA-EL-A3TA 
       57.01         4.18        45.40        43.36       130.72        66.90 
TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EM-A22M TCGA-EM-A22P 
       53.06        52.50        45.53         7.07        14.53        11.15 
TCGA-EM-A2CP TCGA-EM-A2P1 TCGA-EM-A3AR TCGA-EM-A3FQ TCGA-EM-A4FO TCGA-EM-A4FV 
        2.99        17.46        16.77        16.18         8.38        12.72 
TCGA-ET-A39M TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A3BS TCGA-ET-A3DQ TCGA-ET-A3DT 
       84.89        57.11        55.10         5.56        59.87        17.98 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-FE-A232 TCGA-FY-A3R6 TCGA-FY-A3R7 
        4.80         5.03         2.14        44.25         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        11.24        31.82         2.47 
TCGA-KS-A4ID 
       33.24 

$subtype4
TCGA-BJ-A0Z5 TCGA-BJ-A290 TCGA-BJ-A45J TCGA-CE-A13K TCGA-CE-A3MD TCGA-CE-A481 
       14.73        30.21         5.06         0.53         0.20        11.38 
TCGA-CE-A482 TCGA-DE-A3KN TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13V 
       10.68        15.85         3.22       137.88        25.35        11.90 
TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PQ TCGA-DJ-A2PU 
        7.99        18.51        14.96         8.88         8.48        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
        8.28         7.69        10.09        15.88        15.09        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V9 TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DO-A1JZ 
       31.46        36.33        20.48        18.97        18.21        54.90 
TCGA-E3-A3E0 TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CP 
       66.38        14.04        14.43        20.68        31.66       158.83 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GQ TCGA-EL-A3GV TCGA-EL-A3GZ TCGA-EL-A3MW 
        1.45        74.30        30.18        50.37       139.99       108.66 
TCGA-EL-A3MX TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZL TCGA-EL-A4K0 
       57.63        41.29        95.38        82.82        50.33        31.04 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CV 
       41.13        37.78        29.95        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-A3FO TCGA-EM-A3O7 TCGA-EM-A3SX TCGA-ET-A25K 
       16.44        27.95        17.49         7.33        15.62        32.35 
TCGA-ET-A25O TCGA-ET-A2MZ TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A3BP 
       27.09        12.26         2.66        71.01        80.02         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BW TCGA-ET-A3DP TCGA-FE-A235 TCGA-FE-A3PA TCGA-FE-A3PD 
        2.43         2.37        69.24       102.90       106.36        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A40K 
       46.06         4.08         0.92        48.10        91.17         4.14 
TCGA-J8-A3YH TCGA-KS-A41F TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4IB 
        5.75       143.57         6.02         6.74        32.45        84.72 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37        21.83        32.45         8.71 

$subtype5
TCGA-BJ-A0ZH TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A4O9 TCGA-CE-A3ME TCGA-CE-A483 
       15.12        18.97        16.01         5.98         0.23         0.10 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A4MD TCGA-DJ-A13U TCGA-DJ-A1QD TCGA-DJ-A1QO 
       15.42        36.46        25.12        13.41        11.01         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2Q4 TCGA-DJ-A3UM TCGA-DJ-A3V7 
        5.95        10.09         7.99         9.44        31.04         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3VA TCGA-DJ-A3VJ TCGA-DJ-A4V2 TCGA-DO-A1K0 TCGA-E3-A3DY 
       21.27        11.93        17.36         3.12        21.53        31.07 
TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E8-A417 TCGA-E8-A418 TCGA-EL-A3CS TCGA-EL-A3CT 
       40.21        30.31        14.27         3.02        45.53        60.95 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H4 TCGA-EL-A3H8 
      102.84        65.39       147.75       101.13        38.66       131.15 
TCGA-EL-A3T3 TCGA-EL-A3ZG TCGA-EL-A3ZK TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EM-A1CT 
      116.91        77.36        31.50        44.65        19.30        18.18 
TCGA-EM-A1CU TCGA-EM-A22O TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A3FK TCGA-EM-A4FN 
       20.91        11.74        12.07        17.59        23.77         8.61 
TCGA-ET-A25N TCGA-ET-A2MX TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BU TCGA-ET-A3BX 
       14.79        54.05        59.15        28.24        38.30         4.50 
TCGA-ET-A3DR TCGA-FE-A231 TCGA-FE-A233 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A3PC 
       43.50        31.59        24.69        66.77        39.95        85.68 
TCGA-FK-A3SE TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3RA TCGA-FY-A4B3 
       22.03         1.15        17.82         1.51        18.08         1.35 
TCGA-FY-A4B4 TCGA-H2-A3RI TCGA-H2-A422 TCGA-IM-A41Y TCGA-J8-A3O1 TCGA-J8-A3YE 
        1.15         2.99        18.61         9.80        27.19        27.85 
TCGA-J8-A3YG TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I3 TCGA-KS-A4IC 
       22.29         2.60        15.68        12.43        35.28 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.72     0.20     0.03     0.20     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
  157.15   132.36   130.72   158.83   147.75 
subtype1 subtype2 subtype3 subtype4 subtype5 
   18.92    14.81    14.14    18.97    18.97 
[1] "0.7 - 157.2 (18.9)" "0.2 - 132.4 (14.8)" "0.0 - 130.7 (14.1)"
[4] "0.2 - 158.8 (19.0)" "0.1 - 147.8 (19.0)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      45        2        39        1        14         1
  subtype2      76       30        21        1         4         2
  subtype3      56        3        18        0         8         0
  subtype4      54       11        19        0         9         2
  subtype5      49        6        11        0        10         1
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I         45       76       56       54       49
  STAGE II         2       30        3       11        6
  STAGE III       39       21       18       19       11
  STAGE IV         1        1        0        0        0
  STAGE IVA       14        4        8        9       10
  STAGE IVC        1        2        0        2        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 16 23 55  8
  subtype2 44 55 34  2
  subtype3 37 22 23  1
  subtype4 26 40 25  4
  subtype5 17 26 28  6
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       16       44       37       26       17
  T2       23       55       22       40       26
  T3       55       34       23       25       28
  T4        8        2        1        4        6
[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 28 66
  subtype2 90 19
  subtype3 38 44
  subtype4 43 45
  subtype5 25 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   66
  subtype2   90   19
  subtype3   38   44
  subtype4   43   45
  subtype5   25   47
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       28       90       38       43       25
  1       66       19       44       45       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  1 48
  subtype2 56  3 75
  subtype3 59  0 26
  subtype4 58  3 35
  subtype5 47  2 28
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       53       56       59       58       47
  M1        1        3        0        3        2
  MX       48       75       26       35       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 83 19
  subtype2 96 39
  subtype3 60 25
  subtype4 74 22
  subtype5 50 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   83   19
  subtype2   96   39
  subtype3   60   25
  subtype4   74   22
  subtype5   50   27
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       83       96       60       74       50
  MALE         19       39       25       22       27
[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              1                                            77
  subtype2              2                                            57
  subtype3              2                                            67
  subtype4              0                                            83
  subtype5              4                                            68
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      2
  subtype2                                                                     76
  subtype3                                                                     10
  subtype4                                                                     11
  subtype5                                                                      1
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  22
  subtype2                                                                   0
  subtype3                                                                   6
  subtype4                                                                   2
  subtype5                                                                   4
D6V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                77
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          22
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                57
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       76
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                67
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           6
                                                                        clus
vv                                                                       subtype4
  OTHER  SPECIFY                                                                0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                83
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       11
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           2
                                                                        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   5  97
  subtype2   1 134
  subtype3   1  84
  subtype4   2  94
  subtype5   5  72
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   97
  subtype2    1  134
  subtype3    1   84
  subtype4    2   94
  subtype5    5   72
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         5        1        1        2        5
  YES       97      134       84       94       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  92   3
  subtype2 111   5
  subtype3  65   6
  subtype4  85   1
  subtype5  63   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92    3
  subtype2  111    5
  subtype3   65    6
  subtype4   85    1
  subtype5   63    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        92      111       65       85       63
  YES        3        5        6        1        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           53                       8   37                   1
  subtype2           15                       1  110                   0
  subtype3           20                       1   61                   0
  subtype4           21                       1   71                   0
  subtype5           21                       5   49                   0
D6V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3 subtype4 subtype5
  MINIMAL (T3)                  53       15       20       21       21
  MODERATE/ADVANCED (T4A)        8        1        1        1        5
  NONE                          37      110       61       71       49
  VERY ADVANCED (T4B)            1        0        0        0        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  68  22   2   6
  subtype2 103  10   0   8
  subtype3  69   4   0   6
  subtype4  76   8   2   6
  subtype5  62   7   0   4
D6V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       68      103       69       76       62
  R1       22       10        4        8        7
  R2        2        0        0        2        0
  RX        6        8        6        6        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 38 64
  subtype2 64 68
  subtype3 43 40
  subtype4 47 46
  subtype5 32 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   64
  subtype2   64   68
  subtype3   43   40
  subtype4   47   46
  subtype5   32   43
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  MULTIFOCAL       38       64       43       47       32
  UNIFOCAL         64       68       40       46       43
[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                                1     4                        10
  subtype2                                0     6                         8
  subtype3                                0    16                         1
  subtype4                                0    12                         6
  subtype5                                0    10                         1
          vv
clus       WHITE
  subtype1    76
  subtype2    73
  subtype3    58
  subtype4    59
  subtype5    56
D6V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   4        6       16       12       10
  BLACK OR AFRICAN AMERICAN              10        8        1        6        1
  WHITE                                  76       73       58       59       56
[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 15 75
  subtype2  9 79
  subtype3  3 69
  subtype4  3 70
  subtype5  8 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   75
  subtype2    9   79
  subtype3    3   69
  subtype4    3   70
  subtype5    8   56
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO           15        9        3        3        8
  NOT HISPANIC OR LATINO       75       79       69       70       56
[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 168  10
  subtype2 147   3
  subtype3 163   1
subtype1 subtype2 subtype3 
     178      150      164 
subtype1 subtype2 subtype3 
      10        3        1 
$subtype1
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-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-A4MA 
        0.10         0.20        11.38         0.10        18.54        30.12 
TCGA-DE-A4MB TCGA-DE-A7U5 TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.57         2.76        14.07        11.01       100.01        18.51 
TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PS 
        7.99         1.45         1.02         5.95        10.09         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PV TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 
        9.60         8.28         8.78         8.42         9.34         9.21 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3UM 
        9.90         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-A4V4 
        7.76        17.36        10.78        14.14        14.70        15.81 
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-A3CN 
       14.96         7.69        13.78        13.58        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-A3D4 
       37.94        57.01         4.18         1.45        74.30        45.40 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3GZ TCGA-EL-A3H5 
        1.41        30.18       102.84       124.04       139.99        52.73 
TCGA-EL-A3H7 TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 
      139.00        57.63        17.52        52.50       147.42       130.72 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
        5.72        66.90        31.50        50.33        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZS TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       52.50         7.07        19.30        37.94        31.04        19.59 
TCGA-EL-A4K4 TCGA-EM-A1CU TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CU TCGA-EM-A2OX 
       33.60        20.91        57.01        11.15        13.15        19.73 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3FQ TCGA-EM-A3O3 
       17.59        17.46        14.60        16.77        16.18        14.50 
TCGA-EM-A4FM TCGA-EM-A4FO TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A2N0 
        4.83         8.38        47.47        14.79        12.33        16.08 
TCGA-ET-A39J TCGA-ET-A39M TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT 
       71.01        84.89        58.72        55.10        28.24        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU 
       38.30        42.25        59.87        43.50        17.98        25.32 
TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A238 
        7.17         2.14         4.01        73.74        81.34        39.95 
TCGA-FE-A3PB TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 TCGA-FY-A3R6 TCGA-FY-A3R7 
       85.15        22.03        48.10        17.82         0.76         0.03 
TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A4B3 
        0.30         6.87         4.14         6.58         4.54         1.35 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A420 TCGA-IM-A4EB 
       12.53        17.00        47.41        10.26         2.96         8.65 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW 
       11.24        31.82        24.69        22.29         2.47         2.60 
TCGA-KS-A4I3 TCGA-KS-A4IC TCGA-L6-A4EU TCGA-MK-A4N6 
       12.43        35.28         0.72        16.64 

$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-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        18.84        25.12 
TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QG 
       17.26         3.39         8.71        14.60         7.99        13.12 
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        24.23         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 
       17.82        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        30.51 
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        69.24         0.30       132.36         3.22         4.80 
TCGA-ET-A4KQ TCGA-FE-A236 TCGA-FE-A239 TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SD 
        1.94        66.77        33.63        78.77        46.06         0.89 
TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 
        1.25         1.64         0.99        16.14        16.57         0.76 
TCGA-FY-A3WA TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3O1 
       17.06        21.67        12.46         9.63        43.17        27.19 
TCGA-KS-A41I TCGA-KS-A41L TCGA-KS-A4IB TCGA-KS-A4ID TCGA-MK-A84Z TCGA-QD-A8IV 
       15.98        86.70        84.72        33.24        10.98         5.19 

$subtype3
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        30.21 
TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J TCGA-BJ-A4O9 TCGA-CE-A13K 
       18.97        16.01        18.64         5.06         5.98         0.53 
TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN 
       10.68         0.10        20.22        15.42        36.46        15.85 
TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U 
       30.02         4.27         3.22       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         8.48        10.45        12.56 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.69         5.52         9.44        10.09        15.88        15.09 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V7 
       12.49        31.46        36.33        20.22        30.61         9.83 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DJ-A4V5 
       11.93        22.92        18.97        18.21         3.12        24.33 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A417 TCGA-E8-A418 
       21.53        31.07        63.19        30.31        14.27         3.02 
TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3D6 TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY 
       20.68        31.66       108.36        50.37       147.75       101.13 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T1 
       43.36        38.66       131.15       108.66        12.16       129.57 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZG 
      116.91        98.24        41.29        95.38        82.82        77.36 
TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JX TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       45.53        44.65        45.96        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CV TCGA-EM-A22I 
       13.32        11.87        26.86        18.18        12.36        14.73 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OZ TCGA-EM-A3AK TCGA-EM-A3AN 
       14.53        11.74        15.19        12.07        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-A4FN 
        7.33        16.41        15.62        12.79        70.65         8.61 
TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O 
        9.80        12.72        29.69        32.35        14.79        27.09 
TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A39K 
       29.49        22.09        12.26        29.19         2.66        80.02 
TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BS 
       61.02        57.11        59.15         5.85         4.18         5.56 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DW TCGA-ET-A40S TCGA-FE-A230 TCGA-FE-A231 
        4.50        80.81        24.72         5.03        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A23A TCGA-FE-A3PA 
       44.25        24.69        68.22       102.90        81.83       106.36 
TCGA-FE-A3PC TCGA-FK-A3SB TCGA-FK-A3SG TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3ON 
       85.68         4.08         0.92        91.17         1.15         1.51 
TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A40N TCGA-FY-A4B4 TCGA-FY-A76V TCGA-H2-A3RI 
        4.67        18.08         0.89         1.15         1.68         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-J8-A3NZ 
       20.05        18.61        48.92        16.90         9.80        17.23 
TCGA-J8-A3YE TCGA-J8-A3YH TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 
       27.85         5.75         0.20       143.57        15.68         6.02 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
        6.74        32.45        87.39        33.40        40.37        21.83 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

subtype1 subtype2 subtype3 
    0.03     0.23     0.10 
subtype1 subtype2 subtype3 
  158.83   132.36   147.75 
subtype1 subtype2 subtype3 
  16.130   16.060   18.195 
[1] "0.0 - 158.8 (16.1)" "0.2 - 132.4 (16.1)" "0.1 - 147.8 (18.2)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      89        6        55        1        25         2
  subtype2      92       29        21        1         5         2
  subtype3      99       17        33        0        15         2
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         89       92       99
  STAGE II         6       29       17
  STAGE III       55       21       33
  STAGE IV         1        1        0
  STAGE IVA       25        5       15
  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 55 38 70 13
  subtype2 43 68 38  2
  subtype3 43 61 56  6
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       55       43       43
  T2       38       68       61
  T3       70       38       56
  T4       13        2        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"
D7V5, binary
          cls
clus         0   1
  subtype1  64 106
  subtype2  96  27
  subtype3  65  88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64  106
  subtype2   96   27
  subtype3   65   88
   clus
vv  subtype1 subtype2 subtype3
  0       64       96       65
  1      106       27       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"
          vv
clus        M0  M1  MX
  subtype1 119   2  58
  subtype2  64   3  83
  subtype3  90   4  72
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      119       64       90
  M1        2        3        4
  MX       58       83       72
[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 134  45
  subtype2 108  43
  subtype3 122  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  134   45
  subtype2  108   43
  subtype3  122   44
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      134      108      122
  MALE         45       43       44
[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              4                                           142
  subtype2              2                                            66
  subtype3              3                                           144
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      8
  subtype2                                                                     83
  subtype3                                                                      9
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  25
  subtype2                                                                   0
  subtype3                                                                  10
D7V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               142
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          25
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                66
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       83
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               144
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          10
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus         0   1
  subtype1   3 176
  subtype2   3 148
  subtype3   8 158
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  176
  subtype2    3  148
  subtype3    8  158
     clus
vv    subtype1 subtype2 subtype3
  NO         3        3        8
  YES      176      148      158
[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 151   7
  subtype2 126   5
  subtype3 140   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  151    7
  subtype2  126    5
  subtype3  140    5
     clus
vv    subtype1 subtype2 subtype3
  NO       151      126      140
  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           63                      12   96                   1
  subtype2           16                       0  127                   0
  subtype3           50                       4  107                   0
D7V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  63       16       50
  MODERATE/ADVANCED (T4A)       12        0        4
  NONE                          96      127      107
  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 130  25   3  12
  subtype2 118  10   0  10
  subtype3 131  16   1   8
D7V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      130      118      131
  R1       25       10       16
  R2        3        0        1
  RX       12       10        8
[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 81 97
  subtype2 66 80
  subtype3 77 85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   81   97
  subtype2   66   80
  subtype3   77   85
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       81       66       77
  UNIFOCAL         97       80       85
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    25                         7
  subtype2                                0     8                        10
  subtype3                                1    16                         9
          vv
clus       WHITE
  subtype1   130
  subtype2    84
  subtype3   108
D7V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  25        8       16
  BLACK OR AFRICAN AMERICAN               7       10        9
  WHITE                                 130       84      108
[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  13 142
  subtype2  10  92
  subtype3  15 116
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  142
  subtype2   10   92
  subtype3   15  116
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13       10       15
  NOT HISPANIC OR LATINO      142       92      116
[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 164  10
  subtype2 126   3
  subtype3 188   1
subtype1 subtype2 subtype3 
     174      129      189 
subtype1 subtype2 subtype3 
      10        3        1 
$subtype1
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        11.38         0.10        18.54        11.57 
TCGA-DE-A7U5 TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QM 
        2.76        14.07        11.01       100.01         7.99         1.45 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PV 
        1.02         5.95        10.09         1.51         9.60         8.28 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 
        8.78         8.42         9.34         9.21         8.61         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3UW 
       10.36        12.43        31.04        19.56        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       11.34        21.37        12.76        25.02        14.56        19.20 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A4UQ 
       21.27        20.48        21.01         7.76        17.36        10.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-E3-A3E1 
       14.14        14.70        17.82        15.81         2.33        40.21 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       14.07        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.78        13.58        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
        4.18         1.45        74.30         1.41        30.18       102.84 
TCGA-EL-A3GU TCGA-EL-A3GZ TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3MX TCGA-EL-A3MY 
      124.04       139.99        52.73       139.00        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T9 TCGA-EL-A3TA 
       52.50       147.42       130.72       129.57         5.72        66.90 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS 
       31.50        50.33        53.06        47.38        52.50         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 
       44.65        19.30        37.94        31.04        19.59        33.60 
TCGA-EL-A4KG TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CU TCGA-EM-A2OX TCGA-EM-A2P0 
       13.32        57.01        11.15        13.15        19.73        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3O3 TCGA-EM-A4FF TCGA-EM-A4FM 
       17.46        14.60        16.77        14.50        70.65         4.83 
TCGA-EM-A4FO TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25R TCGA-ET-A2N0 
        8.38        47.47        14.79        12.33        29.49        16.08 
TCGA-ET-A39J TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BT TCGA-ET-A3BV 
       71.01        58.72        55.10        28.24        24.72        42.25 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A40Q TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z 
       59.87        43.50         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        17.82 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K 
        0.76         0.03         4.67         0.30         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-IM-A3U2 TCGA-IM-A420 
        6.58         1.35        12.53        17.00        10.26         2.96 
TCGA-IM-A4EB TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S 
        8.65        11.24        31.82        24.69        22.29         2.47 
TCGA-J8-A4HW TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4IC TCGA-L6-A4EU TCGA-MK-A4N6 
        2.60        12.43         6.74        35.28         0.72        16.64 

$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-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-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3F0 
       22.88        18.38        16.57        20.48         7.04        13.94 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45K TCGA-CE-A484 
        5.75         6.48         3.45         6.35         8.98         0.39 
TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W 
        5.98        18.84        17.26         3.39         8.71        14.60 
TCGA-DJ-A1QG TCGA-DJ-A1QL TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2QB 
       13.12         7.20         5.33         8.12         6.77        10.85 
TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR 
       16.41        24.23         8.32        17.23        27.62        10.98 
TCGA-E3-A3DZ TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW 
       12.07        58.82        45.40        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 
       30.51        28.73         8.71        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N 
       54.21        54.08        14.50        15.75        10.45        10.65 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        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-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-A39N TCGA-ET-A3DS TCGA-ET-A3DV 
       19.76        58.22        13.74        98.56         0.30       132.36 
TCGA-ET-A40P TCGA-ET-A4KQ TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3I5 
        3.22         1.94        33.63         0.89         1.25         1.64 
TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-H2-A2K9 
        0.99        16.14        16.57         0.76        17.06        21.67 
TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-KS-A41I TCGA-KS-A41L 
       12.46         9.63        43.17        27.19        15.98        86.70 
TCGA-KS-A4ID TCGA-MK-A84Z TCGA-QD-A8IV 
       33.24        10.98         5.19 

$subtype3
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-A28Z TCGA-BJ-A290 TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J TCGA-BJ-A4O9 
        1.22        30.21        16.01        18.64         5.06         5.98 
TCGA-CE-A13K TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ 
        0.53         0.20         0.23        10.68         0.10        20.22 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD 
       15.42        36.46        15.85        30.12        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13X 
        4.27         3.22       137.88        25.35        13.41         7.99 
TCGA-DJ-A1QF TCGA-DJ-A1QI TCGA-DJ-A1QN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       18.51        14.96         8.88         7.99         8.48        10.45 
TCGA-DJ-A2PU TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 
       12.56         7.69         5.52         9.44         9.90        10.09 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3US 
       15.88        15.09        12.49        31.46        36.33        32.81 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       20.22        30.61         9.83        11.93        22.92        18.97 
TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
       18.21         3.12        24.33        54.90        21.53        31.07 
TCGA-E3-A3E0 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A417 TCGA-E8-A418 
       66.38        63.19        30.31        14.04        14.27         3.02 
TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CX TCGA-EL-A3D6 TCGA-EL-A3GS TCGA-EL-A3GV 
       20.68        31.66        80.91       108.36        65.39        50.37 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3MW 
      147.75       101.13        43.36        38.66       131.15       108.66 
TCGA-EL-A3N2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB 
       12.16       116.91        98.24        41.29        95.38        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZQ TCGA-EL-A4JX TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       77.36        45.53        45.96        41.13        37.78        29.95 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I 
       11.87        26.86        18.18        20.91        12.36        14.73 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A2CS TCGA-EM-A2OZ TCGA-EM-A3AK TCGA-EM-A3AN 
       14.53        11.74        15.19        12.07        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-A3FQ TCGA-EM-A3O7 TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FN 
       16.18         7.33        16.41        15.62        12.79         8.61 
TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O 
        9.80        12.72        29.69        32.35        14.79        27.09 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A39K 
       54.05        22.09        12.26        29.19         2.66        80.02 
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        69.24        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-A3SG TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3ON 
       78.77        46.06         0.92        91.17         1.15         1.51 
TCGA-FY-A3RA TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B4 TCGA-FY-A76V TCGA-H2-A3RI 
       18.08         4.54         0.89         1.15         1.68         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y 
       20.05        18.61        48.92        47.41        16.90         9.80 
TCGA-J8-A3NZ TCGA-J8-A3YE TCGA-J8-A3YH TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J 
       17.23        27.85         5.75         0.20       143.57        15.68 
TCGA-KS-A4I1 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4EQ 
        6.02        32.45        87.39        84.72        33.40        40.37 
TCGA-L6-A4ET TCGA-MK-A4N7 TCGA-MK-A4N9 
       21.83        32.45         8.71 

subtype1 subtype2 subtype3 
    0.03     0.30     0.10 
subtype1 subtype2 subtype3 
  158.83   132.36   147.75 
subtype1 subtype2 subtype3 
  14.875   15.020   18.640 
[1] "0.0 - 158.8 (14.9)" "0.3 - 132.4 (15.0)" "0.1 - 147.8 (18.6)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      86        5        56        1        24         2
  subtype2      74       28        20        1         4         2
  subtype3     120       19        33        0        17         2
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         86       74      120
  STAGE II         5       28       19
  STAGE III       56       20       33
  STAGE IV         1        1        0
  STAGE IVA       24        4       17
  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 53 38 69 13
  subtype2 42 53 34  1
  subtype3 46 76 61  7
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       53       42       46
  T2       38       53       76
  T3       69       34       61
  T4       13        1        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"
D8V5, binary
          cls
clus         0   1
  subtype1  65 100
  subtype2  86  19
  subtype3  74 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65  100
  subtype2   86   19
  subtype3   74  102
   clus
vv  subtype1 subtype2 subtype3
  0       65       86       74
  1      100       19      102
[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 120   2  53
  subtype2  55   3  71
  subtype3  98   4  89
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      120       55       98
  M1        2        3        4
  MX       53       71       89
[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 133  42
  subtype2  92  38
  subtype3 139  52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  133   42
  subtype2   92   38
  subtype3  139   52
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      133       92      139
  MALE         42       38       52
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  subtype1              3                                           138
  subtype2              2                                            51
  subtype3              4                                           163
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      9
  subtype2                                                                     77
  subtype3                                                                     14
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  25
  subtype2                                                                   0
  subtype3                                                                  10
D8V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               138
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          25
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                51
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       77
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               163
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       14
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          10
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus         0   1
  subtype1   2 173
  subtype2   1 129
  subtype3  11 180
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  173
  subtype2    1  129
  subtype3   11  180
     clus
vv    subtype1 subtype2 subtype3
  NO         2        1       11
  YES      173      129      180
[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 149   6
  subtype2 107   5
  subtype3 161   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  149    6
  subtype2  107    5
  subtype3  161    6
     clus
vv    subtype1 subtype2 subtype3
  NO       149      107      161
  YES        6        5        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           66                      12   89                   1
  subtype2           15                       0  107                   0
  subtype3           48                       4  134                   0
D8V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  66       15       48
  MODERATE/ADVANCED (T4A)       12        0        4
  NONE                          89      107      134
  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 126  25   3  13
  subtype2 101   9   0   7
  subtype3 152  17   1  10
D8V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      126      101      152
  R1       25        9       17
  R2        3        0        1
  RX       13        7       10
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, continuous
D8V14, binary
          cls
clus        0  1
  subtype1 75 98
  subtype2 62 66
  subtype3 87 98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75   98
  subtype2   62   66
  subtype3   87   98
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       75       62       87
  UNIFOCAL         98       66       98
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    26                         6
  subtype2                                0     5                         8
  subtype3                                1    18                        12
          vv
clus       WHITE
  subtype1   127
  subtype2    70
  subtype3   125
D8V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  26        5       18
  BLACK OR AFRICAN AMERICAN               6        8       12
  WHITE                                 127       70      125
[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  13 139
  subtype2   8  74
  subtype3  17 137
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  139
  subtype2    8   74
  subtype3   17  137
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        8       17
  NOT HISPANIC OR LATINO      139       74      137
[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 146  10
  subtype2 162   2
  subtype3 140   2
subtype1 subtype2 subtype3 
     156      164      142 
subtype1 subtype2 subtype3 
      10        2        2 
$subtype1
TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
        4.01        20.71         2.79        11.31        17.52         1.22 
TCGA-BJ-A291 TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H 
       22.88        18.97        15.48        23.31         0.03         7.82 
TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A485 TCGA-DE-A4M8 TCGA-DE-A4MB TCGA-DE-A7U5 
        6.18         4.93         0.10        18.54        11.57         2.76 
TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH TCGA-DJ-A1QM TCGA-DJ-A1QO 
       14.07        11.01       100.01         7.99         1.45         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PT TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PY TCGA-DJ-A2PZ 
        5.95         9.60         8.28         7.69         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A3UM 
        9.34         9.21         8.61         7.07        10.36        31.04 
TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V0 
       19.56        17.69        43.00        11.34        21.37        25.02 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF 
       14.56        19.20        21.27        20.48        21.01         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-DO-A2HM 
       17.36        14.14        14.70        17.82        15.81         2.33 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A44K 
       14.07        14.43        14.70        14.10        14.96        13.78 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
       26.73       155.54        97.74         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D6 
      157.15        37.94        57.01         4.18         1.45       108.36 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3H7 
        1.41        30.18       102.84       124.04        52.73       139.00 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       57.63        17.52        52.50       147.42       130.72       129.57 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3ZK TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS 
        5.72        66.90        31.50        47.38        52.50         7.07 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 
       19.30        45.96        37.94        31.04        19.59        33.60 
TCGA-EL-A4KG TCGA-EM-A1CU TCGA-EM-A1YD TCGA-EM-A22P TCGA-EM-A2CR TCGA-EM-A2P1 
       13.32        20.91        57.01        11.15        13.64        17.46 
TCGA-EM-A2P3 TCGA-EM-A3FM TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A4FM TCGA-EM-A4FO 
       14.60        21.01        16.18        14.50         4.83         8.38 
TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A3BU 
       47.47        14.79        12.33        84.89        61.02        38.30 
TCGA-ET-A3BV TCGA-ET-A3DO TCGA-ET-A3DQ TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40Q 
       42.25        80.81        59.87        17.98        25.32         7.17 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SB 
        2.14         4.01        73.74        81.34        85.15         4.08 
TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3R6 TCGA-FY-A3R7 
       22.03        48.10        17.82         1.64         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A4B3 
        4.67         0.30         6.87         4.14         6.58         1.35 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A421 TCGA-IM-A3U2 TCGA-IM-A420 TCGA-IM-A4EB 
       12.53        17.00        20.05        10.26         2.96         8.65 
TCGA-J8-A3O2 TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-L6-A4EU TCGA-MK-A4N6 
       11.24        24.69        22.29         2.47         0.72        16.64 

$subtype2
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        18.21        16.34        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
        7.56        15.12        23.34        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28V TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PU 
        4.87        21.04         5.10        16.01        13.94        18.64 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN 
        0.10         0.20         0.23        15.42        36.46        15.85 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13X TCGA-DJ-A1QF 
      137.88         3.39         8.71        25.35         7.99        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QN TCGA-DJ-A2PN TCGA-DJ-A2PP 
       13.12        14.96         7.20         8.88        10.09         5.33 
TCGA-DJ-A2PR TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A3UR TCGA-DJ-A3VA TCGA-DJ-A3VB 
       10.45         8.12         6.77        36.33        11.93        22.92 
TCGA-DJ-A3VE TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
       18.97        17.23        27.62        54.90        21.53        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A417 TCGA-E8-A418 TCGA-EL-A3CP TCGA-EL-A3D1 TCGA-EL-A3D5 TCGA-EL-A3GO 
       14.27         3.02       158.83        74.30        33.47        39.32 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H2 TCGA-EL-A3H3 
       37.25       147.75       101.13       139.99        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T6 TCGA-EL-A3T8 TCGA-EL-A3TB 
       38.66       108.66        12.16        98.24        95.38        82.82 
TCGA-EL-A3ZH TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EM-A1CS 
       78.97        50.33        53.06        45.53        44.65        26.86 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A2CO 
       12.36        18.05        19.79        19.46        54.08         6.05 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P2 
       22.16        13.84        19.73        12.07        17.59        17.29 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FN 
        8.35        16.44        16.77        27.95        23.77        12.07 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       15.02        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
        7.82        29.69        32.35        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MZ TCGA-ET-A39K TCGA-ET-A39P TCGA-ET-A39R 
       29.49        54.05        12.26        80.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BW 
       55.10        59.15        28.24         2.43         5.56         2.37 
TCGA-ET-A3BX TCGA-ET-A3DR TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A40R TCGA-FE-A230 
        4.50        43.50       132.36         3.22         4.80        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        33.63        81.83       106.36        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SD TCGA-FY-A3BL TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON 
       46.06         0.89         1.15         0.99        16.14         1.51 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3WA TCGA-FY-A40N TCGA-H2-A3RH TCGA-H2-A3RI 
       16.57        18.08        17.06         0.89        12.46         2.99 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3O1 
       18.61        48.92        47.41         9.63        43.17        27.19 
TCGA-KS-A41F TCGA-KS-A41J 
      143.57        15.68 

$subtype3
TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A45C 
       30.21        18.38        16.57        20.48         7.04         5.75 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O9 
        6.48         3.45         6.35         5.06         8.98         5.98 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A2OL 
       11.38        10.68         0.10         0.39        20.22         5.98 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DJ-A2PO 
       18.84        30.12        30.02         4.27         3.22         7.99 
TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PX TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.48         1.51        12.56         5.52         9.44         9.90 
TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UN 
       10.09        12.43        10.85        15.88        15.09        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-DJ-A3UZ TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       31.46        16.41        24.23        12.76        20.22        30.61 
TCGA-DJ-A3VG TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4V2 TCGA-DJ-A4V5 
        8.32        18.21        10.78        10.98         3.12        24.33 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3GV TCGA-EL-A3H1 
        7.69        20.68        13.58        31.66        50.37        49.32 
TCGA-EL-A3H8 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T7 TCGA-EL-A3ZG TCGA-EL-A3ZR 
      131.15        32.48       116.91        41.29        77.36        48.16 
TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       45.80        30.51        28.73        41.13        37.78        29.95 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       11.87         8.71        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        10.65        11.74        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       13.18        23.51         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SZ 
       13.15        17.49        17.39        11.51        16.41        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
       70.65        16.90         8.61         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       12.72         0.95        22.09        16.08        29.19        19.76 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39N TCGA-ET-A3BO TCGA-ET-A3BP 
       58.22        13.74        71.01        98.56         5.85         4.18 
TCGA-ET-A3DP TCGA-ET-A3DS TCGA-ET-A40S TCGA-ET-A4KQ TCGA-FK-A3SG TCGA-FK-A4UB 
       69.24         0.30         5.03         1.94         0.92        91.17 
TCGA-FY-A2QD TCGA-FY-A3W9 TCGA-FY-A40M TCGA-FY-A4B4 TCGA-FY-A76V TCGA-H2-A2K9 
        1.25         0.76         4.54         1.15         1.68        21.67 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-J8-A3NZ TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YH 
       16.90         9.80        17.23        31.82        27.85         5.75 
TCGA-J8-A4HW TCGA-KS-A41I TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
        2.60        15.98         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       87.39        35.28        33.24        33.40        40.37        21.83 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

subtype1 subtype2 subtype3 
    0.03     0.10     0.10 
subtype1 subtype2 subtype3 
  157.15   158.83   131.15 
subtype1 subtype2 subtype3 
   15.22    18.56    13.99 
[1] "0.0 - 157.2 (15.2)" "0.1 - 158.8 (18.6)" "0.1 - 131.2 (14.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      77        6        51        1        21         2
  subtype2     105       27        21        0         8         2
  subtype3      82       17        30        1        11         2
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         77      105       82
  STAGE II         6       27       17
  STAGE III       51       21       30
  STAGE IV         1        0        1
  STAGE IVA       21        8       11
  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 41 36 67 13
  subtype2 47 66 45  5
  subtype3 46 55 40  2
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       41       47       46
  T2       36       66       55
  T3       67       45       40
  T4       13        5        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"
D9V5, binary
          cls
clus        0  1
  subtype1 58 93
  subtype2 87 58
  subtype3 66 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58   93
  subtype2   87   58
  subtype3   66   57
   clus
vv  subtype1 subtype2 subtype3
  0       58       87       66
  1       93       58       57
[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 105   2  51
  subtype2  71   4  89
  subtype3  81   3  59
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      105       71       81
  M1        2        4        3
  MX       51       89       59
[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 118  40
  subtype2 119  45
  subtype3 105  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  118   40
  subtype2  119   45
  subtype3  105   39
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      118      119      105
  MALE         40       45       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              3                                           124
  subtype2              2                                           113
  subtype3              4                                            99
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      7
  subtype2                                                                     46
  subtype3                                                                     37
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  24
  subtype2                                                                   3
  subtype3                                                                   4
D9V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               124
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          24
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               113
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       46
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           3
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                99
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       37
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           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"
D9V9, binary
          cls
clus         0   1
  subtype1   2 156
  subtype2  12 152
  subtype3   0 144
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  156
  subtype2   12  152
  subtype3    0  144
     clus
vv    subtype1 subtype2 subtype3
  NO         2       12        0
  YES      156      152      144
[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 132   5
  subtype2 136   8
  subtype3 124   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  132    5
  subtype2  136    8
  subtype3  124    3
     clus
vv    subtype1 subtype2 subtype3
  NO       132      136      124
  YES        5        8        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           60                      12   78                   1
  subtype2           30                       2  127                   0
  subtype3           32                       1  104                   0
D9V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  60       30       32
  MODERATE/ADVANCED (T4A)       12        2        1
  NONE                          78      127      104
  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 110  24   3   9
  subtype2 137   9   1  11
  subtype3 108  15   0   9
D9V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      110      137      108
  R1       24        9       15
  R2        3        1        0
  RX        9       11        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
D9V14, binary
          cls
clus        0  1
  subtype1 74 84
  subtype2 71 87
  subtype3 68 74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   74   84
  subtype2   71   87
  subtype3   68   74
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       74       71       68
  UNIFOCAL         84       87       74
[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    18                         5
  subtype2                                0    11                         7
  subtype3                                1    17                        13
          vv
clus       WHITE
  subtype1   121
  subtype2   106
  subtype3    77
D9V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  18       11       17
  BLACK OR AFRICAN AMERICAN               5        7       13
  WHITE                                 121      106       77
[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  14 128
  subtype2  12 114
  subtype3   9  90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  128
  subtype2   12  114
  subtype3    9   90
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           14       12        9
  NOT HISPANIC OR LATINO      128      114       90
[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 150  10
  subtype2 123   3
  subtype3 175   1
subtype1 subtype2 subtype3 
     160      126      176 
subtype1 subtype2 subtype3 
      10        3        1 
$subtype1
TCGA-BJ-A0ZB TCGA-BJ-A18Z TCGA-BJ-A28T TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
        4.01        20.71         2.79        11.31        17.52         1.22 
TCGA-BJ-A291 TCGA-BJ-A2NA TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A45E TCGA-BJ-A45H 
       22.88        18.97        15.48        23.31         0.03         7.82 
TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-CE-A27D TCGA-CE-A481 TCGA-CE-A485 TCGA-DE-A4M8 
        6.18         4.93         0.10        11.38         0.10        18.54 
TCGA-DE-A4MB TCGA-DE-A7U5 TCGA-DJ-A13O TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QH 
       11.57         2.76        14.07        11.01       100.01         7.99 
TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PV 
        1.45         1.02         5.95         1.51         9.60         8.28 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 
        8.78         8.42         9.34         9.21         8.61         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UU TCGA-DJ-A3UW 
       10.36        12.43        31.04        19.56        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       11.34        21.37        12.76        25.02        14.56        19.20 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VD TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A4UQ 
       21.27        20.48        21.01         7.76        17.36        10.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A2HM 
       14.14        14.70        17.82        15.81        24.33         2.33 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       14.07        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CO TCGA-EL-A3CR TCGA-EL-A3CS 
       13.78        13.58        26.73        97.74         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3D0 
       60.95       157.15        37.94        57.01         4.18         1.45 
TCGA-EL-A3D1 TCGA-EL-A3GP TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3H7 
       74.30         1.41       102.84       124.04        52.73       139.00 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T9 
       57.63        17.52        52.50       147.42       130.72         5.72 
TCGA-EL-A3TA TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZS 
       66.90        31.50        53.06        47.38        52.50         7.07 
TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K4 TCGA-EM-A1YD 
       19.30        37.94        31.04        19.59        33.60        57.01 
TCGA-EM-A22P TCGA-EM-A2CU TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AR TCGA-EM-A3O3 
       11.15        13.15        17.46        14.60        16.77        14.50 
TCGA-EM-A4FM TCGA-EM-A4FO TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25R 
        4.83         8.38        47.47        14.79        12.33        29.49 
TCGA-ET-A2N0 TCGA-ET-A39M TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A3BN TCGA-ET-A3BV 
       16.08        84.89        58.72        55.10        28.24        42.25 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A40Q TCGA-ET-A40T 
       59.87        43.50        17.98        25.32         7.17         2.14 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A237 TCGA-FE-A3PB TCGA-FK-A3SE TCGA-FK-A3SH 
        4.01        73.74        81.34        85.15        22.03        48.10 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3TY TCGA-FY-A3YR 
       17.82         1.64         0.76         0.03         0.30         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U 
        4.14         6.58         1.35         1.15        12.53        17.00 
TCGA-IM-A3U2 TCGA-IM-A4EB TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF TCGA-J8-A3YG 
       10.26         8.65        11.24        31.82        24.69        22.29 
TCGA-J8-A4HW TCGA-KS-A4I3 TCGA-KS-A4IC TCGA-L6-A4EU 
        2.60        12.43        35.28         0.72 

$subtype2
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        18.21        16.34        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-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3F0 
        5.10        18.38        16.57        20.48         7.04        13.94 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45K TCGA-CE-A484 
        5.75         6.48         3.45         6.35         8.98         0.39 
TCGA-DE-A2OL TCGA-DE-A4M9 TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A1QL 
        5.98        18.84         3.39         8.71        13.12         7.20 
TCGA-DJ-A2PP TCGA-DJ-A2Q0 TCGA-DJ-A2Q2 TCGA-DJ-A2Q4 TCGA-DJ-A2QB TCGA-DJ-A3UP 
        5.33         8.12         6.77         9.44        10.85        16.41 
TCGA-DJ-A3UT TCGA-DJ-A3VG TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-DO-A1JZ 
       24.23         8.32        17.23        27.62        10.98        54.90 
TCGA-E3-A3DZ TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 
       12.07        33.47        39.32        37.25        49.32        33.50 
TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 
       32.48        78.97        48.16        45.80        30.51        28.73 
TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KI TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       41.13        29.95         8.71        18.05        19.79        19.46 
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-A2P2 
       12.30        13.64        10.49        22.16        13.84        17.29 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AP TCGA-EM-A3FN TCGA-EM-A3FP 
       17.46        18.97        14.14         8.35        12.07        17.39 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       15.02        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A4FH TCGA-EM-A4FR TCGA-EM-A4FU 
        7.82        11.51        16.41        16.90         5.03        37.87 
TCGA-EM-A4G1 TCGA-ET-A25P TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I 
        0.95        18.38        29.19        19.76        58.22        13.74 
TCGA-ET-A39N TCGA-ET-A39T TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40P TCGA-ET-A4KQ 
       98.56        59.15         0.30       132.36         3.22         1.94 
TCGA-FE-A236 TCGA-FE-A239 TCGA-FK-A3SD TCGA-FY-A2QD TCGA-FY-A3NM TCGA-FY-A3NP 
       66.77        33.63         0.89         1.25         0.99        16.14 
TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40M TCGA-FY-A76V TCGA-H2-A2K9 
       16.57         0.76        17.06         4.54         1.68        21.67 
TCGA-H2-A3RH TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-KS-A41I TCGA-MK-A84Z TCGA-QD-A8IV 
       12.46         9.63        43.17        15.98        10.98         5.19 

$subtype3
TCGA-BJ-A0ZH TCGA-BJ-A28R TCGA-BJ-A290 TCGA-BJ-A3EZ TCGA-BJ-A3PU TCGA-BJ-A45J 
       15.12         4.87        30.21        16.01        18.64         5.06 
TCGA-BJ-A4O9 TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A483 TCGA-DE-A0XZ 
        5.98         0.20         0.23        10.68         0.10        20.22 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A69J 
       15.42        36.46        15.85        30.12        30.02         4.27 
TCGA-DE-A69K TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13X TCGA-DJ-A1QF TCGA-DJ-A1QI 
        3.22       137.88        25.35         7.99        18.51        14.96 
TCGA-DJ-A1QN TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PU 
        8.88        10.09         7.99         8.48        10.45        12.56 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.69         5.52         9.90        10.09        15.88        15.09 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UR TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3VA 
       12.49        31.46        36.33        20.22        30.61        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A4UL TCGA-DJ-A4V2 TCGA-DO-A1K0 TCGA-E3-A3DY 
       22.92        18.97        18.21         3.12        21.53        31.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A417 
       66.38        40.21        63.19        30.31        14.04        14.27 
TCGA-E8-A418 TCGA-E8-A438 TCGA-EL-A3CL TCGA-EL-A3CN TCGA-EL-A3CP TCGA-EL-A3D6 
        3.02        20.68        31.66       155.54       158.83       108.36 
TCGA-EL-A3GQ TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H3 
       30.18        50.37       147.75       101.13       139.99        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3N2 TCGA-EL-A3T1 TCGA-EL-A3T3 
       38.66       131.15       108.66        12.16       129.57       116.91 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZL 
       98.24        41.29        95.38        82.82        77.36        50.33 
TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JX TCGA-EL-A4K9 TCGA-EL-A4KG TCGA-EL-A4KH 
       45.53        44.65        45.96        37.78        13.32        11.87 
TCGA-EM-A1CS TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O 
       26.86        20.91        12.36        14.73        14.53        11.74 
TCGA-EM-A2CS TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A3AK TCGA-EM-A3AN 
       15.19        19.73        12.07        17.59        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-A3FQ TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV 
       16.18        12.79        70.65         8.61         9.80        12.72 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A2MX TCGA-ET-A2MY 
       29.69        32.35        14.79        27.09        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A3BO 
       12.26        71.01        80.02        61.02        57.11         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-A40R TCGA-ET-A40S TCGA-FE-A230 TCGA-FE-A231 
       80.81        69.24         4.80         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-A3S3 TCGA-FK-A3SB TCGA-FK-A3SG 
      106.36        85.68        78.77        46.06         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-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-A3O1 TCGA-J8-A3YE TCGA-J8-A3YH 
        9.80         2.96        17.23        27.19        27.85         5.75 
TCGA-J8-A42S TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 
        2.47       143.57        15.68         6.02         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 
       87.39        33.24        33.40        40.37        21.83        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

subtype1 subtype2 subtype3 
    0.03     0.30     0.10 
subtype1 subtype2 subtype3 
  157.15   132.36   158.83 
subtype1 subtype2 subtype3 
   14.70    14.19    19.89 
[1] "0.0 - 157.2 (14.7)" "0.3 - 132.4 (14.2)" "0.1 - 158.8 (19.9)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  subtype1      75        4        57        1        22         2
  subtype2      70       27        23        1         3         2
  subtype3     119       19        22        0        15         2
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         75       70      119
  STAGE II         4       27       19
  STAGE III       57       23       22
  STAGE IV         1        1        0
  STAGE IVA       22        3       15
  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 45 34 67 13
  subtype2 39 54 33  1
  subtype3 50 69 52  6
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       45       39       50
  T2       34       54       69
  T3       67       33       52
  T4       13        1        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"
D10V5, binary
          cls
clus        0  1
  subtype1 58 95
  subtype2 80 22
  subtype3 73 91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58   95
  subtype2   80   22
  subtype3   73   91
   clus
vv  subtype1 subtype2 subtype3
  0       58       80       73
  1       95       22       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 110   2  49
  subtype2  51   3  72
  subtype3  96   4  78
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      110       51       96
  M1        2        3        4
  MX       49       72       78
[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"
D10V7, binary
          cls
clus         0   1
  subtype1 123  38
  subtype2  85  42
  subtype3 134  44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  123   38
  subtype2   85   42
  subtype3  134   44
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      123       85      134
  MALE         38       42       44
[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              3                                           127
  subtype2              2                                            56
  subtype3              4                                           153
          vv
clus       THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  subtype1                                                                      7
  subtype2                                                                     69
  subtype3                                                                     14
          vv
clus       THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  subtype1                                                                  24
  subtype2                                                                   0
  subtype3                                                                   7
D10V8, multiclass
                                                                        clus
vv                                                                       subtype1
  OTHER  SPECIFY                                                                3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               127
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)        7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)          24
                                                                        clus
vv                                                                       subtype2
  OTHER  SPECIFY                                                                2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                56
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       69
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           0
                                                                        clus
vv                                                                       subtype3
  OTHER  SPECIFY                                                                4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                               153
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)       14
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)           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"
D10V9, binary
          cls
clus         0   1
  subtype1   2 159
  subtype2   3 124
  subtype3   9 169
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  159
  subtype2    3  124
  subtype3    9  169
     clus
vv    subtype1 subtype2 subtype3
  NO         2        3        9
  YES      159      124      169
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
          cls
clus         0   1
  subtype1 135   6
  subtype2 106   5
  subtype3 151   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  135    6
  subtype2  106    5
  subtype3  151    5
     clus
vv    subtype1 subtype2 subtype3
  NO       135      106      151
  YES        6        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           62                      12   79                   1
  subtype2           17                       0  103                   0
  subtype3           43                       3  127                   0
D10V11, multiclass
                         clus
vv                        subtype1 subtype2 subtype3
  MINIMAL (T3)                  62       17       43
  MODERATE/ADVANCED (T4A)       12        0        3
  NONE                          79      103      127
  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 112  26   2  11
  subtype2  97   9   0   9
  subtype3 146  13   2   9
D10V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      112       97      146
  R1       26        9       13
  R2        2        0        2
  RX       11        9        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
D10V14, binary
          cls
clus        0  1
  subtype1 71 89
  subtype2 62 62
  subtype3 80 94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   71   89
  subtype2   62   62
  subtype3   80   94
            clus
vv           subtype1 subtype2 subtype3
  MULTIFOCAL       71       62       80
  UNIFOCAL         89       62       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"
D10V15, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    25                         4
  subtype2                                0     6                         9
  subtype3                                1    15                        12
          vv
clus       WHITE
  subtype1   119
  subtype2    68
  subtype3   117
D10V16, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  25        6       15
  BLACK OR AFRICAN AMERICAN               4        9       12
  WHITE                                 119       68      117
[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"
D10V17, binary
          cls
clus         0   1
  subtype1  10 133
  subtype2   7  77
  subtype3  18 122
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  133
  subtype2    7   77
  subtype3   18  122
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           10        7       18
  NOT HISPANIC OR LATINO      133       77      122
[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"
