[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"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[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_Correlate_Genomic_Events_Preprocess/THCA-TP/10685822/transformed.cor.cli.txt"

nPatients in clinical file=497, in cluster file=401, common to both=398
[1] "Reduce the number of clustering variables from 12 to 11."
[1]  11 398
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
           238            160 
  BRAF MUTATED BRAF WILD-TYPE 
           238            160 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            34            364 
  NRAS MUTATED NRAS WILD-TYPE 
            34            364 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            14            384 
  HRAS MUTATED HRAS WILD-TYPE 
            14            384 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              392 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              392 
[1] "NUP93 MUTATION ANALYSIS"
[1] 3
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             394 
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             394 
[1] "PPM1D MUTATION ANALYSIS"
[1] 3
  PPM1D MUTATED PPM1D WILD-TYPE 
              5             393 
  PPM1D MUTATED PPM1D WILD-TYPE 
              5             393 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               3              395 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               3              395 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             4            394 
  KRAS MUTATED KRAS WILD-TYPE 
             4            394 
[1] "DLC1 MUTATION ANALYSIS"
[1] 3
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            394 
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            394 
[1] "ITGAL MUTATION ANALYSIS"
[1] 3
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             394 
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             394 
[1] "NLRP6 MUTATION ANALYSIS"
[1] 3
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             395 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             395 
[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 398 columns.

[1] "Batch" "24"   
[1] "Last Follow UP"
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
         754          419          554          497          251          574 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
         122          352          509          230          460          538 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
         710          630          147          246          148          640 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 
          85          155          533           37          919          559 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 
         504          623          577          214          487          424 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
         471          709          567          197            1          105 
TCGA-BJ-A45G TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
         193          188          154          273          150          182 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
          16            3            6            7          325           12 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
           3          615          469         1109          182          482 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
         564          573          525          428         4194          103 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
         265          771          408          362          444          243 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
         335         3042          563          399          243          455 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
         219           44          270           31          181          307 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
         243          162          258          318           46          292 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
         382          252          234          168          267          256 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
         247          284          206          280          287          301 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
         262          307          215          315          378          330 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
         483          459          944          380          957          499 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
         595         1105          998          737          538         1308 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
         345          650          299          363          697          577 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UT 
         236          528          524          840          554          430 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
         447          542           95          481          740         1670 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
         655           71          945          367         2019         1223 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 
        1922          922          427           35          678          414 
TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 
         420           92           NA          447          455          234 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
         419          413           NA           NA         4731           NA 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
        4831           NA           NA           NA         4780         1154 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
          NA         2461          127         1789           44         2260 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
        1381         1018         3296         1196           43          918 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
        3128         1989         3773         1532         1133         4494 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
        3076         4258           NA           NA         1319         1176 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
        1604         4228         3989         3305           NA           NA 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
          NA          370         4484         3976         3941          988 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
        3556         2988         1256         2901           NA         2035 
TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR 
        2519         2402          958         1614         1385         1465 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
        1358         1393          587         1398         1154          944 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
         928         1022          874          911          405          361 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
         265          817          553          636          376          549 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
         602          592         1649         1734         1645          448 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
         441          479          318          442          324          357 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
         339          433          500          544          401          715 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU 
         184           91          374          415          319          400 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
         674          421          600          535          367          535 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
         531          526          444          531          577          477 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
         430          597          407          254          500          510 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
         850          723          511          639          367          532 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
         529          492          457          441          339          223 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM 
         381          281          423          238          274          147 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
         255          298          153          387           29         1444 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY 
        1466          903          984          824          897          672 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
         373          489          888           81         1771          418 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
        2160         2434         1988         2582         2998         1856 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
        1786         1737         1676         1799          859          178 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
         127           74          169          752         1165         1285 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
          72          137         2458         2106         1821         1323 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S 
           9          547          770         4026          752          153 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
         122         2243         1816          961         1346          751 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB 
        2075         3130         2031         2474         2489         2590 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
        2606         2396         1401          124           27          670 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
          28         1463           38           35          542           50 
TCGA-FY-A3NM TCGA-FY-A3NN TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
          30           NA          491           46           23            1 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K 
         142          504          550           23          519          126 
TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
          41          381          517          659          379           91 
TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ 
         610         1488         1442          312          514          524 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 
        1313          827          847           79          477          205 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
        2658         2577         1016          664           22          506 
TCGA-MK-A4N7 TCGA-MK-A4N9 
         987          265 
Variable 1:'AGE':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=341,	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=18,	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=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR.SIZE':	nDistinctValues=67,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'BATCH.NUMBER':	nDistinctValues=23,	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 398 columns, 1 survival variables, and 16 non-survival variables.
AGE, nv=70, 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 
116 137 127  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
116 137 127  15 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
116 137 127  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
116 137 127  15 
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=28, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR.SIZE, nv=67, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = BRAF MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  BRAF MUTATED   227   9
  BRAF WILD-TYPE 156   4
  BRAF MUTATED BRAF WILD-TYPE 
           236            160 
  BRAF MUTATED BRAF WILD-TYPE 
             9              4 
$`BRAF MUTATED`
TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A18Z TCGA-BJ-A28R 
       16.34         8.25         4.01        15.12        20.71         4.87 
TCGA-BJ-A28S TCGA-BJ-A28X TCGA-BJ-A290 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3PR 
       21.04        17.52        30.21        18.97        16.01        15.48 
TCGA-BJ-A3PU TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A3ME 
       18.64         6.18         5.06         4.93         5.98         0.23 
TCGA-DE-A0XZ TCGA-DE-A0Y3 TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13T TCGA-DJ-A13U 
       20.22        36.46        14.07       137.88        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH 
       11.90         7.99        11.01       100.01        18.51         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.28         7.69         8.78         8.42         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QC 
        9.90         8.61        10.09        10.36        12.43        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       15.09        31.04        12.49        31.46        19.56        36.33 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA 
       17.69        43.00        11.34        21.37         9.83        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL 
       22.92        18.97         7.76        17.36        17.23        18.21 
TCGA-DJ-A4UW TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       14.70         3.12        15.81        21.53         2.33        31.07 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 
       13.61        13.81         3.02        14.70        14.96         7.69 
TCGA-E8-A44K TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CP TCGA-EL-A3CR 
       13.78        31.66        26.73       155.54       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3D0 
       45.53        60.95       157.15        37.94        57.01         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
       74.30       108.36         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H4 
      124.04        50.37       147.75       101.13       139.99        38.66 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       52.73       139.00       131.15       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 
       52.50        12.16       147.42       129.57       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JW 
       41.29        95.38        66.90        45.53        44.65        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K4 TCGA-EL-A4KG TCGA-EL-A4KH 
       45.96        37.94        31.04        33.60        13.32        11.87 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O 
       18.18        20.91        12.36        14.73        14.53        11.74 
TCGA-EM-A22P TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       11.15        19.73        12.07        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AK TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM 
       14.60        15.68        16.77        27.95        23.77        21.01 
TCGA-EM-A3FO TCGA-EM-A3O3 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A4FM TCGA-EM-A4FO 
       17.49        14.50         7.33        12.53         4.83         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O 
        9.80        12.72        47.47        29.69        32.35        27.09 
TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N4 TCGA-ET-A39J 
       29.49        22.09        12.26        16.08         2.66        71.01 
TCGA-ET-A39K TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A39T 
       80.02        84.89        61.02        58.72        55.10        59.15 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DT 
       42.25         2.37         4.50        80.81        69.24        17.98 
TCGA-ET-A3DU TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       25.32        24.72        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A 
       24.69        68.22       102.90        66.77        81.34        81.83 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FK-A3SB TCGA-FK-A3SH TCGA-FY-A3BL TCGA-FY-A3I4 
       85.15        85.68         4.08        48.10         1.15        17.82 
TCGA-FY-A3ON TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A40K TCGA-FY-A4B3 
        1.51         0.03         4.67        18.08         4.14         1.35 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.53        17.00         2.99        20.05        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3YE TCGA-KS-A41J TCGA-KS-A4I5 
       10.26        16.90        17.23        27.85        15.68         6.74 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       87.39        84.72        33.40        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

$`BRAF WILD-TYPE`
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-A191 TCGA-BJ-A192 TCGA-BJ-A28T 
        7.56        17.69        23.34         4.83         8.09         2.79 
TCGA-BJ-A28V TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 
        5.10         1.22        18.38        16.57        20.48         7.04 
TCGA-BJ-A3F0 TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       13.94        23.31         6.48         0.03         3.45         6.35 
TCGA-BJ-A45K TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A482 TCGA-CE-A484 
        8.98         0.53         0.10         0.20        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
        0.10        15.42         5.98        15.85        18.54        18.84 
TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL 
       17.26         3.39         8.71        14.60        13.12         7.20 
TCGA-DJ-A2PP TCGA-DJ-A2PX TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q8 
        5.33         5.52         8.12         9.34         6.77         7.07 
TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3VM TCGA-DJ-A4UT 
       10.85        16.41        32.81        24.23        27.62        14.14 
TCGA-DJ-A4V0 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E8-A44M 
       17.82        24.33        54.90        12.07        66.38        13.58 
TCGA-EL-A3CO TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D4 TCGA-EL-A3D5 
       97.74        80.91         4.18        58.82        45.40        33.47 
TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3T0 
       39.32        37.25        49.32        33.50        43.36       130.72 
TCGA-EL-A3T2 TCGA-EL-A3T9 TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
       32.48         5.72        82.82        78.97        31.50        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-A1CS TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       26.86        18.05        19.79        19.46        54.21        57.01 
TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22Q 
       54.08        14.50        15.75        10.45        10.65        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        13.64        10.49        13.15        22.16        13.84 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       17.59        17.46        18.97        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ 
        8.35        16.44        16.80        12.07        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK 
       15.02        11.15         9.24        13.91         7.82         9.01 
TCGA-EM-A4FR TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A2N1 TCGA-ET-A2N5 TCGA-ET-A39I 
        5.03         0.95        48.20        29.19        58.22        13.74 
TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39R TCGA-ET-A3BN TCGA-ET-A3DQ TCGA-ET-A3DR 
       65.36        98.56        57.11        28.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A3PD TCGA-FK-A3S3 
        0.30       132.36         5.03         4.01        78.77        46.06 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FY-A2QD TCGA-FY-A3I5 TCGA-FY-A3NM 
        0.89        22.03         0.92         1.25         1.64         0.99 
TCGA-FY-A3NP TCGA-FY-A3R6 TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-H2-A2K9 
       16.14         0.76        16.57         0.76        17.06        21.67 
TCGA-H2-A3RH TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A4HW 
       12.46        43.17        27.19         2.60 

  BRAF MUTATED BRAF WILD-TYPE 
          0.03           0.03 
  BRAF MUTATED BRAF WILD-TYPE 
        158.83         132.36 
  BRAF MUTATED BRAF WILD-TYPE 
        17.640         15.995 
[1] "0.0 - 158.8 (17.6)" "0.0 - 132.4 (16.0)"
[1] "hr=" "1.1"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  BRAF MUTATED       130       18        59        0        26         4
  BRAF WILD-TYPE      98       26        24        2         7         2
D1V3, multiclass
           clus
vv          BRAF MUTATED BRAF WILD-TYPE
  STAGE I            130             98
  STAGE II            18             26
  STAGE III           59             24
  STAGE IV             0              2
  STAGE IVA           26              7
  STAGE IVC            4              2
[1] 6 2
[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
  BRAF MUTATED   68 66 89 13
  BRAF WILD-TYPE 48 71 38  2
D1V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1           68             48
  T2           66             71
  T3           89             38
  T4           13              2
[1] 4 2
[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
  BRAF MUTATED    98 119
  BRAF WILD-TYPE  90  50
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     98  119
  BRAF WILD-TYPE   90   50
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0           98             90
  1          119             50
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  BRAF MUTATED   140   5  93
  BRAF WILD-TYPE  79   2  78
D1V6, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  M0          140             79
  M1            5              2
  MX           93             78
[1] 3 2
[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
  BRAF MUTATED   173  65
  BRAF WILD-TYPE 124  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    173   65
  BRAF WILD-TYPE  124   36
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE          173            124
  MALE             65             36
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  BRAF MUTATED                3                                           193
  BRAF WILD-TYPE              3                                            87
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  BRAF MUTATED                                                                       15
  BRAF WILD-TYPE                                                                     68
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  BRAF MUTATED                                                                    27
  BRAF WILD-TYPE                                                                   2
D1V8, multiclass
                                                                        clus
vv                                                                       BRAF MUTATED
  OTHER  SPECIFY                                                                    3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                   193
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)           15
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)              27
                                                                        clus
vv                                                                       BRAF WILD-TYPE
  OTHER  SPECIFY                                                                      3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      87
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             68
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 2
[1] 4 2
[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
  BRAF MUTATED    11 227
  BRAF WILD-TYPE   1 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     11  227
  BRAF WILD-TYPE    1  159
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            11              1
  YES          227            159
[1] 2 2
[1] FALSE
D1V10, binary
                cls
clus               0   1
  BRAF MUTATED   204   8
  BRAF WILD-TYPE 130   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    204    8
  BRAF WILD-TYPE  130    7
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO           204            130
  YES            8              7
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  BRAF MUTATED             79                      11  142                   0
  BRAF WILD-TYPE           23                       0  128                   1
D1V11, multiclass
                         clus
vv                        BRAF MUTATED BRAF WILD-TYPE
  MINIMAL (T3)                      79             23
  MODERATE/ADVANCED (T4A)           11              0
  NONE                             142            128
  VERY ADVANCED (T4B)                0              1
[1] 4 2
[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
  BRAF MUTATED   183  25   3  15
  BRAF WILD-TYPE 128  12   0   7
D1V12, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0          183            128
  R1           25             12
  R2            3              0
  RX           15              7
[1] 4 2
[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
  BRAF MUTATED   108 127
  BRAF WILD-TYPE  72  82
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    108  127
  BRAF WILD-TYPE   72   82
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  MULTIFOCAL          108             72
  UNIFOCAL            127             82
[1] 2 2
[1] FALSE
D1V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED      22                        11   168
  BRAF WILD-TYPE    13                         7    90
D1V16, multiclass
                           clus
vv                          BRAF MUTATED BRAF WILD-TYPE
  ASIAN                               22             13
  BLACK OR AFRICAN AMERICAN           11              7
  WHITE                              168             90
[1] 3 2
[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
  BRAF MUTATED    22 179
  BRAF WILD-TYPE   9 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     22  179
  BRAF WILD-TYPE    9  104
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO               22              9
  NOT HISPANIC OR LATINO          179            104
[1] 2 2
[1] FALSE

Clustering(2) Variable = NRAS MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  NRAS MUTATED    34   0
  NRAS WILD-TYPE 349  13
  NRAS MUTATED NRAS WILD-TYPE 
            34            362 
  NRAS MUTATED NRAS WILD-TYPE 
             0             13 
$`NRAS MUTATED`
TCGA-BJ-A0ZA TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A3PT TCGA-BJ-A45F TCGA-BJ-A45G 
       18.87        18.38        16.57        23.31         3.45         6.35 
TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A2PP TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-EL-A3GW 
        8.71        13.12         5.33        16.41        24.23        37.25 
TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A22J 
       32.48        78.97        30.51        28.73         8.71        14.50 
TCGA-EM-A22L TCGA-EM-A22Q TCGA-EM-A2CN TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A3AP 
       10.45        14.24        23.51        13.64        10.49         8.35 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4G1 TCGA-ET-A25I TCGA-FY-A3NP 
       13.91         7.82         9.01         0.95        48.20        16.14 
TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-H2-A2K9 TCGA-J8-A3O0 
       16.57         0.76        21.67        43.17 

$`NRAS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB 
       24.79        13.78        18.21        16.34         8.25         4.01 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
       11.57        16.73         7.56        15.12        17.69        23.34 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.71         4.83         8.09         4.87        21.04         2.79 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
        5.10        17.52         1.22        30.21        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU TCGA-BJ-A45D 
        7.04        16.01        13.94        15.48        18.64         6.48 
TCGA-BJ-A45E TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        0.03         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
        0.53         0.10         0.20         0.23        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       18.54        18.84        17.26        14.07       137.88         3.39 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       25.35        13.41        11.90        14.60         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
      100.01        18.51         7.99        14.96         7.20         1.45 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ 
        8.88         1.02         5.95        10.09         7.99         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UU 
       12.49        31.46        19.56        36.33        32.81        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       43.00        11.34        21.37         9.83        11.93        22.92 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
       18.97         7.76        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 
       13.61        13.81         3.02        14.70        14.96         7.69 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01        80.91         4.18        58.82         1.45        74.30 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        33.47       108.36        39.32         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY 
      102.84        65.39       124.04        50.37       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      139.99        49.32        33.50        43.36        38.66        52.73 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 
       12.16       147.42       130.72       129.57       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZK 
       41.29        95.38         5.72        66.90        82.82        31.50 
TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       53.06        45.53        48.16        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K4 TCGA-EL-A4KD TCGA-EL-A4KG 
       45.96        37.94        31.04        33.60        29.95        13.32 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       11.87        26.86        18.18        20.91        12.36        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        54.21        57.01        54.08        14.73 
TCGA-EM-A22K TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ 
       15.75        14.53        10.65        11.74        11.15        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CU 
       17.88        13.18         6.05         2.99        12.30        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        19.73        17.59        12.07        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        17.46        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-A3FO TCGA-EM-A3FP 
       23.77        16.80        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        11.15         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV 
        9.24         4.83         8.38         9.80         5.03        12.72 
TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY 
       47.47        29.69        32.35        27.09        29.49        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       12.26        16.08        29.19         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S 
        0.30        17.98        25.32       132.36        24.72         5.03 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        4.01        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB 
       68.22       102.90        66.77        81.34        81.83        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
        0.92        48.10         1.25         1.15        17.82         1.64 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3RA 
        0.99         1.51         0.76         0.03         4.67        18.08 
TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A3RH 
       17.06         4.14         1.35        12.53        17.00        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
        2.99        20.05        48.92        47.41        10.26        16.90 
TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 
       17.23        27.19        27.85         2.60        15.68         6.74 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       87.39        84.72        33.40        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

  NRAS MUTATED NRAS WILD-TYPE 
          0.76           0.03 
  NRAS MUTATED NRAS WILD-TYPE 
         78.97         158.83 
  NRAS MUTATED NRAS WILD-TYPE 
        15.320         17.275 
[1] "0.8 - 79.0 (15.3)"  "0.0 - 158.8 (17.3)"
[1] "hr="     "2.7e+07"
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  NRAS MUTATED        22        6         4        1         0         1
  NRAS WILD-TYPE     206       38        79        1        33         5
D2V3, multiclass
           clus
vv          NRAS MUTATED NRAS WILD-TYPE
  STAGE I             22            206
  STAGE II             6             38
  STAGE III            4             79
  STAGE IV             1              1
  STAGE IVA            0             33
  STAGE IVC            1              5
[1] 6 2
[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
  NRAS MUTATED    10  17   6   1
  NRAS WILD-TYPE 106 120 121  14
D2V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1           10            106
  T2           17            120
  T3            6            121
  T4            1             14
[1] 4 2
[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
  NRAS MUTATED    27   5
  NRAS WILD-TYPE 161 164
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     27    5
  NRAS WILD-TYPE  161  164
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0           27            161
  1            5            164
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  NRAS MUTATED    17   1  16
  NRAS WILD-TYPE 202   6 155
D2V6, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  M0           17            202
  M1            1              6
  MX           16            155
[1] 3 2
[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
  NRAS MUTATED    25   9
  NRAS WILD-TYPE 272  92
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     25    9
  NRAS WILD-TYPE  272   92
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE           25            272
  MALE              9             92
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  NRAS MUTATED                0                                            15
  NRAS WILD-TYPE              6                                           265
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  NRAS MUTATED                                                                       19
  NRAS WILD-TYPE                                                                     64
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  NRAS MUTATED                                                                     0
  NRAS WILD-TYPE                                                                  29
D2V8, multiclass
                                                                        clus
vv                                                                       NRAS MUTATED
  OTHER  SPECIFY                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                    15
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)           19
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       NRAS WILD-TYPE
  OTHER  SPECIFY                                                                      6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     265
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             64
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                29
[1] 4 2
[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
  NRAS MUTATED     0  34
  NRAS WILD-TYPE  12 352
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0   34
  NRAS WILD-TYPE   12  352
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             0             12
  YES           34            352
[1] 2 2
[1] FALSE
D2V10, binary
                cls
clus               0   1
  NRAS MUTATED    28   1
  NRAS WILD-TYPE 306  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     28    1
  NRAS WILD-TYPE  306   14
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            28            306
  YES            1             14
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  NRAS MUTATED              4                       0   27                   0
  NRAS WILD-TYPE           98                      11  243                   1
D2V11, multiclass
                         clus
vv                        NRAS MUTATED NRAS WILD-TYPE
  MINIMAL (T3)                       4             98
  MODERATE/ADVANCED (T4A)            0             11
  NONE                              27            243
  VERY ADVANCED (T4B)                0              1
[1] 4 2
[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
  NRAS MUTATED    27   1   0   1
  NRAS WILD-TYPE 284  36   3  21
D2V12, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0           27            284
  R1            1             36
  R2            0              3
  RX            1             21
[1] 4 2
[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
  NRAS MUTATED    13  21
  NRAS WILD-TYPE 167 188
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     13   21
  NRAS WILD-TYPE  167  188
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  MULTIFOCAL           13            167
  UNIFOCAL             21            188
[1] 2 2
[1] FALSE
D2V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       0                         0    21
  NRAS WILD-TYPE    35                        18   237
D2V16, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                0             35
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                               21            237
[1] 3 2
[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
  NRAS MUTATED     5  18
  NRAS WILD-TYPE  26 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      5   18
  NRAS WILD-TYPE   26  265
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                5             26
  NOT HISPANIC OR LATINO           18            265
[1] 2 2
[1] FALSE

Clustering(3) Variable = HRAS MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  HRAS MUTATED    14   0
  HRAS WILD-TYPE 369  13
  HRAS MUTATED HRAS WILD-TYPE 
            14            382 
  HRAS MUTATED HRAS WILD-TYPE 
             0             13 
$`HRAS MUTATED`
TCGA-BJ-A0Z2 TCGA-BJ-A18Y TCGA-BJ-A2P4 TCGA-BJ-A45D TCGA-DJ-A13M TCGA-DJ-A2QB 
       18.21        23.34         7.04         6.48        17.26        10.85 
TCGA-E3-A3DZ TCGA-EL-A3CZ TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EM-A22K TCGA-EM-A2CK 
       12.07        58.82        48.16        45.80        15.75        17.88 
TCGA-ET-A2N5 TCGA-ET-A39I 
       58.22        13.74 

$`HRAS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB 
       24.79        13.78        16.34         8.25        18.87         4.01 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Z 
       11.57        16.73         7.56        15.12        17.69        20.71 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83         8.09         4.87        21.04         2.79         5.10 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       17.52         1.22        30.21        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       18.97        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K 
        0.03         3.45         6.35         6.18         5.06         8.98 
TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
        4.93         5.98         0.53         0.10         0.20         0.23 
TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       10.68         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13O TCGA-DJ-A13P 
        5.98        15.85        18.54        18.84        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        12.49        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        24.23        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       11.34        21.37         9.83        11.93        22.92        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UT 
        7.76        17.36        17.23        27.62        18.21        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-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
       21.53         2.33        31.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 
       30.31        14.04         1.15        22.29        13.61        13.81 
TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
        3.02        14.70        14.96         7.69        13.78        13.58 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01        80.91 
TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
        4.18         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        38.66        52.73       139.00       131.15 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK 
       95.38         5.72        66.90        82.82        78.97        31.50 
TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
       53.06        45.53        44.65        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG 
       31.04        30.51        33.60        28.73        29.95        13.32 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       11.87         8.71        26.86        18.18        20.91        12.36 
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-A22I TCGA-EM-A22J TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.73        14.50        10.45        14.53        10.65        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       11.15        14.24        16.44        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        13.64        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        19.73        17.59        12.07        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        17.46        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        11.15         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO 
        9.24        13.91         7.82         9.01         4.83         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        9.80         5.03        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       29.69        32.35        27.09        29.49        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
       16.08        29.19         2.66        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89        98.56        61.02        58.72        57.11        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-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 
      132.36        24.72         5.03         4.01        73.74        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-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.34        81.83        85.15        85.68        78.77        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD 
        4.08         0.89        22.03         0.92        48.10         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON 
        1.15        17.82         1.64         0.99        16.14         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 
        0.76         0.03         4.67        16.57        18.08         0.76 
TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       17.06         4.14         1.35        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       12.46         2.99        20.05        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW 
       16.90        17.23        43.17        27.19        27.85         2.60 
TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET 
       15.68         6.74        87.39        84.72        33.40        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
        0.72        16.64        32.45         8.71 

  HRAS MUTATED HRAS WILD-TYPE 
          6.48           0.03 
  HRAS MUTATED HRAS WILD-TYPE 
         58.82         158.83 
  HRAS MUTATED HRAS WILD-TYPE 
         17.57          16.95 
[1] "6.5 - 58.8 (17.6)"  "0.0 - 158.8 (16.9)"
[1] "hr="     "2.6e+07"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  HRAS MUTATED         8        1         2        0         2         1
  HRAS WILD-TYPE     220       43        81        2        31         5
D3V3, multiclass
           clus
vv          HRAS MUTATED HRAS WILD-TYPE
  STAGE I              8            220
  STAGE II             1             43
  STAGE III            2             81
  STAGE IV             0              2
  STAGE IVA            2             31
  STAGE IVC            1              5
[1] 6 2
[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
  HRAS MUTATED     6   6   2   0
  HRAS WILD-TYPE 110 131 125  15
D3V4, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  T1            6            110
  T2            6            131
  T3            2            125
  T4            0             15
[1] 4 2
[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
  HRAS MUTATED     8   4
  HRAS WILD-TYPE 180 165
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      8    4
  HRAS WILD-TYPE  180  165
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0            8            180
  1            4            165
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  HRAS MUTATED     8   1   5
  HRAS WILD-TYPE 211   6 166
D3V6, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  M0            8            211
  M1            1              6
  MX            5            166
[1] 3 2
[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
  HRAS MUTATED    10   4
  HRAS WILD-TYPE 287  97
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     10    4
  HRAS WILD-TYPE  287   97
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE           10            287
  MALE              4             97
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  HRAS MUTATED                0                                             6
  HRAS WILD-TYPE              6                                           274
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  HRAS MUTATED                                                                        8
  HRAS WILD-TYPE                                                                     75
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  HRAS MUTATED                                                                     0
  HRAS WILD-TYPE                                                                  29
D3V8, multiclass
                                                                        clus
vv                                                                       HRAS MUTATED
  OTHER  SPECIFY                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)            8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       HRAS WILD-TYPE
  OTHER  SPECIFY                                                                      6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     274
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             75
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                29
[1] 4 2
[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
  HRAS MUTATED     0  14
  HRAS WILD-TYPE  12 372
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   14
  HRAS WILD-TYPE   12  372
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO             0             12
  YES           14            372
[1] 2 2
[1] FALSE
D3V10, binary
                cls
clus               0   1
  HRAS MUTATED    12   0
  HRAS WILD-TYPE 322  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     12    0
  HRAS WILD-TYPE  322   15
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO            12            322
  YES            0             15
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  HRAS MUTATED              2                       0   11                   0
  HRAS WILD-TYPE          100                      11  259                   1
D3V11, multiclass
                         clus
vv                        HRAS MUTATED HRAS WILD-TYPE
  MINIMAL (T3)                       2            100
  MODERATE/ADVANCED (T4A)            0             11
  NONE                              11            259
  VERY ADVANCED (T4B)                0              1
[1] 4 2
[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
  HRAS MUTATED     9   2   0   2
  HRAS WILD-TYPE 302  35   3  20
D3V12, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  R0            9            302
  R1            2             35
  R2            0              3
  RX            2             20
[1] 4 2
[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
  HRAS MUTATED     7   7
  HRAS WILD-TYPE 173 202
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      7    7
  HRAS WILD-TYPE  173  202
            clus
vv           HRAS MUTATED HRAS WILD-TYPE
  MULTIFOCAL            7            173
  UNIFOCAL              7            202
[1] 2 2
[1] FALSE
D3V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED       2                         2     8
  HRAS WILD-TYPE    33                        16   250
D3V16, multiclass
                           clus
vv                          HRAS MUTATED HRAS WILD-TYPE
  ASIAN                                2             33
  BLACK OR AFRICAN AMERICAN            2             16
  WHITE                                8            250
[1] 3 2
[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
  HRAS MUTATED     0  12
  HRAS WILD-TYPE  31 271
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   12
  HRAS WILD-TYPE   31  271
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO           12            271
[1] 2 2
[1] FALSE

Clustering(4) Variable = EIF1AX MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2                0   1
  EIF1AX MUTATED     5   1
  EIF1AX WILD-TYPE 378  12
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              390 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               1               12 
$`EIF1AX MUTATED`
TCGA-BJ-A0ZG TCGA-EL-A3CO TCGA-EM-A1YA TCGA-EM-A2CL TCGA-EM-A3FN TCGA-EM-A4FV 
        7.56        97.74        19.79        13.18        12.07        12.72 

$`EIF1AX WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        18.21        16.34         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
        4.01        11.57        16.73        15.12        17.69        23.34 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.71         4.83         8.09         4.87        21.04         2.79 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
        5.10        17.52         1.22        30.21        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         6.48         0.03         3.45         6.35 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
        0.10         0.20         0.23        10.68         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        15.85        18.54 
TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
       18.84        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       25.35        13.41        11.90        14.60         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      100.01        18.51        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45         8.88         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28         7.69         5.52         8.78         8.42         8.12 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        9.34         6.77         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF 
       21.37         9.83        11.93        22.92        18.97         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UT TCGA-DJ-A4UW 
       17.36        17.23        27.62        18.21        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 
       30.31        14.04         1.15        22.29        13.61        13.81 
TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
        3.02        14.70        14.96         7.69        13.78        13.58 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       31.66        26.73       155.54       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        38.66        52.73       139.00       131.15 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK 
       95.38         5.72        66.90        82.82        78.97        31.50 
TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       53.06        45.53        48.16        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       45.96        37.94        31.04        30.51        33.60        28.73 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       20.91        12.36        18.05        19.46        54.21        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        13.64        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FO 
       16.77        27.95        23.77        16.80        21.01        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM 
       12.53         9.24        13.91         7.82         9.01         4.83 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        8.38         9.80         5.03         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       29.69        32.35        27.09        29.49        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       16.08        29.19         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN 
       17.98        25.32       132.36        24.72         5.03         4.01 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC 
      102.90        66.77        81.34        81.83        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       48.10         1.25         1.15        17.82         1.64         0.99 
TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       16.14         1.51         0.76         0.03         4.67        16.57 
TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 
       18.08         0.76        17.06         4.14         1.35        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB 
       17.00        21.67        12.46         2.99        20.05        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       47.41        10.26        16.90        17.23        43.17        27.19 
TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB 
       27.85         2.60        15.68         6.74        87.39        84.72 
TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        21.83         0.72        16.64        32.45         8.71 

  EIF1AX MUTATED EIF1AX WILD-TYPE 
            7.56             0.03 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
           97.74           158.83 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
          12.950           17.145 
[1] "7.6 - 97.7 (12.9)"  "0.0 - 158.8 (17.1)"
[1] "hr=" "5.1"
D4V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  EIF1AX MUTATED         4        1         1        0         0         0
  EIF1AX WILD-TYPE     224       43        82        2        33         6
D4V3, multiclass
           clus
vv          EIF1AX MUTATED EIF1AX WILD-TYPE
  STAGE I                4              224
  STAGE II               1               43
  STAGE III              1               82
  STAGE IV               0                2
  STAGE IVA              0               33
  STAGE IVC              0                6
[1] 6 2
[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
  EIF1AX MUTATED     2   2   2   0
  EIF1AX WILD-TYPE 114 135 125  15
D4V4, multiclass
    clus
vv   EIF1AX MUTATED EIF1AX WILD-TYPE
  T1              2              114
  T2              2              135
  T3              2              125
  T4              0               15
[1] 4 2
[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
  EIF1AX MUTATED     3   1
  EIF1AX WILD-TYPE 185 168
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      3    1
  EIF1AX WILD-TYPE  185  168
   clus
vv  EIF1AX MUTATED EIF1AX WILD-TYPE
  0              3              185
  1              1              168
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  EIF1AX MUTATED     2   0   4
  EIF1AX WILD-TYPE 217   7 167
D4V6, multiclass
    clus
vv   EIF1AX MUTATED EIF1AX WILD-TYPE
  M0              2              217
  M1              0                7
  MX              4              167
[1] 3 2
[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
  EIF1AX MUTATED     3   3
  EIF1AX WILD-TYPE 294  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      3    3
  EIF1AX WILD-TYPE  294   98
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  FEMALE              3              294
  MALE                3               98
[1] 2 2
[1] FALSE
                  vv
clus               OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  EIF1AX MUTATED                0                                             2
  EIF1AX WILD-TYPE              6                                           278
                  vv
clus               THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  EIF1AX MUTATED                                                                        4
  EIF1AX WILD-TYPE                                                                     79
                  vv
clus               THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  EIF1AX MUTATED                                                                     0
  EIF1AX WILD-TYPE                                                                  29
D4V8, multiclass
                                                                        clus
vv                                                                       EIF1AX MUTATED
  OTHER  SPECIFY                                                                      0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 0
                                                                        clus
vv                                                                       EIF1AX WILD-TYPE
  OTHER  SPECIFY                                                                        6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       278
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               79
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  29
[1] 4 2
[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
  EIF1AX MUTATED     0   6
  EIF1AX WILD-TYPE  12 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      0    6
  EIF1AX WILD-TYPE   12  380
     clus
vv    EIF1AX MUTATED EIF1AX WILD-TYPE
  NO               0               12
  YES              6              380
[1] 2 2
[1] FALSE
D4V10, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     6   0
  EIF1AX WILD-TYPE 328  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      6    0
  EIF1AX WILD-TYPE  328   15
     clus
vv    EIF1AX MUTATED EIF1AX WILD-TYPE
  NO               6              328
  YES              0               15
[1] 2 2
[1] FALSE
                  vv
clus               MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  EIF1AX MUTATED              1                       0    5
  EIF1AX WILD-TYPE          101                      11  265
                  vv
clus               VERY ADVANCED (T4B)
  EIF1AX MUTATED                     0
  EIF1AX WILD-TYPE                   1
D4V11, multiclass
                         clus
vv                        EIF1AX MUTATED EIF1AX WILD-TYPE
  MINIMAL (T3)                         1              101
  MODERATE/ADVANCED (T4A)              0               11
  NONE                                 5              265
  VERY ADVANCED (T4B)                  0                1
[1] 4 2
[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
  EIF1AX MUTATED     4   1   0   1
  EIF1AX WILD-TYPE 307  36   3  21
D4V12, multiclass
    clus
vv   EIF1AX MUTATED EIF1AX WILD-TYPE
  R0              4              307
  R1              1               36
  R2              0                3
  RX              1               21
[1] 4 2
[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
  EIF1AX MUTATED     3   2
  EIF1AX WILD-TYPE 177 207
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      3    2
  EIF1AX WILD-TYPE  177  207
            clus
vv           EIF1AX MUTATED EIF1AX WILD-TYPE
  MULTIFOCAL              3              177
  UNIFOCAL                2              207
[1] 2 2
[1] FALSE
D4V15, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF1AX MUTATED       0                         0     2
  EIF1AX WILD-TYPE    35                        18   256
D4V16, multiclass
[1] "Remove cluster labels:" "EIF1AX MUTATED"        
clus
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               2              309 
      TCGA-BJ-A0YZ       TCGA-BJ-A0Z2       TCGA-BJ-A0Z3       TCGA-BJ-A0Z9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A0ZA       TCGA-BJ-A0ZB       TCGA-BJ-A0ZC       TCGA-BJ-A0ZE 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A0ZH       TCGA-BJ-A0ZJ       TCGA-BJ-A18Y       TCGA-BJ-A18Z 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A191       TCGA-BJ-A192       TCGA-BJ-A28R       TCGA-BJ-A28S 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A28T       TCGA-BJ-A28V       TCGA-BJ-A28X       TCGA-BJ-A28Z 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A290       TCGA-BJ-A2N7       TCGA-BJ-A2N8       TCGA-BJ-A2N9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A2NA       TCGA-BJ-A2P4       TCGA-BJ-A3EZ       TCGA-BJ-A3F0 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A3PR       TCGA-BJ-A3PT       TCGA-BJ-A3PU       TCGA-BJ-A45D 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A45E       TCGA-BJ-A45F       TCGA-BJ-A45G       TCGA-BJ-A45I 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A45J       TCGA-BJ-A45K       TCGA-BJ-A4O8       TCGA-BJ-A4O9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-CE-A13K       TCGA-CE-A27D       TCGA-CE-A3MD       TCGA-CE-A3ME 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-CE-A482       TCGA-CE-A484       TCGA-CE-A485       TCGA-DE-A0XZ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DE-A0Y2       TCGA-DE-A0Y3       TCGA-DE-A2OL       TCGA-DE-A3KN 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DE-A4M8       TCGA-DE-A4M9       TCGA-DJ-A13M       TCGA-DJ-A13O 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A13P       TCGA-DJ-A13R       TCGA-DJ-A13S       TCGA-DJ-A13T 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A13U       TCGA-DJ-A13W       TCGA-DJ-A1QD       TCGA-DJ-A1QE 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A1QF       TCGA-DJ-A1QG       TCGA-DJ-A1QH       TCGA-DJ-A1QI 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A1QM       TCGA-DJ-A1QO       TCGA-DJ-A1QQ       TCGA-DJ-A2PN 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2PO       TCGA-DJ-A2PQ       TCGA-DJ-A2PR       TCGA-DJ-A2PT 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2PU       TCGA-DJ-A2PV       TCGA-DJ-A2PW       TCGA-DJ-A2PX 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2PY       TCGA-DJ-A2PZ       TCGA-DJ-A2Q0       TCGA-DJ-A2Q1 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2Q2       TCGA-DJ-A2Q3       TCGA-DJ-A2Q4       TCGA-DJ-A2Q5 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2Q6       TCGA-DJ-A2Q7       TCGA-DJ-A2Q9       TCGA-DJ-A2QA 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2QB       TCGA-DJ-A3UK       TCGA-DJ-A3UM       TCGA-DJ-A3UN 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A3UO       TCGA-DJ-A3UQ       TCGA-DJ-A3UR       TCGA-DJ-A3US 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A3UT       TCGA-DJ-A3UU       TCGA-DJ-A3UW       TCGA-DJ-A3UX 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A3UY       TCGA-DJ-A3V7       TCGA-DJ-A3VE       TCGA-DJ-A3VF 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A3VJ       TCGA-DJ-A3VL       TCGA-DJ-A3VM       TCGA-DJ-A4UL 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A4UT       TCGA-DJ-A4UW       TCGA-DJ-A4V0       TCGA-DJ-A4V4 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A4V5       TCGA-DO-A1JZ       TCGA-DO-A1K0       TCGA-DO-A2HM 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E3-A3DY       TCGA-E3-A3DZ       TCGA-E3-A3E0       TCGA-E3-A3E1 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E3-A3E2       TCGA-E3-A3E3       TCGA-E3-A3E5       TCGA-E8-A242 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E8-A2EA       TCGA-E8-A413       TCGA-E8-A415       TCGA-E8-A418 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E8-A419       TCGA-E8-A433       TCGA-E8-A436       TCGA-E8-A437 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E8-A44K       TCGA-E8-A44M       TCGA-EL-A3CL       TCGA-EL-A3CM 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3CN       TCGA-EL-A3CP       TCGA-EL-A3CR       TCGA-EL-A3CS 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3CT       TCGA-EL-A3CU       TCGA-EL-A3CV       TCGA-EL-A3CW 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3CX       TCGA-EL-A3CY       TCGA-EL-A3CZ       TCGA-EL-A3D0 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3D1       TCGA-EL-A3D4       TCGA-EL-A3D5       TCGA-EL-A3D6 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3GO       TCGA-EL-A3GP       TCGA-EL-A3GQ       TCGA-EL-A3GR 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3GS       TCGA-EL-A3GU       TCGA-EL-A3GV       TCGA-EL-A3GW 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3GX       TCGA-EL-A3GY       TCGA-EL-A3GZ       TCGA-EL-A3H1 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3H2       TCGA-EL-A3H3       TCGA-EL-A3H4       TCGA-EL-A3H5 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3H7       TCGA-EL-A3H8       TCGA-EL-A3MW       TCGA-EL-A3MX 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3MY       TCGA-EL-A3MZ       TCGA-EL-A3N2       TCGA-EL-A3N3 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3T0       TCGA-EL-A3T1       TCGA-EL-A3T2       TCGA-EL-A3T3 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3T6       TCGA-EL-A3T7       TCGA-EL-A3T8       TCGA-EL-A3T9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3TA       TCGA-EL-A3TB       TCGA-EL-A3ZH       TCGA-EL-A3ZK 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3ZN       TCGA-EL-A3ZQ       TCGA-EL-A3ZR       TCGA-EL-A3ZT 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A4JV       TCGA-EL-A4JW       TCGA-EL-A4JX       TCGA-EL-A4JZ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A4K0       TCGA-EL-A4K2       TCGA-EL-A4K4       TCGA-EL-A4K6 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A4KD       TCGA-EL-A4KG       TCGA-EL-A4KH       TCGA-EL-A4KI 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A25G       TCGA-ET-A25I       TCGA-ET-A25J       TCGA-ET-A25K 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A25O       TCGA-ET-A25R       TCGA-ET-A2MY       TCGA-ET-A2MZ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A2N0       TCGA-ET-A2N1       TCGA-ET-A2N4       TCGA-ET-A2N5 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A39I       TCGA-ET-A39J       TCGA-ET-A39K       TCGA-ET-A39M 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A39N       TCGA-ET-A39O       TCGA-ET-A39P       TCGA-ET-A39R 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A39S       TCGA-ET-A39T       TCGA-ET-A3BN       TCGA-ET-A3BO 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3BQ       TCGA-ET-A3BS       TCGA-ET-A3BT       TCGA-ET-A3BU 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3BV       TCGA-ET-A3BW       TCGA-ET-A3DO       TCGA-ET-A3DP 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3DQ       TCGA-ET-A3DR       TCGA-ET-A3DS       TCGA-ET-A3DT 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3DU       TCGA-ET-A3DV       TCGA-ET-A3DW       TCGA-ET-A40S 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A4KN       TCGA-FE-A22Z       TCGA-FE-A230       TCGA-FE-A231 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FE-A232       TCGA-FE-A233       TCGA-FE-A234       TCGA-FE-A235 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FE-A236       TCGA-FE-A237       TCGA-FE-A23A       TCGA-FE-A3PB 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FE-A3PC       TCGA-FE-A3PD       TCGA-FK-A3S3       TCGA-FK-A3SB 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FK-A3SD       TCGA-FK-A3SE       TCGA-FK-A3SG       TCGA-FK-A3SH 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A2QD       TCGA-FY-A3BL       TCGA-FY-A3I4       TCGA-FY-A3I5 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A3NM       TCGA-FY-A3NP       TCGA-FY-A3ON       TCGA-FY-A3R6 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A3R7       TCGA-FY-A3R8       TCGA-FY-A3R9       TCGA-FY-A3RA 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A3W9       TCGA-FY-A3WA       TCGA-FY-A40K       TCGA-FY-A4B3 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-GE-A2C6       TCGA-H2-A26U       TCGA-H2-A2K9       TCGA-H2-A3RH 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-H2-A3RI       TCGA-H2-A421       TCGA-IM-A3EB       TCGA-IM-A3ED 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-IM-A3U2       TCGA-IM-A3U3       TCGA-J8-A3NZ       TCGA-J8-A3O0 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-J8-A3O1       TCGA-J8-A3YE       TCGA-J8-A4HW       TCGA-KS-A41J 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-KS-A4I5       TCGA-KS-A4I9       TCGA-KS-A4IB       TCGA-L6-A4EP 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-L6-A4ET       TCGA-L6-A4EU       TCGA-MK-A4N6       TCGA-MK-A4N7 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-MK-A4N9 
"EIF1AX WILD-TYPE" 
D4V17, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     0   2
  EIF1AX WILD-TYPE  31 281
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      0    2
  EIF1AX WILD-TYPE   31  281
                        clus
vv                       EIF1AX MUTATED EIF1AX WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              2              281
[1] 2 2
[1] FALSE

Clustering(5) Variable = NUP93 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  NUP93 MUTATED     4   0
  NUP93 WILD-TYPE 379  13
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             392 
  NUP93 MUTATED NUP93 WILD-TYPE 
              0              13 
$`NUP93 MUTATED`
TCGA-BJ-A191 TCGA-DJ-A2Q4 TCGA-EM-A4FQ TCGA-L6-A4EU 
        4.83         9.44         9.80         0.72 

$`NUP93 WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        18.21        16.34         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       23.34        20.71         8.09         4.87        21.04         2.79 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
        5.10        17.52         1.22        30.21        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         6.48         0.03         3.45         6.35 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
        0.10         0.20         0.23        10.68         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        15.85        18.54 
TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
       18.84        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       25.35        13.41        11.90        14.60         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      100.01        18.51        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45         8.88         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28         7.69         5.52         8.78         8.42         8.12 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        9.34         6.77         9.21         9.90         8.61        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.07        10.36        12.43        10.85        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        12.49        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        43.00        11.34        21.37 
TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ 
        9.83        11.93        22.92        18.97         7.76        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       17.23        27.62        18.21        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 
       14.04         1.15        22.29        13.61        13.81         3.02 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.70        14.96         7.69        13.78        13.58        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        38.66        52.73       139.00       131.15 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK 
       95.38         5.72        66.90        82.82        78.97        31.50 
TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       53.06        45.53        48.16        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       45.96        37.94        31.04        30.51        33.60        28.73 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        11.74        11.15        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-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       13.64        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        17.59        17.46        17.29        14.60 
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-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FV 
        7.82         9.01         4.83         8.38         5.03        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O 
        0.95        47.47        48.20        29.69        32.35        27.09 
TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 
       29.49        22.09        12.26        16.08        29.19         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       24.72         5.03         4.01        73.74        59.70        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-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
       81.83        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL 
        0.89        22.03         0.92        48.10         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 
       17.82         1.64         0.99        16.14         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA 
        0.03         4.67        16.57        18.08         0.76        17.06 
TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        4.14         1.35        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
        2.99        20.05        48.92        47.41        10.26        16.90 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J 
       17.23        43.17        27.19        27.85         2.60        15.68 
TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-MK-A4N6 
        6.74        87.39        84.72        33.40        21.83        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

  NUP93 MUTATED NUP93 WILD-TYPE 
           0.72            0.03 
  NUP93 MUTATED NUP93 WILD-TYPE 
           9.80          158.83 
  NUP93 MUTATED NUP93 WILD-TYPE 
          7.135          17.230 
[1] "0.7 - 9.8 (7.1)"    "0.0 - 158.8 (17.2)"
[1] "hr="    "450000"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  NUP93 MUTATED         2        0         2        0         0         0
  NUP93 WILD-TYPE     226       44        81        2        33         6
D5V3, multiclass
           clus
vv          NUP93 MUTATED NUP93 WILD-TYPE
  STAGE I               2             226
  STAGE II              0              44
  STAGE III             2              81
  STAGE IV              0               2
  STAGE IVA             0              33
  STAGE IVC             0               6
[1] 6 2
[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
  NUP93 MUTATED     2   1   1   0
  NUP93 WILD-TYPE 114 136 126  15
D5V4, multiclass
    clus
vv   NUP93 MUTATED NUP93 WILD-TYPE
  T1             2             114
  T2             1             136
  T3             1             126
  T4             0              15
[1] 4 2
[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
  NUP93 MUTATED     1   3
  NUP93 WILD-TYPE 187 166
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      1    3
  NUP93 WILD-TYPE  187  166
   clus
vv  NUP93 MUTATED NUP93 WILD-TYPE
  0             1             187
  1             3             166
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  NUP93 MUTATED     3   0   1
  NUP93 WILD-TYPE 216   7 170
D5V6, multiclass
    clus
vv   NUP93 MUTATED NUP93 WILD-TYPE
  M0             3             216
  M1             0               7
  MX             1             170
[1] 3 2
[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
  NUP93 MUTATED     3   1
  NUP93 WILD-TYPE 294 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      3    1
  NUP93 WILD-TYPE  294  100
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  FEMALE             3             294
  MALE               1             100
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  NUP93 MUTATED                1                                             1
  NUP93 WILD-TYPE              5                                           279
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  NUP93 MUTATED                                                                        1
  NUP93 WILD-TYPE                                                                     82
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  NUP93 MUTATED                                                                     1
  NUP93 WILD-TYPE                                                                  28
D5V8, multiclass
                                                                        clus
vv                                                                       NUP93 MUTATED
  OTHER  SPECIFY                                                                     1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                1
                                                                        clus
vv                                                                       NUP93 WILD-TYPE
  OTHER  SPECIFY                                                                       5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      279
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              82
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 28
[1] 4 2
[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
  NUP93 MUTATED     0   4
  NUP93 WILD-TYPE  12 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      0    4
  NUP93 WILD-TYPE   12  382
     clus
vv    NUP93 MUTATED NUP93 WILD-TYPE
  NO              0              12
  YES             4             382
[1] 2 2
[1] FALSE
D5V10, binary
                 cls
clus                0   1
  NUP93 MUTATED     3   0
  NUP93 WILD-TYPE 331  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      3    0
  NUP93 WILD-TYPE  331   15
     clus
vv    NUP93 MUTATED NUP93 WILD-TYPE
  NO              3             331
  YES             0              15
[1] 2 2
[1] FALSE
                 vv
clus              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  NUP93 MUTATED              1                       0    3                   0
  NUP93 WILD-TYPE          101                      11  267                   1
D5V11, multiclass
                         clus
vv                        NUP93 MUTATED NUP93 WILD-TYPE
  MINIMAL (T3)                        1             101
  MODERATE/ADVANCED (T4A)             0              11
  NONE                                3             267
  VERY ADVANCED (T4B)                 0               1
[1] 4 2
[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
  NUP93 MUTATED     3   1   0   0
  NUP93 WILD-TYPE 308  36   3  22
D5V12, multiclass
    clus
vv   NUP93 MUTATED NUP93 WILD-TYPE
  R0             3             308
  R1             1              36
  R2             0               3
  RX             0              22
[1] 4 2
[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
  NUP93 MUTATED     3   1
  NUP93 WILD-TYPE 177 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      3    1
  NUP93 WILD-TYPE  177  208
            clus
vv           NUP93 MUTATED NUP93 WILD-TYPE
  MULTIFOCAL             3             177
  UNIFOCAL               1             208
[1] 2 2
[1] FALSE
D5V15, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUP93 MUTATED       0                         1     2
  NUP93 WILD-TYPE    35                        17   256
D5V16, multiclass
                           clus
vv                          NUP93 MUTATED NUP93 WILD-TYPE
  ASIAN                                 0              35
  BLACK OR AFRICAN AMERICAN             1              17
  WHITE                                 2             256
[1] 3 2
[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
  NUP93 MUTATED     0   3
  NUP93 WILD-TYPE  31 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      0    3
  NUP93 WILD-TYPE   31  280
                        clus
vv                       NUP93 MUTATED NUP93 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             3             280
[1] 2 2
[1] FALSE

Clustering(6) Variable = PPM1D MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  PPM1D MUTATED     4   0
  PPM1D WILD-TYPE 379  13
  PPM1D MUTATED PPM1D WILD-TYPE 
              4             392 
  PPM1D MUTATED PPM1D WILD-TYPE 
              0              13 
$`PPM1D MUTATED`
TCGA-DJ-A1QL TCGA-DJ-A2PW TCGA-E8-A418 TCGA-ET-A3BW 
        7.20         7.69         3.02         2.37 

$`PPM1D WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        18.21        16.34         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         4.83         8.09         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 
        2.79         5.10        17.52         1.22        30.21        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 
       16.57        20.48        18.97         7.04        16.01        13.94 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       15.48        23.31        18.64         6.48         0.03         3.45 
TCGA-BJ-A45G TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        6.35         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
        0.53         0.10         0.20         0.23        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       18.54        18.84        17.26        14.07       137.88         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        25.35        13.41        11.90        14.60         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45         8.88         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
        8.28         5.52         8.78         8.42         8.12         9.34 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77         9.21         9.44         9.90         8.61        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.07        10.36        12.43        10.85        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        12.49        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        24.23        17.69        43.00        11.34        21.37 
TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ 
        9.83        11.93        22.92        18.97         7.76        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       17.23        27.62        18.21        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A433 
       14.04         1.15        22.29        13.61        13.81        14.70 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       14.96         7.69        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       147.75       101.13       139.99        49.32        33.50 
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-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
        5.72        66.90        82.82        78.97        31.50        53.06 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       45.53        48.16        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD 
       37.94        31.04        30.51        33.60        28.73        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR 
       13.18        23.51         6.05         2.99        12.30        13.64 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV 
        9.01         4.83         8.38         9.80         5.03        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O 
        0.95        47.47        48.20        29.69        32.35        27.09 
TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 
       29.49        22.09        12.26        16.08        29.19         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       38.30        42.25         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        5.03         4.01        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A 
       24.69        68.22       102.90        66.77        81.34        81.83 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
       22.03         0.92        48.10         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.64         0.99        16.14         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K 
        4.67        16.57        18.08         0.76        17.06         4.14 
TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.35        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ 
       20.05        48.92        47.41        10.26        16.90        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 
       43.17        27.19        27.85         2.60        15.68         6.74 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       87.39        84.72        33.40        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

  PPM1D MUTATED PPM1D WILD-TYPE 
           2.37            0.03 
  PPM1D MUTATED PPM1D WILD-TYPE 
           7.69          158.83 
  PPM1D MUTATED PPM1D WILD-TYPE 
           5.11           17.23 
[1] "2.4 - 7.7 (5.1)"    "0.0 - 158.8 (17.2)"
[1] "hr="    "450000"
D6V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  PPM1D MUTATED         1        1         2        0         1         0
  PPM1D WILD-TYPE     227       43        81        2        32         6
D6V3, multiclass
           clus
vv          PPM1D MUTATED PPM1D WILD-TYPE
  STAGE I               1             227
  STAGE II              1              43
  STAGE III             2              81
  STAGE IV              0               2
  STAGE IVA             1              32
  STAGE IVC             0               6
[1] 6 2
[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
  PPM1D MUTATED     1   2   1   1
  PPM1D WILD-TYPE 115 135 126  14
D6V4, multiclass
    clus
vv   PPM1D MUTATED PPM1D WILD-TYPE
  T1             1             115
  T2             2             135
  T3             1             126
  T4             1              14
[1] 4 2
[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
  PPM1D MUTATED     2   2
  PPM1D WILD-TYPE 186 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      2    2
  PPM1D WILD-TYPE  186  167
   clus
vv  PPM1D MUTATED PPM1D WILD-TYPE
  0             2             186
  1             2             167
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  PPM1D MUTATED     3   0   2
  PPM1D WILD-TYPE 216   7 169
D6V6, multiclass
    clus
vv   PPM1D MUTATED PPM1D WILD-TYPE
  M0             3             216
  M1             0               7
  MX             2             169
[1] 3 2
[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
  PPM1D MUTATED     3   2
  PPM1D WILD-TYPE 294  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      3    2
  PPM1D WILD-TYPE  294   99
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  FEMALE             3             294
  MALE               2              99
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  PPM1D MUTATED                0                                             4
  PPM1D WILD-TYPE              6                                           276
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  PPM1D MUTATED                                                                        1
  PPM1D WILD-TYPE                                                                     82
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  PPM1D MUTATED                                                                     0
  PPM1D WILD-TYPE                                                                  29
D6V8, multiclass
                                                                        clus
vv                                                                       PPM1D MUTATED
  OTHER  SPECIFY                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                0
                                                                        clus
vv                                                                       PPM1D WILD-TYPE
  OTHER  SPECIFY                                                                       6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      276
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              82
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 29
[1] 4 2
[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
  PPM1D MUTATED     0   5
  PPM1D WILD-TYPE  12 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      0    5
  PPM1D WILD-TYPE   12  381
     clus
vv    PPM1D MUTATED PPM1D WILD-TYPE
  NO              0              12
  YES             5             381
[1] 2 2
[1] FALSE
D6V10, binary
                 cls
clus                0   1
  PPM1D MUTATED     4   0
  PPM1D WILD-TYPE 330  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      4    0
  PPM1D WILD-TYPE  330   15
     clus
vv    PPM1D MUTATED PPM1D WILD-TYPE
  NO              4             330
  YES             0              15
[1] 2 2
[1] FALSE
                 vv
clus              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  PPM1D MUTATED              0                       1    4                   0
  PPM1D WILD-TYPE          102                      10  266                   1
D6V11, multiclass
                         clus
vv                        PPM1D MUTATED PPM1D WILD-TYPE
  MINIMAL (T3)                        0             102
  MODERATE/ADVANCED (T4A)             1              10
  NONE                                4             266
  VERY ADVANCED (T4B)                 0               1
[1] 4 2
[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
  PPM1D MUTATED     4   0   0   1
  PPM1D WILD-TYPE 307  37   3  21
D6V12, multiclass
    clus
vv   PPM1D MUTATED PPM1D WILD-TYPE
  R0             4             307
  R1             0              37
  R2             0               3
  RX             1              21
[1] 4 2
[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
[1] "Remove cluster labels:" "PPM1D MUTATED"         
clus
  PPM1D MUTATED PPM1D WILD-TYPE 
              2             308 
     TCGA-BJ-A0Z0      TCGA-BJ-A0Z3      TCGA-BJ-A0Z9      TCGA-BJ-A0ZA 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A0ZB      TCGA-BJ-A0ZH      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A18Z      TCGA-BJ-A191      TCGA-BJ-A28R      TCGA-BJ-A28T 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A28X      TCGA-BJ-A28Z      TCGA-BJ-A290      TCGA-BJ-A2N8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A2N9      TCGA-BJ-A2NA      TCGA-BJ-A3EZ      TCGA-BJ-A3PR 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A3PU      TCGA-BJ-A45D      TCGA-BJ-A45E      TCGA-BJ-A45G 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A45I      TCGA-BJ-A45J      TCGA-BJ-A45K      TCGA-BJ-A4O8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A4O9      TCGA-CE-A13K      TCGA-CE-A3MD      TCGA-DE-A0XZ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DE-A0Y2      TCGA-DE-A0Y3      TCGA-DE-A3KN      TCGA-DE-A4M8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A13M      TCGA-DJ-A13O      TCGA-DJ-A13P      TCGA-DJ-A13R 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A13T      TCGA-DJ-A13U      TCGA-DJ-A13V      TCGA-DJ-A13W 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A13X      TCGA-DJ-A1QG      TCGA-DJ-A1QH      TCGA-DJ-A1QM 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2PO      TCGA-DJ-A2PP      TCGA-DJ-A2PQ      TCGA-DJ-A2PR 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2PS      TCGA-DJ-A2PT      TCGA-DJ-A2PU      TCGA-DJ-A2PV 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2PX      TCGA-DJ-A2PY      TCGA-DJ-A2PZ      TCGA-DJ-A2Q0 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2Q1      TCGA-DJ-A2Q2      TCGA-DJ-A2Q3      TCGA-DJ-A2Q4 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2Q5      TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2Q9      TCGA-DJ-A2QA      TCGA-DJ-A2QB      TCGA-DJ-A3UK 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3UM      TCGA-DJ-A3UN      TCGA-DJ-A3UO      TCGA-DJ-A3UP 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3UQ      TCGA-DJ-A3UR      TCGA-DJ-A3UU      TCGA-DJ-A3UW 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3UX      TCGA-DJ-A3V7      TCGA-DJ-A3VA      TCGA-DJ-A3VB 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3VF      TCGA-DJ-A3VJ      TCGA-DJ-A3VL      TCGA-DJ-A4UL 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A4UW      TCGA-DJ-A4V2      TCGA-DJ-A4V5      TCGA-DO-A1K0 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DO-A2HM      TCGA-E3-A3DY      TCGA-E3-A3DZ      TCGA-E3-A3E0 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E3-A3E1      TCGA-E3-A3E2      TCGA-E3-A3E3      TCGA-E3-A3E5 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E8-A242      TCGA-E8-A2EA      TCGA-E8-A415      TCGA-E8-A419 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E8-A433      TCGA-E8-A436      TCGA-E8-A44K      TCGA-EL-A3CM 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3CN      TCGA-EL-A3CO      TCGA-EL-A3CR      TCGA-EL-A3CS 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3CT      TCGA-EL-A3CU      TCGA-EL-A3CV      TCGA-EL-A3CW 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3CX      TCGA-EL-A3CY      TCGA-EL-A3CZ      TCGA-EL-A3D0 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3D1      TCGA-EL-A3D4      TCGA-EL-A3D5      TCGA-EL-A3D6 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3GO      TCGA-EL-A3GP      TCGA-EL-A3GQ      TCGA-EL-A3GS 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3GU      TCGA-EL-A3GV      TCGA-EL-A3GX      TCGA-EL-A3H3 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3H4      TCGA-EL-A3H5      TCGA-EL-A3H7      TCGA-EL-A3H8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3MW      TCGA-EL-A3MX      TCGA-EL-A3MZ      TCGA-EL-A3N2 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3T0      TCGA-EL-A3T1      TCGA-EL-A3T2      TCGA-EL-A3TB 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3ZH      TCGA-EL-A3ZK      TCGA-EL-A3ZN      TCGA-EL-A4JV 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A4JW      TCGA-EL-A4JX      TCGA-EL-A4JZ      TCGA-EL-A4K0 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A4K2      TCGA-EL-A4K4      TCGA-EL-A4K6      TCGA-EL-A4KD 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A4KG      TCGA-EL-A4KI      TCGA-EM-A1CS      TCGA-EM-A1CT 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A1CU      TCGA-EM-A1CV      TCGA-EM-A1CW      TCGA-EM-A1YA 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A1YB      TCGA-EM-A1YC      TCGA-EM-A1YD      TCGA-EM-A1YE 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22K      TCGA-EM-A22L 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A22M      TCGA-EM-A22N      TCGA-EM-A22O      TCGA-EM-A22P 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A22Q      TCGA-EM-A2CK      TCGA-EM-A2CN      TCGA-EM-A2CP 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CT      TCGA-EM-A2CU 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A2OV      TCGA-EM-A2OW      TCGA-EM-A2OX      TCGA-EM-A2OY 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A2OZ      TCGA-EM-A2P0      TCGA-EM-A2P1      TCGA-EM-A2P2 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A2P3      TCGA-EM-A3AJ      TCGA-EM-A3AK      TCGA-EM-A3AL 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3AN      TCGA-EM-A3AO      TCGA-EM-A3AQ      TCGA-EM-A3AR 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3FJ      TCGA-EM-A3FK      TCGA-EM-A3FL      TCGA-EM-A3FM 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3FN      TCGA-EM-A3FO      TCGA-EM-A3FP      TCGA-EM-A3FQ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3FR      TCGA-EM-A3O3      TCGA-EM-A3O7      TCGA-EM-A3O8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3O9      TCGA-EM-A3OA      TCGA-EM-A3OB      TCGA-EM-A4FK 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A4FM      TCGA-EM-A4FO      TCGA-EM-A4FQ      TCGA-EM-A4FR 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A4FV      TCGA-EM-A4G1      TCGA-ET-A25G      TCGA-ET-A25I 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A25J      TCGA-ET-A25K      TCGA-ET-A25O      TCGA-ET-A2MZ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A2N0      TCGA-ET-A2N1      TCGA-ET-A2N4      TCGA-ET-A39K 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A39L      TCGA-ET-A39O      TCGA-ET-A39P      TCGA-ET-A39R 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A39S      TCGA-ET-A39T      TCGA-ET-A3BO      TCGA-ET-A3BP 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3BQ      TCGA-ET-A3BS      TCGA-ET-A3BT      TCGA-ET-A3BU 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3BV      TCGA-ET-A3BX      TCGA-ET-A3DQ      TCGA-ET-A3DR 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3DS      TCGA-ET-A3DT      TCGA-ET-A3DU      TCGA-ET-A3DV 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3DW      TCGA-ET-A40S      TCGA-ET-A4KN      TCGA-FE-A22Z 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FE-A230      TCGA-FE-A231      TCGA-FE-A232      TCGA-FE-A233 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FE-A23A      TCGA-FE-A3PB      TCGA-FE-A3PC      TCGA-FE-A3PD 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FK-A3S3      TCGA-FK-A3SB      TCGA-FK-A3SE      TCGA-FK-A3SG 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FK-A3SH      TCGA-FY-A2QD      TCGA-FY-A3I4      TCGA-FY-A3I5 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FY-A3NM      TCGA-FY-A3ON      TCGA-FY-A3R6      TCGA-FY-A3R7 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FY-A3R9      TCGA-FY-A3W9      TCGA-FY-A40K      TCGA-FY-A4B3 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-GE-A2C6      TCGA-H2-A26U      TCGA-H2-A2K9      TCGA-H2-A3RH 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-H2-A3RI      TCGA-H2-A421      TCGA-IM-A3EB      TCGA-IM-A3ED 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-IM-A3U2      TCGA-IM-A3U3      TCGA-J8-A3NZ      TCGA-J8-A3O0 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-J8-A3O1      TCGA-J8-A3YE      TCGA-J8-A4HW      TCGA-KS-A41J 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-KS-A4I5      TCGA-KS-A4I9      TCGA-KS-A4IB      TCGA-L6-A4EP 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-L6-A4EU      TCGA-MK-A4N6      TCGA-MK-A4N7      TCGA-MK-A4N9 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
D6V14, binary
                 cls
clus                0   1
  PPM1D MUTATED     2   3
  PPM1D WILD-TYPE 178 206
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      2    3
  PPM1D WILD-TYPE  178  206
            clus
vv           PPM1D MUTATED PPM1D WILD-TYPE
  MULTIFOCAL             2             178
  UNIFOCAL               3             206
[1] 2 2
[1] FALSE
D6V15, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPM1D MUTATED       0                         0     3
  PPM1D WILD-TYPE    35                        18   255
D6V16, multiclass
                           clus
vv                          PPM1D MUTATED PPM1D WILD-TYPE
  ASIAN                                 0              35
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 3             255
[1] 3 2
[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
  PPM1D MUTATED     0   4
  PPM1D WILD-TYPE  31 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      0    4
  PPM1D WILD-TYPE   31  279
                        clus
vv                       PPM1D MUTATED PPM1D WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             4             279
[1] 2 2
[1] FALSE

Clustering(7) Variable = DNMT3A MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  DNMT3A MUTATED     2   1
  DNMT3A WILD-TYPE 381  12
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               3              393 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               1               12 
$`DNMT3A MUTATED`
TCGA-DJ-A2Q2 TCGA-EL-A3CR TCGA-FY-A3NM 
        6.77         7.66         0.99 

$`DNMT3A WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        18.21        16.34         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         4.83         8.09         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 
        2.79         5.10        17.52         1.22        30.21        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 
       16.57        20.48        18.97         7.04        16.01        13.94 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       15.48        23.31        18.64         6.48         0.03         3.45 
TCGA-BJ-A45G TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        6.35         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
        0.53         0.10         0.20         0.23        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       18.54        18.84        17.26        14.07       137.88         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        25.35        13.41        11.90        14.60         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        8.12         9.34         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF 
       21.37         9.83        11.93        22.92        18.97         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UT TCGA-DJ-A4UW 
       17.36        17.23        27.62        18.21        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 
       30.31        14.04         1.15        22.29        13.61        13.81 
TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
        3.02        14.70        14.96         7.69        13.78        13.58 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CS 
       31.66        26.73       155.54        97.74       158.83        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        38.66        52.73       139.00       131.15 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK 
       95.38         5.72        66.90        82.82        78.97        31.50 
TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       53.06        45.53        48.16        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       45.96        37.94        31.04        30.51        33.60        28.73 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        11.74        11.15        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-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       13.64        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        17.59        17.46        17.29        14.60 
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-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        7.82         9.01         4.83         8.38         9.80         5.03 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       27.09        29.49        22.09        12.26        16.08        29.19 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89        98.56        61.02        58.72        57.11        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-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 
      132.36        24.72         5.03         4.01        73.74        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-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.34        81.83        85.15        85.68        78.77        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD 
        4.08         0.89        22.03         0.92        48.10         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 
        1.15        17.82         1.64        16.14         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA 
        0.03         4.67        16.57        18.08         0.76        17.06 
TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        4.14         1.35        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
        2.99        20.05        48.92        47.41        10.26        16.90 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J 
       17.23        43.17        27.19        27.85         2.60        15.68 
TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU 
        6.74        87.39        84.72        33.40        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       16.64        32.45         8.71 

  DNMT3A MUTATED DNMT3A WILD-TYPE 
            0.99             0.03 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
            7.66           158.83 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
            6.77            17.23 
[1] "1.0 - 7.7 (6.8)"    "0.0 - 158.8 (17.2)"
[1] "hr=" "230"
D7V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  DNMT3A MUTATED         0        0         3        0         0         0
  DNMT3A WILD-TYPE     228       44        80        2        33         6
D7V3, multiclass
           clus
vv          DNMT3A MUTATED DNMT3A WILD-TYPE
  STAGE I                0              228
  STAGE II               0               44
  STAGE III              3               80
  STAGE IV               0                2
  STAGE IVA              0               33
  STAGE IVC              0                6
[1] 6 2
[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
  DNMT3A MUTATED     0   0   3   0
  DNMT3A WILD-TYPE 116 137 124  15
D7V4, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  T1              0              116
  T2              0              137
  T3              3              124
  T4              0               15
[1] 4 2
[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
  DNMT3A MUTATED     2   1
  DNMT3A WILD-TYPE 186 168
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      2    1
  DNMT3A WILD-TYPE  186  168
   clus
vv  DNMT3A MUTATED DNMT3A WILD-TYPE
  0              2              186
  1              1              168
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  DNMT3A MUTATED     2   0   1
  DNMT3A WILD-TYPE 217   7 170
D7V6, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  M0              2              217
  M1              0                7
  MX              1              170
[1] 3 2
[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
  DNMT3A MUTATED     3   0
  DNMT3A WILD-TYPE 294 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      3    0
  DNMT3A WILD-TYPE  294  101
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE              3              294
  MALE                0              101
[1] 2 2
[1] FALSE
                  vv
clus               OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DNMT3A MUTATED                0                                             2
  DNMT3A WILD-TYPE              6                                           278
                  vv
clus               THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DNMT3A MUTATED                                                                        1
  DNMT3A WILD-TYPE                                                                     82
                  vv
clus               THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DNMT3A MUTATED                                                                     0
  DNMT3A WILD-TYPE                                                                  29
D7V8, multiclass
                                                                        clus
vv                                                                       DNMT3A MUTATED
  OTHER  SPECIFY                                                                      0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 0
                                                                        clus
vv                                                                       DNMT3A WILD-TYPE
  OTHER  SPECIFY                                                                        6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       278
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               82
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  29
[1] 4 2
[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
  DNMT3A MUTATED     0   3
  DNMT3A WILD-TYPE  12 383
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      0    3
  DNMT3A WILD-TYPE   12  383
     clus
vv    DNMT3A MUTATED DNMT3A WILD-TYPE
  NO               0               12
  YES              3              383
[1] 2 2
[1] FALSE
D7V10, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     2   1
  DNMT3A WILD-TYPE 332  14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      2    1
  DNMT3A WILD-TYPE  332   14
     clus
vv    DNMT3A MUTATED DNMT3A WILD-TYPE
  NO               2              332
  YES              1               14
[1] 2 2
[1] FALSE
                  vv
clus               MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DNMT3A MUTATED              2                       0    1
  DNMT3A WILD-TYPE          100                      11  269
                  vv
clus               VERY ADVANCED (T4B)
  DNMT3A MUTATED                     0
  DNMT3A WILD-TYPE                   1
D7V11, multiclass
                         clus
vv                        DNMT3A MUTATED DNMT3A WILD-TYPE
  MINIMAL (T3)                         2              100
  MODERATE/ADVANCED (T4A)              0               11
  NONE                                 1              269
  VERY ADVANCED (T4B)                  0                1
[1] 4 2
[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
  DNMT3A MUTATED     2   1   0   0
  DNMT3A WILD-TYPE 309  36   3  22
D7V12, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  R0              2              309
  R1              1               36
  R2              0                3
  RX              0               22
[1] 4 2
[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
  DNMT3A MUTATED     1   2
  DNMT3A WILD-TYPE 179 207
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      1    2
  DNMT3A WILD-TYPE  179  207
            clus
vv           DNMT3A MUTATED DNMT3A WILD-TYPE
  MULTIFOCAL              1              179
  UNIFOCAL                2              207
[1] 2 2
[1] FALSE
D7V15, continuous
[1] "Remove cluster labels:" "DNMT3A MUTATED"        
clus
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               2              322 
      TCGA-BJ-A0Z2       TCGA-BJ-A0Z3       TCGA-BJ-A0Z9       TCGA-BJ-A0ZA 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A0ZB       TCGA-BJ-A0ZC       TCGA-BJ-A0ZE       TCGA-BJ-A0ZG 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A0ZH       TCGA-BJ-A0ZJ       TCGA-BJ-A18Y       TCGA-BJ-A18Z 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A191       TCGA-BJ-A192       TCGA-BJ-A28R       TCGA-BJ-A28S 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A28T       TCGA-BJ-A28V       TCGA-BJ-A28Z       TCGA-BJ-A290 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A2N8       TCGA-BJ-A2N9       TCGA-BJ-A2P4       TCGA-BJ-A3PU 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A45D       TCGA-BJ-A45E       TCGA-BJ-A45F       TCGA-BJ-A45G 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A45I       TCGA-BJ-A45J       TCGA-BJ-A45K       TCGA-BJ-A4O8 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A4O9       TCGA-CE-A13K       TCGA-CE-A27D       TCGA-CE-A3MD 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CE-A3ME       TCGA-CE-A482       TCGA-CE-A484       TCGA-CE-A485 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DE-A0XZ       TCGA-DE-A0Y2       TCGA-DE-A0Y3       TCGA-DE-A2OL 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DE-A3KN       TCGA-DE-A4M8       TCGA-DE-A4M9       TCGA-DJ-A13M 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A13O       TCGA-DJ-A13R       TCGA-DJ-A13S       TCGA-DJ-A13U 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A13V       TCGA-DJ-A13W       TCGA-DJ-A13X       TCGA-DJ-A1QD 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A1QE       TCGA-DJ-A1QF       TCGA-DJ-A1QG       TCGA-DJ-A1QH 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A1QI       TCGA-DJ-A1QL       TCGA-DJ-A1QM       TCGA-DJ-A1QN 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A1QO       TCGA-DJ-A1QQ       TCGA-DJ-A2PN       TCGA-DJ-A2PO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PP       TCGA-DJ-A2PQ       TCGA-DJ-A2PR       TCGA-DJ-A2PS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PT       TCGA-DJ-A2PU       TCGA-DJ-A2PV       TCGA-DJ-A2PW 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PY       TCGA-DJ-A2PZ       TCGA-DJ-A2Q0       TCGA-DJ-A2Q1 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2Q3       TCGA-DJ-A2Q4       TCGA-DJ-A2Q5       TCGA-DJ-A2Q6 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2Q7       TCGA-DJ-A2Q8       TCGA-DJ-A2Q9       TCGA-DJ-A2QA 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2QC       TCGA-DJ-A3UK       TCGA-DJ-A3UM       TCGA-DJ-A3UN 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A3UO       TCGA-DJ-A3UP       TCGA-DJ-A3UQ       TCGA-DJ-A3UR 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A3US       TCGA-DJ-A3UT       TCGA-DJ-A3UU       TCGA-DJ-A3UW 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A3UX       TCGA-DJ-A3UY       TCGA-DJ-A3V7       TCGA-DJ-A3VA 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A3VB       TCGA-DJ-A3VE       TCGA-DJ-A3VF       TCGA-DJ-A3VJ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A3VL       TCGA-DJ-A3VM       TCGA-DJ-A4UL       TCGA-DJ-A4UT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A4V0       TCGA-DJ-A4V2       TCGA-DJ-A4V4       TCGA-DJ-A4V5 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DO-A1JZ       TCGA-DO-A1K0       TCGA-DO-A2HM       TCGA-E3-A3DY 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-E3-A3DZ       TCGA-E3-A3E0       TCGA-E3-A3E1       TCGA-E3-A3E2 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-E3-A3E3       TCGA-E8-A419       TCGA-EL-A3CN       TCGA-EL-A3CO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CS       TCGA-EL-A3CT       TCGA-EL-A3CU       TCGA-EL-A3CV 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CW       TCGA-EL-A3CX       TCGA-EL-A3CY       TCGA-EL-A3CZ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3D0       TCGA-EL-A3D1       TCGA-EL-A3D4       TCGA-EL-A3D5 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3D6       TCGA-EL-A3GO       TCGA-EL-A3GP       TCGA-EL-A3GQ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GR       TCGA-EL-A3GS       TCGA-EL-A3GU       TCGA-EL-A3GV 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GW       TCGA-EL-A3GX       TCGA-EL-A3GY       TCGA-EL-A3GZ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3H2       TCGA-EL-A3H3       TCGA-EL-A3H4       TCGA-EL-A3H5 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3H7       TCGA-EL-A3H8       TCGA-EL-A3MW       TCGA-EL-A3MX 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3MY       TCGA-EL-A3MZ       TCGA-EL-A3N2       TCGA-EL-A3N3 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3T1       TCGA-EL-A3T2       TCGA-EL-A3T3       TCGA-EL-A3T6 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3T7       TCGA-EL-A3T8       TCGA-EL-A3T9       TCGA-EL-A3TA 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3TB       TCGA-EL-A3ZH       TCGA-EL-A3ZK       TCGA-EL-A3ZN 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3ZQ       TCGA-EL-A3ZR       TCGA-EL-A3ZT       TCGA-EL-A4JV 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A4JW       TCGA-EL-A4JX       TCGA-EL-A4JZ       TCGA-EL-A4K0 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A4K2       TCGA-EL-A4K4       TCGA-EL-A4K6       TCGA-EL-A4KD 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A4KG       TCGA-EL-A4KH       TCGA-EL-A4KI       TCGA-EM-A1CS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A1CT       TCGA-EM-A1CU       TCGA-EM-A1CV       TCGA-EM-A1CW 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A1YA       TCGA-EM-A1YB       TCGA-EM-A1YC       TCGA-EM-A1YD 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A1YE       TCGA-EM-A22I       TCGA-EM-A22J       TCGA-EM-A22K 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A22L       TCGA-EM-A22N       TCGA-EM-A22O       TCGA-EM-A22P 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A22Q       TCGA-EM-A2CJ       TCGA-EM-A2CK       TCGA-EM-A2CL 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2CN       TCGA-EM-A2CO       TCGA-EM-A2CP       TCGA-EM-A2CQ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2CR       TCGA-EM-A2CT       TCGA-EM-A2CU       TCGA-EM-A2OW 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2OX       TCGA-EM-A2OY       TCGA-EM-A2P0       TCGA-EM-A2P1 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2P2       TCGA-EM-A2P3       TCGA-EM-A3AI       TCGA-EM-A3AJ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3AK       TCGA-EM-A3AL       TCGA-EM-A3AN       TCGA-EM-A3AO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3AP       TCGA-EM-A3AQ       TCGA-EM-A3AR       TCGA-EM-A3FJ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3FM       TCGA-EM-A3FN       TCGA-EM-A3FO       TCGA-EM-A3FP 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3FR       TCGA-EM-A3O3       TCGA-EM-A3O6       TCGA-EM-A3O7 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3O8       TCGA-EM-A3O9       TCGA-EM-A3OA       TCGA-EM-A3OB 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A4FK       TCGA-EM-A4FM       TCGA-EM-A4FQ       TCGA-EM-A4FR 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A4FV       TCGA-EM-A4G1       TCGA-ET-A25G       TCGA-ET-A25I 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A25J       TCGA-ET-A25K       TCGA-ET-A25O       TCGA-ET-A25R 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A2MY       TCGA-ET-A2MZ       TCGA-ET-A2N0       TCGA-ET-A2N5 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A39J       TCGA-ET-A39M       TCGA-ET-A39N       TCGA-ET-A39O 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A39P       TCGA-ET-A39T       TCGA-ET-A3BN       TCGA-ET-A3BO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3BP       TCGA-ET-A3BQ       TCGA-ET-A3BS       TCGA-ET-A3BT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3BU       TCGA-ET-A3BV       TCGA-ET-A3BW       TCGA-ET-A3BX 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3DO       TCGA-ET-A3DS       TCGA-ET-A3DT       TCGA-ET-A40S 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A4KN       TCGA-FE-A22Z       TCGA-FE-A230       TCGA-FE-A232 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A233       TCGA-FE-A234       TCGA-FE-A235       TCGA-FE-A236 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A237       TCGA-FE-A23A       TCGA-FE-A3PB       TCGA-FE-A3PC 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A3PD       TCGA-FY-A2QD       TCGA-FY-A3I4       TCGA-FY-A3I5 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FY-A3ON       TCGA-FY-A3R8       TCGA-FY-A3W9       TCGA-FY-A40K 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FY-A4B3       TCGA-GE-A2C6       TCGA-H2-A421       TCGA-IM-A3EB 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-IM-A3ED       TCGA-IM-A3U2       TCGA-IM-A3U3       TCGA-J8-A3O0 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KS-A41J       TCGA-KS-A4I5       TCGA-KS-A4I9       TCGA-KS-A4IB 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-L6-A4EP       TCGA-L6-A4ET       TCGA-L6-A4EU       TCGA-MK-A4N6 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-MK-A4N7       TCGA-MK-A4N9 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNMT3A MUTATED       0                         0     3
  DNMT3A WILD-TYPE    35                        18   255
D7V16, multiclass
                           clus
vv                          DNMT3A MUTATED DNMT3A WILD-TYPE
  ASIAN                                  0               35
  BLACK OR AFRICAN AMERICAN              0               18
  WHITE                                  3              255
[1] 3 2
[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
  DNMT3A MUTATED     0   3
  DNMT3A WILD-TYPE  31 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      0    3
  DNMT3A WILD-TYPE   31  280
                        clus
vv                       DNMT3A MUTATED DNMT3A WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              3              280
[1] 2 2
[1] FALSE

Clustering(8) Variable = KRAS MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     4   0
  KRAS WILD-TYPE 379  13
  KRAS MUTATED KRAS WILD-TYPE 
             4            392 
  KRAS MUTATED KRAS WILD-TYPE 
             0             13 
$`KRAS MUTATED`
TCGA-BJ-A0ZE TCGA-EM-A2CQ TCGA-EM-A4FV TCGA-H2-A3RH 
       16.73        12.30        12.72        12.46 

$`KRAS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        18.21        16.34         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
        4.01        11.57         7.56        15.12        17.69        23.34 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.71         4.83         8.09         4.87        21.04         2.79 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
        5.10        17.52         1.22        30.21        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         6.48         0.03         3.45         6.35 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
        0.10         0.20         0.23        10.68         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        15.85        18.54 
TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
       18.84        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       25.35        13.41        11.90        14.60         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      100.01        18.51        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45         8.88         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28         7.69         5.52         8.78         8.42         8.12 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        9.34         6.77         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF 
       21.37         9.83        11.93        22.92        18.97         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UT TCGA-DJ-A4UW 
       17.36        17.23        27.62        18.21        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 
       30.31        14.04         1.15        22.29        13.61        13.81 
TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
        3.02        14.70        14.96         7.69        13.78        13.58 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82         1.45        74.30        45.40        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        39.32         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      124.04        50.37        37.25       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       129.57        32.48       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH 
       41.29        95.38         5.72        66.90        82.82        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV 
       31.50        53.06        45.53        48.16        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 
       19.30        45.96        37.94        31.04        30.51        33.60 
TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       28.73        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       54.21        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        11.74        11.15        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-A2CR TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       13.64        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        17.59        17.46        17.29        14.60 
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-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        7.82         9.01         4.83         8.38         9.80         5.03 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O 
        0.95        47.47        48.20        29.69        32.35        27.09 
TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 
       29.49        22.09        12.26        16.08        29.19         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       24.72         5.03         4.01        73.74        59.70        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-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
       81.83        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL 
        0.89        22.03         0.92        48.10         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 
       17.82         1.64         0.99        16.14         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA 
        0.03         4.67        16.57        18.08         0.76        17.06 
TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RI 
        4.14         1.35        12.53        17.00        21.67         2.99 
TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ 
       20.05        48.92        47.41        10.26        16.90        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 
       43.17        27.19        27.85         2.60        15.68         6.74 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       87.39        84.72        33.40        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

  KRAS MUTATED KRAS WILD-TYPE 
         12.30           0.03 
  KRAS MUTATED KRAS WILD-TYPE 
         16.73         158.83 
  KRAS MUTATED KRAS WILD-TYPE 
         12.59          17.23 
[1] "12.3 - 16.7 (12.6)" "0.0 - 158.8 (17.2)"
[1] "hr="     "1200000"
D8V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  KRAS MUTATED         3        0         1        0         0         0
  KRAS WILD-TYPE     225       44        82        2        33         6
D8V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE I              3            225
  STAGE II             0             44
  STAGE III            1             82
  STAGE IV             0              2
  STAGE IVA            0             33
  STAGE IVC            0              6
[1] 6 2
[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
  KRAS MUTATED     3   0   1   0
  KRAS WILD-TYPE 113 137 126  15
D8V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            3            113
  T2            0            137
  T3            1            126
  T4            0             15
[1] 4 2
[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
  KRAS MUTATED     3   1
  KRAS WILD-TYPE 185 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      3    1
  KRAS WILD-TYPE  185  168
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            3            185
  1            1            168
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  KRAS MUTATED     2   0   2
  KRAS WILD-TYPE 217   7 169
D8V6, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  M0            2            217
  M1            0              7
  MX            2            169
[1] 3 2
[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
  KRAS MUTATED     4   0
  KRAS WILD-TYPE 293 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4    0
  KRAS WILD-TYPE  293  101
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            4            293
  MALE              0            101
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  KRAS MUTATED                0                                             2
  KRAS WILD-TYPE              6                                           278
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  KRAS MUTATED                                                                        2
  KRAS WILD-TYPE                                                                     81
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  KRAS MUTATED                                                                     0
  KRAS WILD-TYPE                                                                  29
D8V8, multiclass
                                                                        clus
vv                                                                       KRAS MUTATED
  OTHER  SPECIFY                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)            2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       KRAS WILD-TYPE
  OTHER  SPECIFY                                                                      6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     278
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             81
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                29
[1] 4 2
[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
  KRAS MUTATED     0   4
  KRAS WILD-TYPE  12 382
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    4
  KRAS WILD-TYPE   12  382
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             0             12
  YES            4            382
[1] 2 2
[1] FALSE
D8V10, binary
                cls
clus               0   1
  KRAS MUTATED     4   0
  KRAS WILD-TYPE 330  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4    0
  KRAS WILD-TYPE  330   15
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             4            330
  YES            0             15
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  KRAS MUTATED              1                       0    3                   0
  KRAS WILD-TYPE          101                      11  267                   1
D8V11, multiclass
                         clus
vv                        KRAS MUTATED KRAS WILD-TYPE
  MINIMAL (T3)                       1            101
  MODERATE/ADVANCED (T4A)            0             11
  NONE                               3            267
  VERY ADVANCED (T4B)                0              1
[1] 4 2
[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
  KRAS MUTATED     2   1   0   0
  KRAS WILD-TYPE 309  36   3  22
D8V12, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0            2            309
  R1            1             36
  R2            0              3
  RX            0             22
[1] 4 2
[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
  KRAS MUTATED     2   2
  KRAS WILD-TYPE 178 207
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2    2
  KRAS WILD-TYPE  178  207
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  MULTIFOCAL            2            178
  UNIFOCAL              2            207
[1] 2 2
[1] FALSE
D8V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0     2
  KRAS WILD-TYPE    35                        18   256
D8V16, multiclass
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2            309 
    TCGA-BJ-A0YZ     TCGA-BJ-A0Z2     TCGA-BJ-A0Z3     TCGA-BJ-A0Z9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A0ZA     TCGA-BJ-A0ZB     TCGA-BJ-A0ZC     TCGA-BJ-A0ZG 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A0ZH     TCGA-BJ-A0ZJ     TCGA-BJ-A18Y     TCGA-BJ-A18Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A191     TCGA-BJ-A192     TCGA-BJ-A28R     TCGA-BJ-A28S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A28T     TCGA-BJ-A28V     TCGA-BJ-A28X     TCGA-BJ-A28Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A290     TCGA-BJ-A2N7     TCGA-BJ-A2N8     TCGA-BJ-A2N9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A2NA     TCGA-BJ-A2P4     TCGA-BJ-A3EZ     TCGA-BJ-A3F0 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A3PR     TCGA-BJ-A3PT     TCGA-BJ-A3PU     TCGA-BJ-A45D 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A45E     TCGA-BJ-A45F     TCGA-BJ-A45G     TCGA-BJ-A45I 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A45J     TCGA-BJ-A45K     TCGA-BJ-A4O8     TCGA-BJ-A4O9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CE-A13K     TCGA-CE-A27D     TCGA-CE-A3MD     TCGA-CE-A3ME 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CE-A482     TCGA-CE-A484     TCGA-CE-A485     TCGA-DE-A0XZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DE-A0Y2     TCGA-DE-A0Y3     TCGA-DE-A2OL     TCGA-DE-A3KN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DE-A4M8     TCGA-DE-A4M9     TCGA-DJ-A13M     TCGA-DJ-A13O 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A13P     TCGA-DJ-A13R     TCGA-DJ-A13S     TCGA-DJ-A13T 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A13U     TCGA-DJ-A13W     TCGA-DJ-A1QD     TCGA-DJ-A1QE 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A1QF     TCGA-DJ-A1QG     TCGA-DJ-A1QH     TCGA-DJ-A1QI 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A1QM     TCGA-DJ-A1QO     TCGA-DJ-A1QQ     TCGA-DJ-A2PN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2PO     TCGA-DJ-A2PQ     TCGA-DJ-A2PR     TCGA-DJ-A2PT 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2PU     TCGA-DJ-A2PV     TCGA-DJ-A2PW     TCGA-DJ-A2PX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2PY     TCGA-DJ-A2PZ     TCGA-DJ-A2Q0     TCGA-DJ-A2Q1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q2     TCGA-DJ-A2Q3     TCGA-DJ-A2Q4     TCGA-DJ-A2Q5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q6     TCGA-DJ-A2Q7     TCGA-DJ-A2Q9     TCGA-DJ-A2QA 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2QB     TCGA-DJ-A3UK     TCGA-DJ-A3UM     TCGA-DJ-A3UN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A3UO     TCGA-DJ-A3UQ     TCGA-DJ-A3UR     TCGA-DJ-A3US 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A3UT     TCGA-DJ-A3UU     TCGA-DJ-A3UW     TCGA-DJ-A3UX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A3UY     TCGA-DJ-A3V7     TCGA-DJ-A3VE     TCGA-DJ-A3VF 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A3VJ     TCGA-DJ-A3VL     TCGA-DJ-A3VM     TCGA-DJ-A4UL 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A4UT     TCGA-DJ-A4UW     TCGA-DJ-A4V0     TCGA-DJ-A4V4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A4V5     TCGA-DO-A1JZ     TCGA-DO-A1K0     TCGA-DO-A2HM 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E3-A3DY     TCGA-E3-A3DZ     TCGA-E3-A3E0     TCGA-E3-A3E1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E3-A3E2     TCGA-E3-A3E3     TCGA-E3-A3E5     TCGA-E8-A242 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A2EA     TCGA-E8-A413     TCGA-E8-A415     TCGA-E8-A418 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A419     TCGA-E8-A433     TCGA-E8-A436     TCGA-E8-A437 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A44K     TCGA-E8-A44M     TCGA-EL-A3CL     TCGA-EL-A3CM 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CN     TCGA-EL-A3CO     TCGA-EL-A3CP     TCGA-EL-A3CR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CS     TCGA-EL-A3CT     TCGA-EL-A3CU     TCGA-EL-A3CV 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CW     TCGA-EL-A3CX     TCGA-EL-A3CY     TCGA-EL-A3CZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3D0     TCGA-EL-A3D1     TCGA-EL-A3D4     TCGA-EL-A3D5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3D6     TCGA-EL-A3GO     TCGA-EL-A3GP     TCGA-EL-A3GQ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GR     TCGA-EL-A3GS     TCGA-EL-A3GU     TCGA-EL-A3GV 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GW     TCGA-EL-A3GX     TCGA-EL-A3GY     TCGA-EL-A3GZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3H1     TCGA-EL-A3H2     TCGA-EL-A3H3     TCGA-EL-A3H4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3H5     TCGA-EL-A3H7     TCGA-EL-A3H8     TCGA-EL-A3MW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3MX     TCGA-EL-A3MY     TCGA-EL-A3MZ     TCGA-EL-A3N2 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3N3     TCGA-EL-A3T0     TCGA-EL-A3T1     TCGA-EL-A3T2 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3T3     TCGA-EL-A3T6     TCGA-EL-A3T7     TCGA-EL-A3T8 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3T9     TCGA-EL-A3TA     TCGA-EL-A3TB     TCGA-EL-A3ZH 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3ZK     TCGA-EL-A3ZN     TCGA-EL-A3ZQ     TCGA-EL-A3ZR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3ZT     TCGA-EL-A4JV     TCGA-EL-A4JW     TCGA-EL-A4JX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A4JZ     TCGA-EL-A4K0     TCGA-EL-A4K2     TCGA-EL-A4K4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A4K6     TCGA-EL-A4KD     TCGA-EL-A4KG     TCGA-EL-A4KH 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A4KI     TCGA-ET-A25G     TCGA-ET-A25I     TCGA-ET-A25J 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A25K     TCGA-ET-A25O     TCGA-ET-A25R     TCGA-ET-A2MY 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A2MZ     TCGA-ET-A2N0     TCGA-ET-A2N1     TCGA-ET-A2N4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A2N5     TCGA-ET-A39I     TCGA-ET-A39J     TCGA-ET-A39K 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39M     TCGA-ET-A39N     TCGA-ET-A39O     TCGA-ET-A39P 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39R     TCGA-ET-A39S     TCGA-ET-A39T     TCGA-ET-A3BN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BO     TCGA-ET-A3BQ     TCGA-ET-A3BS     TCGA-ET-A3BT 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BU     TCGA-ET-A3BV     TCGA-ET-A3BW     TCGA-ET-A3DO 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3DP     TCGA-ET-A3DQ     TCGA-ET-A3DR     TCGA-ET-A3DS 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3DT     TCGA-ET-A3DU     TCGA-ET-A3DV     TCGA-ET-A3DW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A40S     TCGA-ET-A4KN     TCGA-FE-A22Z     TCGA-FE-A230 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A231     TCGA-FE-A232     TCGA-FE-A233     TCGA-FE-A234 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A235     TCGA-FE-A236     TCGA-FE-A237     TCGA-FE-A23A 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A3PB     TCGA-FE-A3PC     TCGA-FE-A3PD     TCGA-FK-A3S3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FK-A3SB     TCGA-FK-A3SD     TCGA-FK-A3SE     TCGA-FK-A3SG 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FK-A3SH     TCGA-FY-A2QD     TCGA-FY-A3BL     TCGA-FY-A3I4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A3I5     TCGA-FY-A3NM     TCGA-FY-A3NP     TCGA-FY-A3ON 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A3R6     TCGA-FY-A3R7     TCGA-FY-A3R8     TCGA-FY-A3R9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A3RA     TCGA-FY-A3W9     TCGA-FY-A3WA     TCGA-FY-A40K 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A4B3     TCGA-GE-A2C6     TCGA-H2-A26U     TCGA-H2-A2K9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-H2-A3RI     TCGA-H2-A421     TCGA-IM-A3EB     TCGA-IM-A3ED 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IM-A3U2     TCGA-IM-A3U3     TCGA-J8-A3NZ     TCGA-J8-A3O0 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-J8-A3O1     TCGA-J8-A3YE     TCGA-J8-A4HW     TCGA-KS-A41J 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KS-A4I5     TCGA-KS-A4I9     TCGA-KS-A4IB     TCGA-L6-A4EP 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-L6-A4ET     TCGA-L6-A4EU     TCGA-MK-A4N6     TCGA-MK-A4N7 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-MK-A4N9 
"KRAS WILD-TYPE" 
D8V17, binary
                cls
clus               0   1
  KRAS MUTATED     0   2
  KRAS WILD-TYPE  31 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    2
  KRAS WILD-TYPE   31  281
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO            2            281
[1] 2 2
[1] FALSE

Clustering(9) Variable = DLC1 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  DLC1 MUTATED     3   1
  DLC1 WILD-TYPE 380  12
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            392 
  DLC1 MUTATED DLC1 WILD-TYPE 
             1             12 
$`DLC1 MUTATED`
TCGA-EL-A3CR TCGA-EL-A3N2 TCGA-EL-A3T3 TCGA-EM-A2OW 
        7.66        12.16       116.91        13.84 

$`DLC1 WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        18.21        16.34         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         4.83         8.09         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 
        2.79         5.10        17.52         1.22        30.21        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 
       16.57        20.48        18.97         7.04        16.01        13.94 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       15.48        23.31        18.64         6.48         0.03         3.45 
TCGA-BJ-A45G TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        6.35         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
        0.53         0.10         0.20         0.23        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       18.54        18.84        17.26        14.07       137.88         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        25.35        13.41        11.90        14.60         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.12         9.34         6.77         9.21         9.44         9.90 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
        8.61        10.09         7.07        10.36        12.43        10.85 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        12.49        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        24.23        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       11.34        21.37         9.83        11.93        22.92        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UT 
        7.76        17.36        17.23        27.62        18.21        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-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 
       63.19        30.31        14.04         1.15        22.29        13.61 
TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K 
       13.81         3.02        14.70        14.96         7.69        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82         1.45        74.30        45.40        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        39.32         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      124.04        50.37        37.25       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N3 
      131.15       108.66        57.63        17.52        52.50       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      130.72       129.57        32.48        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
        5.72        66.90        82.82        78.97        31.50        53.06 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       45.53        48.16        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD 
       37.94        31.04        30.51        33.60        28.73        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR 
       13.18        23.51         6.05         2.99        12.30        13.64 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       10.49        13.15        22.16        19.73        17.59        12.07 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK 
        7.33        12.53         9.24        13.91         7.82         9.01 
TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 
        4.83         8.38         9.80         5.03        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R 
       47.47        48.20        29.69        32.35        27.09        29.49 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 
       22.09        12.26        16.08        29.19         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        5.03         4.01        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A 
       24.69        68.22       102.90        66.77        81.34        81.83 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
       22.03         0.92        48.10         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.64         0.99        16.14         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K 
        4.67        16.57        18.08         0.76        17.06         4.14 
TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.35        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ 
       20.05        48.92        47.41        10.26        16.90        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 
       43.17        27.19        27.85         2.60        15.68         6.74 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       87.39        84.72        33.40        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

  DLC1 MUTATED DLC1 WILD-TYPE 
          7.66           0.03 
  DLC1 MUTATED DLC1 WILD-TYPE 
        116.91         158.83 
  DLC1 MUTATED DLC1 WILD-TYPE 
        13.000         17.145 
[1] "7.7 - 116.9 (13.0)" "0.0 - 158.8 (17.1)"
[1] "hr=" "5.6"
D9V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  DLC1 MUTATED         2        1         1        0         0         0
  DLC1 WILD-TYPE     226       43        82        2        33         6
D9V3, multiclass
           clus
vv          DLC1 MUTATED DLC1 WILD-TYPE
  STAGE I              2            226
  STAGE II             1             43
  STAGE III            1             82
  STAGE IV             0              2
  STAGE IVA            0             33
  STAGE IVC            0              6
[1] 6 2
[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
  DLC1 MUTATED     1   2   1   0
  DLC1 WILD-TYPE 115 135 126  15
D9V4, multiclass
    clus
vv   DLC1 MUTATED DLC1 WILD-TYPE
  T1            1            115
  T2            2            135
  T3            1            126
  T4            0             15
[1] 4 2
[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
  DLC1 MUTATED     1   2
  DLC1 WILD-TYPE 187 167
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      1    2
  DLC1 WILD-TYPE  187  167
   clus
vv  DLC1 MUTATED DLC1 WILD-TYPE
  0            1            187
  1            2            167
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  DLC1 MUTATED     3   0   1
  DLC1 WILD-TYPE 216   7 170
D9V6, multiclass
    clus
vv   DLC1 MUTATED DLC1 WILD-TYPE
  M0            3            216
  M1            0              7
  MX            1            170
[1] 3 2
[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
  DLC1 MUTATED     3   1
  DLC1 WILD-TYPE 294 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      3    1
  DLC1 WILD-TYPE  294  100
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  FEMALE            3            294
  MALE              1            100
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DLC1 MUTATED                0                                             3
  DLC1 WILD-TYPE              6                                           277
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DLC1 MUTATED                                                                        1
  DLC1 WILD-TYPE                                                                     82
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DLC1 MUTATED                                                                     0
  DLC1 WILD-TYPE                                                                  29
D9V8, multiclass
                                                                        clus
vv                                                                       DLC1 MUTATED
  OTHER  SPECIFY                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)            1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       DLC1 WILD-TYPE
  OTHER  SPECIFY                                                                      6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     277
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             82
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                29
[1] 4 2
[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
  DLC1 MUTATED     0   4
  DLC1 WILD-TYPE  12 382
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      0    4
  DLC1 WILD-TYPE   12  382
     clus
vv    DLC1 MUTATED DLC1 WILD-TYPE
  NO             0             12
  YES            4            382
[1] 2 2
[1] FALSE
D9V10, binary
                cls
clus               0   1
  DLC1 MUTATED     4   0
  DLC1 WILD-TYPE 330  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      4    0
  DLC1 WILD-TYPE  330   15
     clus
vv    DLC1 MUTATED DLC1 WILD-TYPE
  NO             4            330
  YES            0             15
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  DLC1 MUTATED              2                       0    2                   0
  DLC1 WILD-TYPE          100                      11  268                   1
D9V11, multiclass
                         clus
vv                        DLC1 MUTATED DLC1 WILD-TYPE
  MINIMAL (T3)                       2            100
  MODERATE/ADVANCED (T4A)            0             11
  NONE                               2            268
  VERY ADVANCED (T4B)                0              1
[1] 4 2
[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
  DLC1 MUTATED     3   1   0   0
  DLC1 WILD-TYPE 308  36   3  22
D9V12, multiclass
    clus
vv   DLC1 MUTATED DLC1 WILD-TYPE
  R0            3            308
  R1            1             36
  R2            0              3
  RX            0             22
[1] 4 2
[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
  DLC1 MUTATED     1   3
  DLC1 WILD-TYPE 179 206
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      1    3
  DLC1 WILD-TYPE  179  206
            clus
vv           DLC1 MUTATED DLC1 WILD-TYPE
  MULTIFOCAL            1            179
  UNIFOCAL              3            206
[1] 2 2
[1] FALSE
D9V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DLC1 MUTATED       0                         0     3
  DLC1 WILD-TYPE    35                        18   255
D9V16, multiclass
                           clus
vv                          DLC1 MUTATED DLC1 WILD-TYPE
  ASIAN                                0             35
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                                3            255
[1] 3 2
[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
  DLC1 MUTATED     1   2
  DLC1 WILD-TYPE  30 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      1    2
  DLC1 WILD-TYPE   30  281
                        clus
vv                       DLC1 MUTATED DLC1 WILD-TYPE
  HISPANIC OR LATINO                1             30
  NOT HISPANIC OR LATINO            2            281
[1] 2 2
[1] FALSE

Clustering(10) Variable = ITGAL MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  ITGAL MUTATED     3   1
  ITGAL WILD-TYPE 380  12
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             392 
  ITGAL MUTATED ITGAL WILD-TYPE 
              1              12 
$`ITGAL MUTATED`
TCGA-BJ-A0ZB TCGA-EL-A3T3 TCGA-EL-A3T9 TCGA-EM-A3AO 
        4.01       116.91         5.72        13.38 

$`ITGAL WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        18.21        16.34         8.25        18.87 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
       11.57        16.73         7.56        15.12        17.69        23.34 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.71         4.83         8.09         4.87        21.04         2.79 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
        5.10        17.52         1.22        30.21        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        15.48 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         6.48         0.03         3.45         6.35 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
        0.10         0.20         0.23        10.68         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        15.85        18.54 
TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
       18.84        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       25.35        13.41        11.90        14.60         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      100.01        18.51        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45         8.88         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28         7.69         5.52         8.78         8.42         8.12 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        9.34         6.77         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF 
       21.37         9.83        11.93        22.92        18.97         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UT TCGA-DJ-A4UW 
       17.36        17.23        27.62        18.21        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 
       30.31        14.04         1.15        22.29        13.61        13.81 
TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
        3.02        14.70        14.96         7.69        13.78        13.58 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82         1.45        74.30        45.40        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        39.32         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      124.04        50.37        37.25       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T6 TCGA-EL-A3T7 
      147.42       130.72       129.57        32.48        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
       95.38        66.90        82.82        78.97        31.50        53.06 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       45.53        48.16        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD 
       37.94        31.04        30.51        33.60        28.73        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR 
       13.18        23.51         6.05         2.99        12.30        13.64 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AP TCGA-EM-A3AQ 
       18.97        15.68        14.14        19.63         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK 
        7.33        12.53         9.24        13.91         7.82         9.01 
TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 
        4.83         8.38         9.80         5.03        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R 
       47.47        48.20        29.69        32.35        27.09        29.49 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 
       22.09        12.26        16.08        29.19         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        5.03         4.01        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A 
       24.69        68.22       102.90        66.77        81.34        81.83 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
       22.03         0.92        48.10         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.64         0.99        16.14         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K 
        4.67        16.57        18.08         0.76        17.06         4.14 
TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.35        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ 
       20.05        48.92        47.41        10.26        16.90        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 
       43.17        27.19        27.85         2.60        15.68         6.74 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       87.39        84.72        33.40        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

  ITGAL MUTATED ITGAL WILD-TYPE 
           4.01            0.03 
  ITGAL MUTATED ITGAL WILD-TYPE 
         116.91          158.83 
  ITGAL MUTATED ITGAL WILD-TYPE 
          9.550          17.145 
[1] "4.0 - 116.9 (9.6)"  "0.0 - 158.8 (17.1)"
[1] "hr=" "5.9"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  ITGAL MUTATED         0        1         0        1         2         0
  ITGAL WILD-TYPE     228       43        83        1        31         6
D10V3, multiclass
           clus
vv          ITGAL MUTATED ITGAL WILD-TYPE
  STAGE I               0             228
  STAGE II              1              43
  STAGE III             0              83
  STAGE IV              1               1
  STAGE IVA             2              31
  STAGE IVC             0               6
[1] 6 2
[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
  ITGAL MUTATED     0   2   1   1
  ITGAL WILD-TYPE 116 135 126  14
D10V4, multiclass
    clus
vv   ITGAL MUTATED ITGAL WILD-TYPE
  T1             0             116
  T2             2             135
  T3             1             126
  T4             1              14
[1] 4 2
[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
  ITGAL MUTATED     1   3
  ITGAL WILD-TYPE 187 166
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    3
  ITGAL WILD-TYPE  187  166
   clus
vv  ITGAL MUTATED ITGAL WILD-TYPE
  0             1             187
  1             3             166
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  ITGAL MUTATED     2   0   2
  ITGAL WILD-TYPE 217   7 169
D10V6, multiclass
    clus
vv   ITGAL MUTATED ITGAL WILD-TYPE
  M0             2             217
  M1             0               7
  MX             2             169
[1] 3 2
[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
  ITGAL MUTATED     1   3
  ITGAL WILD-TYPE 296  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    3
  ITGAL WILD-TYPE  296   98
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  FEMALE             1             296
  MALE               3              98
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  ITGAL MUTATED                0                                             4
  ITGAL WILD-TYPE              6                                           276
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  ITGAL MUTATED                                                                        0
  ITGAL WILD-TYPE                                                                     83
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  ITGAL MUTATED                                                                     0
  ITGAL WILD-TYPE                                                                  29
D10V8, multiclass
                                                                        clus
vv                                                                       ITGAL MUTATED
  OTHER  SPECIFY                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                0
                                                                        clus
vv                                                                       ITGAL WILD-TYPE
  OTHER  SPECIFY                                                                       6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      276
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              83
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 29
[1] 4 2
[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
  ITGAL MUTATED     0   4
  ITGAL WILD-TYPE  12 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      0    4
  ITGAL WILD-TYPE   12  382
     clus
vv    ITGAL MUTATED ITGAL WILD-TYPE
  NO              0              12
  YES             4             382
[1] 2 2
[1] FALSE
D10V10, binary
                 cls
clus                0   1
  ITGAL MUTATED     4   0
  ITGAL WILD-TYPE 330  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      4    0
  ITGAL WILD-TYPE  330   15
     clus
vv    ITGAL MUTATED ITGAL WILD-TYPE
  NO              4             330
  YES             0              15
[1] 2 2
[1] FALSE
                 vv
clus              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  ITGAL MUTATED              0                       1    2                   1
  ITGAL WILD-TYPE          102                      10  268                   0
D10V11, multiclass
                         clus
vv                        ITGAL MUTATED ITGAL WILD-TYPE
  MINIMAL (T3)                        0             102
  MODERATE/ADVANCED (T4A)             1              10
  NONE                                2             268
  VERY ADVANCED (T4B)                 1               0
[1] 4 2
[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
  ITGAL MUTATED     2   2   0   0
  ITGAL WILD-TYPE 309  35   3  22
D10V12, multiclass
    clus
vv   ITGAL MUTATED ITGAL WILD-TYPE
  R0             2             309
  R1             2              35
  R2             0               3
  RX             0              22
[1] 4 2
[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
[1] "Remove cluster labels:" "ITGAL MUTATED"         
clus
  ITGAL MUTATED ITGAL WILD-TYPE 
              2             308 
     TCGA-BJ-A0Z0      TCGA-BJ-A0Z3      TCGA-BJ-A0Z9      TCGA-BJ-A0ZA 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A0ZH      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y      TCGA-BJ-A18Z 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A191      TCGA-BJ-A28R      TCGA-BJ-A28T      TCGA-BJ-A28X 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A28Z      TCGA-BJ-A290      TCGA-BJ-A2N8      TCGA-BJ-A2N9 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A2NA      TCGA-BJ-A3EZ      TCGA-BJ-A3PR      TCGA-BJ-A3PU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A45D      TCGA-BJ-A45E      TCGA-BJ-A45G      TCGA-BJ-A45I 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A45J      TCGA-BJ-A45K      TCGA-BJ-A4O8      TCGA-BJ-A4O9 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-CE-A13K      TCGA-CE-A3MD      TCGA-DE-A0XZ      TCGA-DE-A0Y2 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DE-A0Y3      TCGA-DE-A3KN      TCGA-DE-A4M8      TCGA-DJ-A13M 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A13O      TCGA-DJ-A13P      TCGA-DJ-A13R      TCGA-DJ-A13T 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A13U      TCGA-DJ-A13V      TCGA-DJ-A13W      TCGA-DJ-A13X 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A1QG      TCGA-DJ-A1QH      TCGA-DJ-A1QM      TCGA-DJ-A2PO 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PP      TCGA-DJ-A2PQ      TCGA-DJ-A2PR      TCGA-DJ-A2PS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PT      TCGA-DJ-A2PU      TCGA-DJ-A2PV      TCGA-DJ-A2PW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PX      TCGA-DJ-A2PY      TCGA-DJ-A2PZ      TCGA-DJ-A2Q0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q1      TCGA-DJ-A2Q2      TCGA-DJ-A2Q3      TCGA-DJ-A2Q4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q5      TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q8 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q9      TCGA-DJ-A2QA      TCGA-DJ-A2QB      TCGA-DJ-A3UK 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3UM      TCGA-DJ-A3UN      TCGA-DJ-A3UO      TCGA-DJ-A3UP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3UQ      TCGA-DJ-A3UR      TCGA-DJ-A3UU      TCGA-DJ-A3UW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3UX      TCGA-DJ-A3V7      TCGA-DJ-A3VA      TCGA-DJ-A3VB 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3VF      TCGA-DJ-A3VJ      TCGA-DJ-A3VL      TCGA-DJ-A4UL 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A4UW      TCGA-DJ-A4V2      TCGA-DJ-A4V5      TCGA-DO-A1K0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DO-A2HM      TCGA-E3-A3DY      TCGA-E3-A3DZ      TCGA-E3-A3E0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E3-A3E1      TCGA-E3-A3E2      TCGA-E3-A3E3      TCGA-E3-A3E5 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E8-A242      TCGA-E8-A2EA      TCGA-E8-A415      TCGA-E8-A419 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E8-A433      TCGA-E8-A436      TCGA-E8-A44K      TCGA-EL-A3CM 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CN      TCGA-EL-A3CO      TCGA-EL-A3CR      TCGA-EL-A3CS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CT      TCGA-EL-A3CU      TCGA-EL-A3CV      TCGA-EL-A3CW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CX      TCGA-EL-A3CY      TCGA-EL-A3CZ      TCGA-EL-A3D0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3D1      TCGA-EL-A3D4      TCGA-EL-A3D5      TCGA-EL-A3D6 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GO      TCGA-EL-A3GP      TCGA-EL-A3GQ      TCGA-EL-A3GS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GU      TCGA-EL-A3GV      TCGA-EL-A3GX      TCGA-EL-A3H3 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3H4      TCGA-EL-A3H5      TCGA-EL-A3H7      TCGA-EL-A3H8 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3MW      TCGA-EL-A3MX      TCGA-EL-A3MZ      TCGA-EL-A3N2 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3T0      TCGA-EL-A3T1      TCGA-EL-A3T2      TCGA-EL-A3TB 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3ZH      TCGA-EL-A3ZK      TCGA-EL-A3ZN      TCGA-EL-A4JV 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A4JW      TCGA-EL-A4JX      TCGA-EL-A4JZ      TCGA-EL-A4K0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A4K2      TCGA-EL-A4K4      TCGA-EL-A4K6      TCGA-EL-A4KD 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A4KG      TCGA-EL-A4KI      TCGA-EM-A1CS      TCGA-EM-A1CT 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1CU      TCGA-EM-A1CV      TCGA-EM-A1CW      TCGA-EM-A1YA 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1YB      TCGA-EM-A1YC      TCGA-EM-A1YD      TCGA-EM-A1YE 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22K      TCGA-EM-A22L 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A22M      TCGA-EM-A22N      TCGA-EM-A22O      TCGA-EM-A22P 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A22Q      TCGA-EM-A2CK      TCGA-EM-A2CN      TCGA-EM-A2CP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CT      TCGA-EM-A2CU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2OV      TCGA-EM-A2OW      TCGA-EM-A2OX      TCGA-EM-A2OY 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2OZ      TCGA-EM-A2P0      TCGA-EM-A2P1      TCGA-EM-A2P2 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2P3      TCGA-EM-A3AJ      TCGA-EM-A3AK      TCGA-EM-A3AL 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3AN      TCGA-EM-A3AQ      TCGA-EM-A3AR      TCGA-EM-A3FJ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3FK      TCGA-EM-A3FL      TCGA-EM-A3FM      TCGA-EM-A3FN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3FO      TCGA-EM-A3FP      TCGA-EM-A3FQ      TCGA-EM-A3FR 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3O3      TCGA-EM-A3O7      TCGA-EM-A3O8      TCGA-EM-A3O9 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3OA      TCGA-EM-A3OB      TCGA-EM-A4FK      TCGA-EM-A4FM 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A4FO      TCGA-EM-A4FQ      TCGA-EM-A4FR      TCGA-EM-A4FV 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A4G1      TCGA-ET-A25G      TCGA-ET-A25I      TCGA-ET-A25J 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A25K      TCGA-ET-A25O      TCGA-ET-A2MZ      TCGA-ET-A2N0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A2N1      TCGA-ET-A2N4      TCGA-ET-A39K      TCGA-ET-A39L 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A39O      TCGA-ET-A39P      TCGA-ET-A39R      TCGA-ET-A39S 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A39T      TCGA-ET-A3BO      TCGA-ET-A3BP      TCGA-ET-A3BQ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3BS      TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3BX      TCGA-ET-A3DQ      TCGA-ET-A3DR      TCGA-ET-A3DS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3DT      TCGA-ET-A3DU      TCGA-ET-A3DV      TCGA-ET-A3DW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A40S      TCGA-ET-A4KN      TCGA-FE-A22Z      TCGA-FE-A230 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A231      TCGA-FE-A232      TCGA-FE-A233      TCGA-FE-A234 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237      TCGA-FE-A23A 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A3PB      TCGA-FE-A3PC      TCGA-FE-A3PD      TCGA-FK-A3S3 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FK-A3SB      TCGA-FK-A3SE      TCGA-FK-A3SG      TCGA-FK-A3SH 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FY-A2QD      TCGA-FY-A3I4      TCGA-FY-A3I5      TCGA-FY-A3NM 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FY-A3NN      TCGA-FY-A3ON      TCGA-FY-A3R6      TCGA-FY-A3R7 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FY-A3R9      TCGA-FY-A3W9      TCGA-FY-A40K      TCGA-FY-A4B3 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-GE-A2C6      TCGA-H2-A26U      TCGA-H2-A2K9      TCGA-H2-A3RH 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-H2-A3RI      TCGA-H2-A421      TCGA-IM-A3EB      TCGA-IM-A3ED 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-IM-A3U2      TCGA-IM-A3U3      TCGA-J8-A3NZ      TCGA-J8-A3O0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-J8-A3O1      TCGA-J8-A3YE      TCGA-J8-A4HW      TCGA-KS-A41J 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-KS-A4I5      TCGA-KS-A4I9      TCGA-KS-A4IB      TCGA-L6-A4EP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-L6-A4EU      TCGA-MK-A4N6      TCGA-MK-A4N7      TCGA-MK-A4N9 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
D10V14, binary
                 cls
clus                0   1
  ITGAL MUTATED     1   3
  ITGAL WILD-TYPE 179 206
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    3
  ITGAL WILD-TYPE  179  206
            clus
vv           ITGAL MUTATED ITGAL WILD-TYPE
  MULTIFOCAL             1             179
  UNIFOCAL               3             206
[1] 2 2
[1] FALSE
D10V15, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITGAL MUTATED       0                         0     3
  ITGAL WILD-TYPE    35                        18   255
D10V16, multiclass
                           clus
vv                          ITGAL MUTATED ITGAL WILD-TYPE
  ASIAN                                 0              35
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 3             255
[1] 3 2
[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
  ITGAL MUTATED     1   2
  ITGAL WILD-TYPE  30 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    2
  ITGAL WILD-TYPE   30  281
                        clus
vv                       ITGAL MUTATED ITGAL WILD-TYPE
  HISPANIC OR LATINO                 1              30
  NOT HISPANIC OR LATINO             2             281
[1] 2 2
[1] FALSE

Clustering(11) Variable = NLRP6 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  NLRP6 MUTATED     3   0
  NLRP6 WILD-TYPE 380  13
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             393 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              0              13 
$`NLRP6 MUTATED`
TCGA-EM-A3FO TCGA-FE-A3PC TCGA-FK-A3S3 
       17.49        85.68        46.06 

$`NLRP6 WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        18.21        16.34         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         4.83         8.09         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 
        2.79         5.10        17.52         1.22        30.21        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 
       16.57        20.48        18.97         7.04        16.01        13.94 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       15.48        23.31        18.64         6.48         0.03         3.45 
TCGA-BJ-A45G TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        6.35         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
        0.53         0.10         0.20         0.23        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       18.54        18.84        17.26        14.07       137.88         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        25.35        13.41        11.90        14.60         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.12         9.34         6.77         9.21         9.44         9.90 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
        8.61        10.09         7.07        10.36        12.43        10.85 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        12.49        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        24.23        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       11.34        21.37         9.83        11.93        22.92        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UT 
        7.76        17.36        17.23        27.62        18.21        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-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 
       63.19        30.31        14.04         1.15        22.29        13.61 
TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K 
       13.81         3.02        14.70        14.96         7.69        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        31.66        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-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
       80.91         4.18        58.82         1.45        74.30        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       33.47       108.36        39.32         1.41        30.18       102.84 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       124.04        50.37        37.25       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      139.99        49.32        33.50        43.36        38.66        52.73 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       12.16       147.42       130.72       129.57        32.48       116.91 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29        95.38         5.72        66.90        82.82 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT 
       78.97        31.50        53.06        45.53        48.16        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 
       45.80        19.30        45.96        37.94        31.04        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       33.60        28.73        29.95        13.32        11.87         8.71 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        12.36        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        54.21        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        11.74        11.15 
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-A2CU TCGA-EM-A2OV 
        2.99        12.30        13.64        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        19.73        17.59        12.07        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        17.46        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        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-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        11.15         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ 
       13.91         7.82         9.01         4.83         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
        5.03        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       32.35        27.09        29.49        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       29.19         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z 
       25.32       132.36        24.72         5.03         4.01        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PD TCGA-FK-A3SB 
       66.77        81.34        81.83        85.15        78.77         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL 
        0.89        22.03         0.92        48.10         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 
       17.82         1.64         0.99        16.14         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA 
        0.03         4.67        16.57        18.08         0.76        17.06 
TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        4.14         1.35        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
        2.99        20.05        48.92        47.41        10.26        16.90 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J 
       17.23        43.17        27.19        27.85         2.60        15.68 
TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU 
        6.74        87.39        84.72        33.40        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       16.64        32.45         8.71 

  NLRP6 MUTATED NLRP6 WILD-TYPE 
          17.49            0.03 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          85.68          158.83 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          46.06           16.90 
[1] "17.5 - 85.7 (46.1)" "0.0 - 158.8 (16.9)"
[1] "hr="     "9100000"
D11V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  NLRP6 MUTATED         3        0         0        0         0         0
  NLRP6 WILD-TYPE     225       44        83        2        33         6
D11V3, multiclass
           clus
vv          NLRP6 MUTATED NLRP6 WILD-TYPE
  STAGE I               3             225
  STAGE II              0              44
  STAGE III             0              83
  STAGE IV              0               2
  STAGE IVA             0              33
  STAGE IVC             0               6
[1] 6 2
[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
  NLRP6 MUTATED     0   0   3   0
  NLRP6 WILD-TYPE 116 137 124  15
D11V4, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  T1             0             116
  T2             0             137
  T3             3             124
  T4             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                 cls
clus                0   1
  NLRP6 MUTATED     1   2
  NLRP6 WILD-TYPE 187 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      1    2
  NLRP6 WILD-TYPE  187  167
   clus
vv  NLRP6 MUTATED NLRP6 WILD-TYPE
  0             1             187
  1             2             167
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  NLRP6 MUTATED     0   0   3
  NLRP6 WILD-TYPE 219   7 168
D11V6, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  M0             0             219
  M1             0               7
  MX             3             168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                 cls
clus                0   1
  NLRP6 MUTATED     2   1
  NLRP6 WILD-TYPE 295 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      2    1
  NLRP6 WILD-TYPE  295  100
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  FEMALE             2             295
  MALE               1             100
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  NLRP6 MUTATED                0                                             2
  NLRP6 WILD-TYPE              6                                           278
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  NLRP6 MUTATED                                                                        1
  NLRP6 WILD-TYPE                                                                     82
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  NLRP6 MUTATED                                                                     0
  NLRP6 WILD-TYPE                                                                  29
D11V8, multiclass
                                                                        clus
vv                                                                       NLRP6 MUTATED
  OTHER  SPECIFY                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                0
                                                                        clus
vv                                                                       NLRP6 WILD-TYPE
  OTHER  SPECIFY                                                                       6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      278
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              82
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   3
  NLRP6 WILD-TYPE  12 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    3
  NLRP6 WILD-TYPE   12  383
     clus
vv    NLRP6 MUTATED NLRP6 WILD-TYPE
  NO              0              12
  YES             3             383
[1] 2 2
[1] FALSE
D11V10, binary
                 cls
clus                0   1
  NLRP6 MUTATED     3   0
  NLRP6 WILD-TYPE 331  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      3    0
  NLRP6 WILD-TYPE  331   15
     clus
vv    NLRP6 MUTATED NLRP6 WILD-TYPE
  NO              3             331
  YES             0              15
[1] 2 2
[1] FALSE
                 vv
clus              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  NLRP6 MUTATED              1                       0    2                   0
  NLRP6 WILD-TYPE          101                      11  268                   1
D11V11, multiclass
                         clus
vv                        NLRP6 MUTATED NLRP6 WILD-TYPE
  MINIMAL (T3)                        1             101
  MODERATE/ADVANCED (T4A)             0              11
  NONE                                2             268
  VERY ADVANCED (T4B)                 0               1
[1] 4 2
[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
  NLRP6 MUTATED     3   0   0   0
  NLRP6 WILD-TYPE 308  37   3  22
D11V12, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  R0             3             308
  R1             0              37
  R2             0               3
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, continuous
D11V14, binary
                 cls
clus                0   1
  NLRP6 MUTATED     2   1
  NLRP6 WILD-TYPE 178 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      2    1
  NLRP6 WILD-TYPE  178  208
            clus
vv           NLRP6 MUTATED NLRP6 WILD-TYPE
  MULTIFOCAL             2             178
  UNIFOCAL               1             208
[1] 2 2
[1] FALSE
D11V15, continuous
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2             322 
     TCGA-BJ-A0Z2      TCGA-BJ-A0Z3      TCGA-BJ-A0Z9      TCGA-BJ-A0ZA 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0ZB      TCGA-BJ-A0ZC      TCGA-BJ-A0ZE      TCGA-BJ-A0ZG 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0ZH      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y      TCGA-BJ-A18Z 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A191      TCGA-BJ-A192      TCGA-BJ-A28R      TCGA-BJ-A28S 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A28T      TCGA-BJ-A28V      TCGA-BJ-A28Z      TCGA-BJ-A290 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A2N8      TCGA-BJ-A2N9      TCGA-BJ-A2P4      TCGA-BJ-A3PU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A45D      TCGA-BJ-A45E      TCGA-BJ-A45F      TCGA-BJ-A45G 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A45I      TCGA-BJ-A45J      TCGA-BJ-A45K      TCGA-BJ-A4O8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A4O9      TCGA-CE-A13K      TCGA-CE-A27D      TCGA-CE-A3MD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-CE-A3ME      TCGA-CE-A482      TCGA-CE-A484      TCGA-CE-A485 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DE-A0XZ      TCGA-DE-A0Y2      TCGA-DE-A0Y3      TCGA-DE-A2OL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DE-A3KN      TCGA-DE-A4M8      TCGA-DE-A4M9      TCGA-DJ-A13M 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13O      TCGA-DJ-A13R      TCGA-DJ-A13S      TCGA-DJ-A13U 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13V      TCGA-DJ-A13W      TCGA-DJ-A13X      TCGA-DJ-A1QD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QE      TCGA-DJ-A1QF      TCGA-DJ-A1QG      TCGA-DJ-A1QH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QI      TCGA-DJ-A1QL      TCGA-DJ-A1QM      TCGA-DJ-A1QN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QO      TCGA-DJ-A1QQ      TCGA-DJ-A2PN      TCGA-DJ-A2PO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PP      TCGA-DJ-A2PQ      TCGA-DJ-A2PR      TCGA-DJ-A2PS 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PT      TCGA-DJ-A2PU      TCGA-DJ-A2PV      TCGA-DJ-A2PW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PY      TCGA-DJ-A2PZ      TCGA-DJ-A2Q0      TCGA-DJ-A2Q1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q2      TCGA-DJ-A2Q3      TCGA-DJ-A2Q4      TCGA-DJ-A2Q5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q8      TCGA-DJ-A2Q9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2QA      TCGA-DJ-A2QC      TCGA-DJ-A3UK      TCGA-DJ-A3UM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UN      TCGA-DJ-A3UO      TCGA-DJ-A3UP      TCGA-DJ-A3UQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UR      TCGA-DJ-A3US      TCGA-DJ-A3UT      TCGA-DJ-A3UU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UW      TCGA-DJ-A3UX      TCGA-DJ-A3UY      TCGA-DJ-A3V7 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3VA      TCGA-DJ-A3VB      TCGA-DJ-A3VE      TCGA-DJ-A3VF 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3VJ      TCGA-DJ-A3VL      TCGA-DJ-A3VM      TCGA-DJ-A4UL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4UT      TCGA-DJ-A4V0      TCGA-DJ-A4V2      TCGA-DJ-A4V4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4V5      TCGA-DO-A1JZ      TCGA-DO-A1K0      TCGA-DO-A2HM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3DY      TCGA-E3-A3DZ      TCGA-E3-A3E0      TCGA-E3-A3E1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3E2      TCGA-E3-A3E3      TCGA-E8-A419      TCGA-EL-A3CN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CO      TCGA-EL-A3CR      TCGA-EL-A3CS      TCGA-EL-A3CT 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CU      TCGA-EL-A3CV      TCGA-EL-A3CW      TCGA-EL-A3CX 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CY      TCGA-EL-A3CZ      TCGA-EL-A3D0      TCGA-EL-A3D1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D4      TCGA-EL-A3D5      TCGA-EL-A3D6      TCGA-EL-A3GO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GP      TCGA-EL-A3GQ      TCGA-EL-A3GR      TCGA-EL-A3GS 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GU      TCGA-EL-A3GV      TCGA-EL-A3GW      TCGA-EL-A3GX 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GY      TCGA-EL-A3GZ      TCGA-EL-A3H2      TCGA-EL-A3H3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H4      TCGA-EL-A3H5      TCGA-EL-A3H7      TCGA-EL-A3H8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3MW      TCGA-EL-A3MX      TCGA-EL-A3MY      TCGA-EL-A3MZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3N2      TCGA-EL-A3N3      TCGA-EL-A3T1      TCGA-EL-A3T2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T3      TCGA-EL-A3T6      TCGA-EL-A3T7      TCGA-EL-A3T8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T9      TCGA-EL-A3TA      TCGA-EL-A3TB      TCGA-EL-A3ZH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3ZK      TCGA-EL-A3ZN      TCGA-EL-A3ZQ      TCGA-EL-A3ZR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3ZT      TCGA-EL-A4JV      TCGA-EL-A4JW      TCGA-EL-A4JX 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4JZ      TCGA-EL-A4K0      TCGA-EL-A4K2      TCGA-EL-A4K4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4K6      TCGA-EL-A4KD      TCGA-EL-A4KG      TCGA-EL-A4KH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4KI      TCGA-EM-A1CS      TCGA-EM-A1CT      TCGA-EM-A1CU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1CV      TCGA-EM-A1CW      TCGA-EM-A1YA      TCGA-EM-A1YB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1YC      TCGA-EM-A1YD      TCGA-EM-A1YE      TCGA-EM-A22I 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A22J      TCGA-EM-A22K      TCGA-EM-A22L      TCGA-EM-A22N 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A22O      TCGA-EM-A22P      TCGA-EM-A22Q      TCGA-EM-A2CJ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CK      TCGA-EM-A2CL      TCGA-EM-A2CN      TCGA-EM-A2CO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CP      TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CT 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CU      TCGA-EM-A2OW      TCGA-EM-A2OX      TCGA-EM-A2OY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2P0      TCGA-EM-A2P1      TCGA-EM-A2P2      TCGA-EM-A2P3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AI      TCGA-EM-A3AJ      TCGA-EM-A3AK      TCGA-EM-A3AL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AN      TCGA-EM-A3AO      TCGA-EM-A3AP      TCGA-EM-A3AQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AR      TCGA-EM-A3FJ      TCGA-EM-A3FM      TCGA-EM-A3FN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3FP      TCGA-EM-A3FR      TCGA-EM-A3O3      TCGA-EM-A3O6 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3O7      TCGA-EM-A3O8      TCGA-EM-A3O9      TCGA-EM-A3OA 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3OB      TCGA-EM-A4FK      TCGA-EM-A4FM      TCGA-EM-A4FQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A4FR      TCGA-EM-A4FV      TCGA-EM-A4G1      TCGA-ET-A25G 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A25I      TCGA-ET-A25J      TCGA-ET-A25K      TCGA-ET-A25O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A25R      TCGA-ET-A2MY      TCGA-ET-A2MZ      TCGA-ET-A2N0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2N5      TCGA-ET-A39J      TCGA-ET-A39M      TCGA-ET-A39N 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39O      TCGA-ET-A39P      TCGA-ET-A39T      TCGA-ET-A3BN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BO      TCGA-ET-A3BP      TCGA-ET-A3BQ      TCGA-ET-A3BS 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV      TCGA-ET-A3BW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BX      TCGA-ET-A3DO      TCGA-ET-A3DS      TCGA-ET-A3DT 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A40S      TCGA-ET-A4KN      TCGA-FE-A22Z      TCGA-FE-A230 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A232      TCGA-FE-A233      TCGA-FE-A234      TCGA-FE-A235 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A236      TCGA-FE-A237      TCGA-FE-A23A      TCGA-FE-A3PB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A3PD      TCGA-FY-A2QD      TCGA-FY-A3I4      TCGA-FY-A3I5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3ON      TCGA-FY-A3R8      TCGA-FY-A3W9      TCGA-FY-A40K 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A4B3      TCGA-GE-A2C6      TCGA-H2-A421      TCGA-IM-A3EB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IM-A3ED      TCGA-IM-A3U2      TCGA-IM-A3U3      TCGA-J8-A3O0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-KS-A41J      TCGA-KS-A4I5      TCGA-KS-A4I9      TCGA-KS-A4IB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-L6-A4EP      TCGA-L6-A4ET      TCGA-L6-A4EU      TCGA-MK-A4N6 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-MK-A4N7      TCGA-MK-A4N9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NLRP6 MUTATED       0                         1     1
  NLRP6 WILD-TYPE    35                        17   257
D11V16, multiclass
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2             309 
     TCGA-BJ-A0YZ      TCGA-BJ-A0Z2      TCGA-BJ-A0Z3      TCGA-BJ-A0Z9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0ZA      TCGA-BJ-A0ZB      TCGA-BJ-A0ZC      TCGA-BJ-A0ZE 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0ZG      TCGA-BJ-A0ZH      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A18Z      TCGA-BJ-A191      TCGA-BJ-A192      TCGA-BJ-A28R 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A28S      TCGA-BJ-A28T      TCGA-BJ-A28V      TCGA-BJ-A28X 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A28Z      TCGA-BJ-A290      TCGA-BJ-A2N7      TCGA-BJ-A2N8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A2N9      TCGA-BJ-A2NA      TCGA-BJ-A2P4      TCGA-BJ-A3EZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A3F0      TCGA-BJ-A3PR      TCGA-BJ-A3PT      TCGA-BJ-A3PU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A45D      TCGA-BJ-A45E      TCGA-BJ-A45F      TCGA-BJ-A45G 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A45I      TCGA-BJ-A45J      TCGA-BJ-A45K      TCGA-BJ-A4O8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A4O9      TCGA-CE-A13K      TCGA-CE-A27D      TCGA-CE-A3MD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-CE-A3ME      TCGA-CE-A482      TCGA-CE-A484      TCGA-CE-A485 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DE-A0XZ      TCGA-DE-A0Y2      TCGA-DE-A0Y3      TCGA-DE-A2OL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DE-A3KN      TCGA-DE-A4M8      TCGA-DE-A4M9      TCGA-DJ-A13M 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13O      TCGA-DJ-A13P      TCGA-DJ-A13R      TCGA-DJ-A13S 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13T      TCGA-DJ-A13U      TCGA-DJ-A13W      TCGA-DJ-A1QD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QE      TCGA-DJ-A1QF      TCGA-DJ-A1QG      TCGA-DJ-A1QH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QI      TCGA-DJ-A1QM      TCGA-DJ-A1QO      TCGA-DJ-A1QQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PN      TCGA-DJ-A2PO      TCGA-DJ-A2PQ      TCGA-DJ-A2PR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PT      TCGA-DJ-A2PU      TCGA-DJ-A2PV      TCGA-DJ-A2PW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PX      TCGA-DJ-A2PY      TCGA-DJ-A2PZ      TCGA-DJ-A2Q0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q1      TCGA-DJ-A2Q2      TCGA-DJ-A2Q3      TCGA-DJ-A2Q4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q5      TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2QA      TCGA-DJ-A2QB      TCGA-DJ-A3UK      TCGA-DJ-A3UM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UN      TCGA-DJ-A3UO      TCGA-DJ-A3UQ      TCGA-DJ-A3UR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3US      TCGA-DJ-A3UT      TCGA-DJ-A3UU      TCGA-DJ-A3UW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UX      TCGA-DJ-A3UY      TCGA-DJ-A3V7      TCGA-DJ-A3VE 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3VF      TCGA-DJ-A3VJ      TCGA-DJ-A3VL      TCGA-DJ-A3VM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4UL      TCGA-DJ-A4UT      TCGA-DJ-A4UW      TCGA-DJ-A4V0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4V4      TCGA-DJ-A4V5      TCGA-DO-A1JZ      TCGA-DO-A1K0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DO-A2HM      TCGA-E3-A3DY      TCGA-E3-A3DZ      TCGA-E3-A3E0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3E1      TCGA-E3-A3E2      TCGA-E3-A3E3      TCGA-E3-A3E5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E8-A242      TCGA-E8-A2EA      TCGA-E8-A413      TCGA-E8-A415 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E8-A418      TCGA-E8-A419      TCGA-E8-A433      TCGA-E8-A436 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E8-A437      TCGA-E8-A44K      TCGA-E8-A44M      TCGA-EL-A3CL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CM      TCGA-EL-A3CN      TCGA-EL-A3CO      TCGA-EL-A3CP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CR      TCGA-EL-A3CS      TCGA-EL-A3CT      TCGA-EL-A3CU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CV      TCGA-EL-A3CW      TCGA-EL-A3CX      TCGA-EL-A3CY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CZ      TCGA-EL-A3D0      TCGA-EL-A3D1      TCGA-EL-A3D4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D5      TCGA-EL-A3D6      TCGA-EL-A3GO      TCGA-EL-A3GP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GQ      TCGA-EL-A3GR      TCGA-EL-A3GS      TCGA-EL-A3GU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GV      TCGA-EL-A3GW      TCGA-EL-A3GX      TCGA-EL-A3GY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GZ      TCGA-EL-A3H1      TCGA-EL-A3H2      TCGA-EL-A3H3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H4      TCGA-EL-A3H5      TCGA-EL-A3H7      TCGA-EL-A3H8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3MW      TCGA-EL-A3MX      TCGA-EL-A3MY      TCGA-EL-A3MZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3N2      TCGA-EL-A3N3      TCGA-EL-A3T0      TCGA-EL-A3T1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T2      TCGA-EL-A3T3      TCGA-EL-A3T6      TCGA-EL-A3T7 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T8      TCGA-EL-A3T9      TCGA-EL-A3TA      TCGA-EL-A3TB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3ZH      TCGA-EL-A3ZK      TCGA-EL-A3ZN      TCGA-EL-A3ZQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3ZR      TCGA-EL-A3ZT      TCGA-EL-A4JV      TCGA-EL-A4JW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4JX      TCGA-EL-A4JZ      TCGA-EL-A4K0      TCGA-EL-A4K2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4K4      TCGA-EL-A4K6      TCGA-EL-A4KD      TCGA-EL-A4KG 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4KH      TCGA-EL-A4KI      TCGA-ET-A25G      TCGA-ET-A25I 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A25J      TCGA-ET-A25K      TCGA-ET-A25O      TCGA-ET-A25R 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2MY      TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2N4      TCGA-ET-A2N5      TCGA-ET-A39I      TCGA-ET-A39J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39K      TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39P      TCGA-ET-A39R      TCGA-ET-A39S      TCGA-ET-A39T 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BN      TCGA-ET-A3BO      TCGA-ET-A3BQ      TCGA-ET-A3BS 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV      TCGA-ET-A3BW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DO      TCGA-ET-A3DP      TCGA-ET-A3DQ      TCGA-ET-A3DR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DS      TCGA-ET-A3DT      TCGA-ET-A3DU      TCGA-ET-A3DV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DW      TCGA-ET-A40S      TCGA-ET-A4KN      TCGA-FE-A22Z 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A230      TCGA-FE-A231      TCGA-FE-A232      TCGA-FE-A233 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A23A      TCGA-FE-A3PB      TCGA-FE-A3PD      TCGA-FK-A3SB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FK-A3SD      TCGA-FK-A3SE      TCGA-FK-A3SG      TCGA-FK-A3SH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A2QD      TCGA-FY-A3BL      TCGA-FY-A3I4      TCGA-FY-A3I5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3NM      TCGA-FY-A3NP      TCGA-FY-A3ON      TCGA-FY-A3R6 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3R7      TCGA-FY-A3R8      TCGA-FY-A3R9      TCGA-FY-A3RA 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3W9      TCGA-FY-A3WA      TCGA-FY-A40K      TCGA-FY-A4B3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-GE-A2C6      TCGA-H2-A26U      TCGA-H2-A2K9      TCGA-H2-A3RH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-H2-A3RI      TCGA-H2-A421      TCGA-IM-A3EB      TCGA-IM-A3ED 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IM-A3U2      TCGA-IM-A3U3      TCGA-J8-A3NZ      TCGA-J8-A3O0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-J8-A3O1      TCGA-J8-A3YE      TCGA-J8-A4HW      TCGA-KS-A41J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-KS-A4I5      TCGA-KS-A4I9      TCGA-KS-A4IB      TCGA-L6-A4EP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-L6-A4ET      TCGA-L6-A4EU      TCGA-MK-A4N6      TCGA-MK-A4N7 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-MK-A4N9 
"NLRP6 WILD-TYPE" 
D11V17, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   2
  NLRP6 WILD-TYPE  31 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    2
  NLRP6 WILD-TYPE   31  281
                        clus
vv                       NLRP6 MUTATED NLRP6 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             2             281
[1] 2 2
[1] FALSE
