[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/11548104/transformed.cor.cli.txt"

nPatients in clinical file=497, in cluster file=501, common to both=495
[1] "Reduce the number of clustering variables from 80 to 57."
[1]  57 495
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               491 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               491 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25               470 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25               470 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               492 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               492 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               490 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               490 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               490 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               490 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               475 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               475 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               16               479 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               16               479 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               17               478 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               17               478 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19               476 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19               476 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               489 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               489 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               488 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               488 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               492 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               492 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               491 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               491 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                489 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                489 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                490 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                490 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                481 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                481 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                480 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                480 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                490 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                490 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                484 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                484 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                480 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                480 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                482 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                482 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                479 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                479 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                478 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                478 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                489 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                489 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                489 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                489 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                487 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                487 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                485 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                485 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                483 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                483 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                483 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                483 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                490 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                490 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9               486 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9               486 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               491 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               491 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               492 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               492 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               485 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               485 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               485 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               485 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               492 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               492 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               491 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               491 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4               491 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4               491 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               488 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               488 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               491 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               491 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               491 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               491 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19               476 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19               476 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23               472 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23               472 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                488 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                488 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                489 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                489 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                488 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                488 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                486 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                486 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                481 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                481 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                487 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                487 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                488 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                488 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                491 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                491 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                491 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                491 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                491 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                491 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                490 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                490 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                487 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                487 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                87                408 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                87                408 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               492 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               492 
[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 495 columns.

[1] "Batch" "24"   
[1] "Last Follow UP"
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
         754          419          554          497          448          251 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
         574          122          352          509          230          460 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
         538          710          630          626          147          246 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
         148          640           85          155          344          533 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
          37          919          696          559          504          623 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
         577          214          487          424          471          709 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
         567          175          197            1          105          193 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
         238          188          154          273          150          182 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
          16            3            6            7          346          325 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
           3           12            3          615          469         1109 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
         182          482          564          573          916          352 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
         913          764          130           98           84          525 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
         428         4194          103          265          771          408 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
         362          444          243          335         3042          563 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
         399          243          455          219           44          270 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
          31          181          307          243          162          258 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
         318           46          292          382          252          234 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
         168          267          256          247          284          206 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
         280          287          301          262          307          215 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
         315          378          330          483          459          944 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
         380          957          499          595         1105          998 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
         737          538         1308          345          650          388 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
         761          615          931          443          584          299 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
         647          623          363          697          639          577 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
         236          253          528          524          840          554 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
         328          334          430          447          542           95 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
         481          740         1670          655           71          945 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
         367         2019         1223         1922          922          427 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
          35          678           NA          596          414          434 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
         420          428          434           92           NA          439 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
         447          429          455          234          629          419 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
         413           NA           NA         4731           NA         4831 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
          NA           NA           NA         4780         1154           NA 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
        2461          127         1789           44         2260         1381 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
        1018         3296         1196           43          918         3128 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
        1989         3773         1532         1133         4494         3076 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
        4258           NA           NA         1319         1176         1604 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
        4228         3989         3305           NA           NA           NA 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
         370         4484         3976         3941          988         3556 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
        2988         1256         2901           NA         2035         2519 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
        2353         2402          958         1531         1614         1441 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
        1597         1385         1465          215         1358         1393 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
         587         1398         1154          944          596          928 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
        1022          874         1251         1149          911          405 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
         361          265          817          553          636          376 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
         549          602          592         1649         1734         1645 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
         448          441          479          318          442          324 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
         357          339          433          500          544          401 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
         715          184           91          374          462          319 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
         400          674          421          600          535          367 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
         535          531          526          444          531          577 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
         477          430          597          407          254          500 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
         510          850          723          511          639          367 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
         532          529          492          457          441          339 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
         223          381          281          423          238          350 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
         499          475          411          389         2149          514 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
         274          147          262          255          298          153 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
        1152          387           29         1444         1466          903 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
         984          450          375          450          824          559 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
         897         1644          672          373          489          888 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
         601           81         1771          418         2160         2434 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
        1988         2582         2998         1856         1786         1737 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
        1676         1799          859          178          127           74 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
         169          752         1165         1285           72          137 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
        2458         2106         1821         1323            9          547 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
         770         4026          752           98          218          146 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
         153           65          122           59         2243         1816 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
         961         1346          751         2075         3130         2031 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
        2474         1215           NA         2489         3235         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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
          28         1463         2773           38           35          542 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NN TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
          50           30           NA           46           23            1 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
         142          504          550            9           23          519 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
         209          126          200          138           27           NA 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
          41           35           51          381          517          659 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
         379           91          610          566         1488         1442 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
         312          514          298          293           90          263 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
         524         1313          827          342          968          847 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
         751          678          175           75           79            6 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
        4367          486          477         2637          183          378 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
         205          987         2658         2577         1073         1011 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
        1016         1228          664           22          506          987 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
         265          334          158 
Variable 1:'AGE':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=407,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONEXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'EXTRATHYROIDAL.EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR.SIZE':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'BATCH.NUMBER':	nDistinctValues=26,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RADIATIONEXPOSURE"                     
[10] "EXTRATHYROIDAL.EXTENSION"              
[11] "COMPLETENESS.OF.RESECTION"             
[12] "NUMBER.OF.LYMPH.NODES"                 
[13] "MULTIFOCALITY"                         
[14] "TUMOR.SIZE"                            
[15] "RACE"                                  
[16] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 495 columns, 1 survival variables, and 16 non-survival variables.
AGE, nv=73, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
140 166 165  21 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
140 166 165  21 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
140 166 165  21 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
140 166 165  21 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RADIATIONEXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL.EXTENSION, nv=4, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=30, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR.SIZE, nv=70, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     3   1
  1P GAIN WILD-TYPE 474  13
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               487 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                13 
$`1P GAIN MUTATED`
TCGA-DO-A2HM TCGA-EL-A3MX TCGA-ET-A3BT TCGA-FY-A3NM 
        2.33        57.63        24.72         0.99 

$`1P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ 
       15.81        24.33        54.90        21.53        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         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-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        4.18         2.43         5.56        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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        39.95        33.63        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         1.64         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.99              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            57.63            158.83 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           13.525            16.570 
[1] "1.0 - 57.6 (13.5)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "9.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  1P GAIN MUTATED         0        0         1        0         2         1
  1P GAIN WILD-TYPE     280       51       108        2        43         5
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0               280
  STAGE II                0                51
  STAGE III               1               108
  STAGE IV                0                 2
  STAGE IVA               2                43
  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
  1P GAIN MUTATED     1   1   1   1
  1P GAIN WILD-TYPE 139 165 164  20
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               1               139
  T2               1               165
  T3               1               164
  T4               1                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"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1   3
  1P GAIN WILD-TYPE 222 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    3
  1P GAIN WILD-TYPE  222  219
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               1               222
  1               3               219
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED     0   1   3
  1P GAIN WILD-TYPE 273   8 209
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               0               273
  M1               1                 8
  MX               3               209
[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
  1P GAIN MUTATED     3   1
  1P GAIN WILD-TYPE 361 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    1
  1P GAIN WILD-TYPE  361  130
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3               361
  MALE                 1               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  1P GAIN MUTATED                0
  1P GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  1P GAIN MUTATED                                               3
  1P GAIN WILD-TYPE                                           350
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  1P GAIN MUTATED                                                                        0
  1P GAIN WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1P GAIN MUTATED                                                                     1
  1P GAIN WILD-TYPE                                                                  34
D1V8, multiclass
                                                                        clus
vv                                                                       1P GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  1
                                                                        clus
vv                                                                       1P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   34
[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
  1P GAIN MUTATED     0   4
  1P GAIN WILD-TYPE  14 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    4
  1P GAIN WILD-TYPE   14  477
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                14
  YES               4               477
[1] 2 2
[1] FALSE
D1V10, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2   1
  1P GAIN WILD-TYPE 415  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    1
  1P GAIN WILD-TYPE  415   16
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                2               415
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  1P GAIN MUTATED              1                       0    3
  1P GAIN WILD-TYPE          129                      16  325
                   vv
clus                VERY ADVANCED (T4B)
  1P GAIN MUTATED                     0
  1P GAIN WILD-TYPE                   1
D1V11, multiclass
                         clus
vv                        1P GAIN MUTATED 1P GAIN WILD-TYPE
  MINIMAL (T3)                          1               129
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  3               325
  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
  1P GAIN MUTATED     2   0   0   2
  1P GAIN WILD-TYPE 376  51   4  28
D1V12, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               2               376
  R1               0                51
  R2               0                 4
  RX               2                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"
D1V13, continuous
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1   3
  1P GAIN WILD-TYPE 223 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    3
  1P GAIN WILD-TYPE  223  258
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  MULTIFOCAL               1               223
  UNIFOCAL                 3               258
[1] 2 2
[1] FALSE
D1V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     0
  1P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           0     4
  1P GAIN WILD-TYPE                        26   317
D1V16, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          4               317
[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"
D1V17, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0   4
  1P GAIN WILD-TYPE  38 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    4
  1P GAIN WILD-TYPE   38  346
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               346
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    21   3
  1Q GAIN WILD-TYPE 456  11
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               24               467 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                11 
$`1Q GAIN MUTATED`
TCGA-BJ-A290 TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DJ-A13U TCGA-DO-A2HM 
       30.21        11.57        30.02        25.12        13.41         2.33 
TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3T9 
        1.41       124.04        52.73        57.63        52.50         5.72 
TCGA-EL-A3ZO TCGA-EL-A4JX TCGA-EM-A3O3 TCGA-ET-A39P TCGA-ET-A3BT TCGA-FE-A231 
       47.38        45.96        14.50        58.72        24.72        31.59 
TCGA-FY-A3NM TCGA-FY-A40L TCGA-IM-A3EB TCGA-J8-A3O1 TCGA-KS-A4IB TCGA-L6-A4EU 
        0.99         6.58        48.92        27.19        84.72         0.72 

$`1Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
        1.22        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A69J TCGA-DE-A69K 
       15.85        18.54        18.84        30.12         4.27         3.22 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       25.35        11.90        14.60         7.99        11.01       100.01 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       18.51        13.12         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-A2PP 
        8.88         1.02         5.95        10.09         7.99         5.33 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
        8.48        10.45         1.51         9.60        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
        7.69         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-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       12.76        25.02        20.22        30.61        14.56        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
        9.83        21.27        20.48        11.93        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        17.36        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       18.21        10.78        10.98        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
        3.12        15.81        24.33        54.90        21.53        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW 
       39.32        30.18       102.84        65.39        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3N2 
       38.66       139.00       131.15       108.66        17.52        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-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29        95.38        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       31.50        50.33        53.06        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 
        7.07        44.65        45.80        19.30        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         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-A39R 
       80.02        65.36        84.89        98.56        61.02        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-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.56        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 
        2.14         4.01         1.94        73.74        59.70        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         1.64         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40M TCGA-FY-A40N 
        0.76        17.06         6.87         4.14         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A3U2 
       12.46         2.99        20.05        18.61        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       43.17        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       87.39        35.28        33.24        33.40        40.37        21.83 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.72              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           124.04            158.83 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           28.605            16.440 
[1] "0.7 - 124.0 (28.6)" "0.0 - 158.8 (16.4)"
[1] "hr=" "3.9"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  1Q GAIN MUTATED         6        0        10        1         7         1
  1Q GAIN WILD-TYPE     274       51        99        1        38         5
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 6               274
  STAGE II                0                51
  STAGE III              10                99
  STAGE IV                1                 1
  STAGE IVA               7                38
  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
  1Q GAIN MUTATED     2   3  15   5
  1Q GAIN WILD-TYPE 138 163 150  16
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               2               138
  T2               3               163
  T3              15               150
  T4               5                16
[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
  1Q GAIN MUTATED     4  20
  1Q GAIN WILD-TYPE 219 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4   20
  1Q GAIN WILD-TYPE  219  202
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               4               219
  1              20               202
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1Q GAIN MUTATED    12   1  12
  1Q GAIN WILD-TYPE 261   8 200
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              12               261
  M1               1                 8
  MX              12               200
[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
  1Q GAIN MUTATED    17   8
  1Q GAIN WILD-TYPE 347 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17    8
  1Q GAIN WILD-TYPE  347  123
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              17               347
  MALE                 8               123
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  1Q GAIN MUTATED                0
  1Q GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  1Q GAIN MUTATED                                              22
  1Q GAIN WILD-TYPE                                           331
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  1Q GAIN MUTATED                                                                        0
  1Q GAIN WILD-TYPE                                                                     98
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1Q GAIN MUTATED                                                                     3
  1Q GAIN WILD-TYPE                                                                  32
D2V8, multiclass
                                                                        clus
vv                                                                       1Q GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       22
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  3
                                                                        clus
vv                                                                       1Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        331
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   32
[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
  1Q GAIN MUTATED     1  24
  1Q GAIN WILD-TYPE  13 457
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   24
  1Q GAIN WILD-TYPE   13  457
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                1                13
  YES              24               457
[1] 2 2
[1] FALSE
D2V10, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    22   1
  1Q GAIN WILD-TYPE 395  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     22    1
  1Q GAIN WILD-TYPE  395   16
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               22               395
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  1Q GAIN MUTATED             11                       3   10
  1Q GAIN WILD-TYPE          119                      13  318
                   vv
clus                VERY ADVANCED (T4B)
  1Q GAIN MUTATED                     1
  1Q GAIN WILD-TYPE                   0
D2V11, multiclass
                         clus
vv                        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  MINIMAL (T3)                         11               119
  MODERATE/ADVANCED (T4A)               3                13
  NONE                                 10               318
  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
  1Q GAIN MUTATED    14   6   0   4
  1Q GAIN WILD-TYPE 364  45   4  26
D2V12, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              14               364
  R1               6                45
  R2               0                 4
  RX               4                26
[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
  1Q GAIN MUTATED     6  19
  1Q GAIN WILD-TYPE 218 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6   19
  1Q GAIN WILD-TYPE  218  242
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  MULTIFOCAL               6               218
  UNIFOCAL                19               242
[1] 2 2
[1] FALSE
D2V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1     1
  1Q GAIN WILD-TYPE                                0    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           4    18
  1Q GAIN WILD-TYPE                        22   303
D2V16, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                48
  BLACK OR AFRICAN AMERICAN                      4                22
  WHITE                                         18               303
[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"
D2V17, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     4  19
  1Q GAIN WILD-TYPE  34 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4   19
  1Q GAIN WILD-TYPE   34  331
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                34
  NOT HISPANIC OR LATINO              19               331
[1] 2 2
[1] FALSE

Clustering(3) Variable = 3P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED     2   1
  3P GAIN WILD-TYPE 475  13
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3               488 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                13 
$`3P GAIN MUTATED`
TCGA-EL-A3MX TCGA-EM-A22N TCGA-EM-A2CO 
       57.63        10.65         6.05 

$`3P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
      108.66        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        11.74        11.15        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       17.88        13.18        23.51         2.99        12.30        15.19 
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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        39.95        33.63        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             6.05              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            57.63            158.83 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           10.650            16.605 
[1] "6.0 - 57.6 (10.7)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "9.4"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  3P GAIN MUTATED         1        1         0        0         0         1
  3P GAIN WILD-TYPE     279       50       109        2        45         5
D3V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 1               279
  STAGE II                1                50
  STAGE III               0               109
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  3P GAIN MUTATED     1   1   0   1
  3P GAIN WILD-TYPE 139 165 165  20
D3V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               1               139
  T2               1               165
  T3               0               165
  T4               1                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"
D3V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     1   1
  3P GAIN WILD-TYPE 222 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    1
  3P GAIN WILD-TYPE  222  221
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               1               222
  1               1               221
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3P GAIN MUTATED     0   1   2
  3P GAIN WILD-TYPE 273   8 210
D3V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               0               273
  M1               1                 8
  MX               2               210
[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
  3P GAIN MUTATED     3   0
  3P GAIN WILD-TYPE 361 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    0
  3P GAIN WILD-TYPE  361  131
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3               361
  MALE                 0               131
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  3P GAIN MUTATED                0
  3P GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  3P GAIN MUTATED                                               1
  3P GAIN WILD-TYPE                                           352
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  3P GAIN MUTATED                                                                        2
  3P GAIN WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  3P GAIN MUTATED                                                                     0
  3P GAIN WILD-TYPE                                                                  35
D3V8, multiclass
                                                                        clus
vv                                                                       3P GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       3P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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
  3P GAIN MUTATED     0   3
  3P GAIN WILD-TYPE  14 478
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    3
  3P GAIN WILD-TYPE   14  478
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                14
  YES               3               478
[1] 2 2
[1] FALSE
D3V10, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3   0
  3P GAIN WILD-TYPE 414  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    0
  3P GAIN WILD-TYPE  414   17
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                3               414
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  3P GAIN MUTATED              0                       0    3
  3P GAIN WILD-TYPE          130                      16  325
                   vv
clus                VERY ADVANCED (T4B)
  3P GAIN MUTATED                     0
  3P GAIN WILD-TYPE                   1
D3V11, multiclass
                         clus
vv                        3P GAIN MUTATED 3P GAIN WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  3               325
  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
  3P GAIN MUTATED     1   0   0   2
  3P GAIN WILD-TYPE 377  51   4  28
D3V12, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               1               377
  R1               0                51
  R2               0                 4
  RX               2                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"
D3V13, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2               389 
       TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZB        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ        TCGA-BJ-A18Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191        TCGA-BJ-A28R 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD        TCGA-DE-A0XZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0        TCGA-EL-A3T1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3T2        TCGA-EL-A3TB        TCGA-EL-A3ZH        TCGA-EL-A3ZK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4KD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS        TCGA-EM-A1CT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22O        TCGA-EM-A22P        TCGA-EM-A22Q 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP        TCGA-EM-A2CQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2CS        TCGA-EM-A2CT        TCGA-EM-A2CU        TCGA-EM-A2OV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2OW        TCGA-EM-A2OX        TCGA-EM-A2OY        TCGA-EM-A2OZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2        TCGA-EM-A2P3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3AJ        TCGA-EM-A3AK        TCGA-EM-A3AL        TCGA-EM-A3AN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3AO        TCGA-EM-A3AQ        TCGA-EM-A3AR        TCGA-EM-A3FJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3FK        TCGA-EM-A3FL        TCGA-EM-A3FM        TCGA-EM-A3FN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ        TCGA-EM-A3FR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3O3        TCGA-EM-A3O7        TCGA-EM-A3O8        TCGA-EM-A3O9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST        TCGA-EM-A3SU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A3SX        TCGA-EM-A3SY        TCGA-EM-A3SZ        TCGA-EM-A4FF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A4FH        TCGA-EM-A4FK        TCGA-EM-A4FM        TCGA-EM-A4FN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR        TCGA-EM-A4FU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A2MX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O        TCGA-ET-A39P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BX        TCGA-ET-A3DQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A3DU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P        TCGA-ET-A40Q 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T        TCGA-ET-A4KN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4        TCGA-FY-A3I5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-QD-A8IV 
"3P GAIN WILD-TYPE" 
D3V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     1   2
  3P GAIN WILD-TYPE 223 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    2
  3P GAIN WILD-TYPE  223  259
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  MULTIFOCAL               1               223
  UNIFOCAL                 2               259
[1] 2 2
[1] FALSE
D3V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           0     1
  3P GAIN WILD-TYPE                        26   320
D3V16, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1               396 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4        TCGA-BJ-A3EZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT        TCGA-BJ-A3PU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BJ-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A13U        TCGA-DJ-A13W        TCGA-DJ-A1QD        TCGA-DJ-A1QE 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QF        TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A1QM        TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PO        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3US 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UT        TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3UY        TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A415        TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A418 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A419        TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E8-A44M        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EL-A3T0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3T7        TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3TB        TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A3ZQ        TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-ET-A25G 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A25R        TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3DO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FK-A3SB        TCGA-FK-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3ON 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3R6        TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A3RA        TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FY-A4B0        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-FY-A76V 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H2-A3RI        TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A3YE        TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-J8-A42S        TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-L6-A4EQ        TCGA-L6-A4ET        TCGA-L6-A4EU        TCGA-MK-A4N6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-MK-A84Z        TCGA-QD-A8IV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D3V17, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0   1
  3P GAIN WILD-TYPE  38 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    1
  3P GAIN WILD-TYPE   38  349
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               1               349
[1] 2 2
[1] FALSE

Clustering(4) Variable = 4P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     4   1
  4P GAIN WILD-TYPE 473  13
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               486 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                13 
$`4P GAIN MUTATED`
TCGA-EM-A1YD TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       57.01        10.65        33.63         1.64         0.99 

$`4P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        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-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        54.21        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         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-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
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-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      102.90        66.77        81.34        39.95        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82         1.51         0.76         0.03         4.67        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
       86.70         6.02        12.43         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        0.72        16.64        32.45         8.71        10.98         5.19 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.99              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            57.01            158.83 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           10.650            16.605 
[1] "1.0 - 57.0 (10.7)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "7.8"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  4P GAIN MUTATED         1        1         3        0         0         0
  4P GAIN WILD-TYPE     279       50       106        2        45         6
D4V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 1               279
  STAGE II                1                50
  STAGE III               3               106
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  4P GAIN MUTATED     1   1   3   0
  4P GAIN WILD-TYPE 139 165 162  21
D4V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               1               139
  T2               1               165
  T3               3               162
  T4               0                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"
D4V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     5   0
  4P GAIN WILD-TYPE 218 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5    0
  4P GAIN WILD-TYPE  218  222
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               5               218
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4P GAIN MUTATED     0   0   5
  4P GAIN WILD-TYPE 273   9 207
D4V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               0               273
  M1               0                 9
  MX               5               207
[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
  4P GAIN MUTATED     4   1
  4P GAIN WILD-TYPE 360 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    1
  4P GAIN WILD-TYPE  360  130
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               4               360
  MALE                 1               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  4P GAIN MUTATED                0
  4P GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  4P GAIN MUTATED                                               2
  4P GAIN WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  4P GAIN MUTATED                                                                        3
  4P GAIN WILD-TYPE                                                                     95
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  4P GAIN MUTATED                                                                     0
  4P GAIN WILD-TYPE                                                                  35
D4V8, multiclass
                                                                        clus
vv                                                                       4P GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       4P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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
  4P GAIN MUTATED     1   4
  4P GAIN WILD-TYPE  13 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    4
  4P GAIN WILD-TYPE   13  477
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                13
  YES               4               477
[1] 2 2
[1] FALSE
D4V10, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   0
  4P GAIN WILD-TYPE 413  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    0
  4P GAIN WILD-TYPE  413   17
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                4               413
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  4P GAIN MUTATED              1                       0    4
  4P GAIN WILD-TYPE          129                      16  324
                   vv
clus                VERY ADVANCED (T4B)
  4P GAIN MUTATED                     0
  4P GAIN WILD-TYPE                   1
D4V11, multiclass
                         clus
vv                        4P GAIN MUTATED 4P GAIN WILD-TYPE
  MINIMAL (T3)                          1               129
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  4               324
  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
  4P GAIN MUTATED     4   0   0   1
  4P GAIN WILD-TYPE 374  51   4  29
D4V12, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               4               374
  R1               0                51
  R2               0                 4
  RX               1                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"
D4V13, continuous
D4V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   1
  4P GAIN WILD-TYPE 220 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    1
  4P GAIN WILD-TYPE  220  260
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  MULTIFOCAL               4               220
  UNIFOCAL                 1               260
[1] 2 2
[1] FALSE
D4V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     0
  4P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           0     3
  4P GAIN WILD-TYPE                        26   318
D4V16, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          3               318
[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"
D4V17, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   3
  4P GAIN WILD-TYPE  38 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    3
  4P GAIN WILD-TYPE   38  347
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               347
[1] 2 2
[1] FALSE

Clustering(5) Variable = 4Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 473  13
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               486 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                13 
$`4Q GAIN MUTATED`
TCGA-EM-A1YD TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       57.01        10.65        33.63         1.64         0.99 

$`4Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        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-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        54.21        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         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-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
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-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      102.90        66.77        81.34        39.95        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82         1.51         0.76         0.03         4.67        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
       86.70         6.02        12.43         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        0.72        16.64        32.45         8.71        10.98         5.19 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.99              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            57.01            158.83 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           10.650            16.605 
[1] "1.0 - 57.0 (10.7)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "7.8"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  4Q GAIN MUTATED         1        1         3        0         0         0
  4Q GAIN WILD-TYPE     279       50       106        2        45         6
D5V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 1               279
  STAGE II                1                50
  STAGE III               3               106
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  4Q GAIN MUTATED     1   1   3   0
  4Q GAIN WILD-TYPE 139 165 162  21
D5V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               1               139
  T2               1               165
  T3               3               162
  T4               0                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"
D5V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5   0
  4Q GAIN WILD-TYPE 218 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5    0
  4Q GAIN WILD-TYPE  218  222
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               5               218
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4Q GAIN MUTATED     0   0   5
  4Q GAIN WILD-TYPE 273   9 207
D5V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               0               273
  M1               0                 9
  MX               5               207
[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
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 360 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    1
  4Q GAIN WILD-TYPE  360  130
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4               360
  MALE                 1               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  4Q GAIN MUTATED                0
  4Q GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  4Q GAIN MUTATED                                               2
  4Q GAIN WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  4Q GAIN MUTATED                                                                        3
  4Q GAIN WILD-TYPE                                                                     95
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  4Q GAIN MUTATED                                                                     0
  4Q GAIN WILD-TYPE                                                                  35
D5V8, multiclass
                                                                        clus
vv                                                                       4Q GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       4Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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
  4Q GAIN MUTATED     1   4
  4Q GAIN WILD-TYPE  13 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    4
  4Q GAIN WILD-TYPE   13  477
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1                13
  YES               4               477
[1] 2 2
[1] FALSE
D5V10, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   0
  4Q GAIN WILD-TYPE 413  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    0
  4Q GAIN WILD-TYPE  413   17
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                4               413
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  4Q GAIN MUTATED              1                       0    4
  4Q GAIN WILD-TYPE          129                      16  324
                   vv
clus                VERY ADVANCED (T4B)
  4Q GAIN MUTATED                     0
  4Q GAIN WILD-TYPE                   1
D5V11, multiclass
                         clus
vv                        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  MINIMAL (T3)                          1               129
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  4               324
  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
  4Q GAIN MUTATED     4   0   0   1
  4Q GAIN WILD-TYPE 374  51   4  29
D5V12, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               4               374
  R1               0                51
  R2               0                 4
  RX               1                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"
D5V13, continuous
D5V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 220 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    1
  4Q GAIN WILD-TYPE  220  260
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  MULTIFOCAL               4               220
  UNIFOCAL                 1               260
[1] 2 2
[1] FALSE
D5V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     3
  4Q GAIN WILD-TYPE                        26   318
D5V16, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          3               318
[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"
D5V17, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   3
  4Q GAIN WILD-TYPE  38 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    3
  4Q GAIN WILD-TYPE   38  347
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               347
[1] 2 2
[1] FALSE

Clustering(6) Variable = 5P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    18   2
  5P GAIN WILD-TYPE 459  12
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               471 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                12 
$`5P GAIN MUTATED`
TCGA-BJ-A0ZB TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EL-A3GU TCGA-EL-A3T9 TCGA-EL-A3ZO 
        4.01        20.58        20.48       124.04         5.72        47.38 
TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
        8.71        54.21        57.01        10.65         6.05        17.59 
TCGA-EM-A3AI TCGA-EM-A3O3 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FE-A239 
       17.46        14.50        13.51        12.26        98.56        33.63 
TCGA-FY-A3I5 TCGA-FY-A3NM 
        1.64         0.99 

$`5P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
       18.87        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-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       22.88        18.38        16.57        18.97         7.04        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D 
       13.94        15.48        23.31        18.64         5.75         6.48 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        0.03         3.45         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
        0.23        11.38        10.68         0.10         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-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12         4.27 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
        3.22         2.76        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-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        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-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
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-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
      102.84        65.39        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-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29        95.38        66.90        82.82        77.36 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       78.97        31.50        50.33        53.06        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       41.13        37.78        29.95        13.32        11.87        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-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-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       15.02        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
       91.17         1.25         1.15        17.82         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       10.26        16.90         9.80         9.63         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.99              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           124.04            158.83 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            15.98             16.57 
[1] "1.0 - 124.0 (16.0)" "0.0 - 158.8 (16.6)"
[1] "hr=" "3.4"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  5P GAIN MUTATED         5        5         8        1         1         0
  5P GAIN WILD-TYPE     275       46       101        1        44         6
D6V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 5               275
  STAGE II                5                46
  STAGE III               8               101
  STAGE IV                1                 1
  STAGE IVA               1                44
  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
  5P GAIN MUTATED     3   7   9   1
  5P GAIN WILD-TYPE 137 159 156  20
D6V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               3               137
  T2               7               159
  T3               9               156
  T4               1                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"
D6V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    11   5
  5P GAIN WILD-TYPE 212 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11    5
  5P GAIN WILD-TYPE  212  217
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              11               212
  1               5               217
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5P GAIN MUTATED     4   0  16
  5P GAIN WILD-TYPE 269   9 196
D6V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               4               269
  M1               0                 9
  MX              16               196
[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
  5P GAIN MUTATED    14   6
  5P GAIN WILD-TYPE 350 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     14    6
  5P GAIN WILD-TYPE  350  125
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              14               350
  MALE                 6               125
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  5P GAIN MUTATED                0
  5P GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  5P GAIN MUTATED                                              12
  5P GAIN WILD-TYPE                                           341
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  5P GAIN MUTATED                                                                        8
  5P GAIN WILD-TYPE                                                                     90
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  5P GAIN MUTATED                                                                     0
  5P GAIN WILD-TYPE                                                                  35
D6V8, multiclass
                                                                        clus
vv                                                                       5P GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       12
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       5P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        341
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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
  5P GAIN MUTATED     1  19
  5P GAIN WILD-TYPE  13 462
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   19
  5P GAIN WILD-TYPE   13  462
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                1                13
  YES              19               462
[1] 2 2
[1] FALSE
D6V10, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    19   0
  5P GAIN WILD-TYPE 398  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     19    0
  5P GAIN WILD-TYPE  398   17
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               19               398
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  5P GAIN MUTATED              4                       1   14
  5P GAIN WILD-TYPE          126                      15  314
                   vv
clus                VERY ADVANCED (T4B)
  5P GAIN MUTATED                     1
  5P GAIN WILD-TYPE                   0
D6V11, multiclass
                         clus
vv                        5P GAIN MUTATED 5P GAIN WILD-TYPE
  MINIMAL (T3)                          4               126
  MODERATE/ADVANCED (T4A)               1                15
  NONE                                 14               314
  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
  5P GAIN MUTATED    15   3   0   2
  5P GAIN WILD-TYPE 363  48   4  28
D6V12, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              15               363
  R1               3                48
  R2               0                 4
  RX               2                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"
D6V13, continuous
D6V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     8  12
  5P GAIN WILD-TYPE 216 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      8   12
  5P GAIN WILD-TYPE  216  249
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  MULTIFOCAL               8               216
  UNIFOCAL                12               249
[1] 2 2
[1] FALSE
D6V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     0
  5P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           0    12
  5P GAIN WILD-TYPE                        26   309
D6V16, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                         12               309
[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"
D6V17, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  11
  5P GAIN WILD-TYPE  37 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   11
  5P GAIN WILD-TYPE   37  339
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                37
  NOT HISPANIC OR LATINO              11               339
[1] 2 2
[1] FALSE

Clustering(7) Variable = 5Q GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    14   2
  5Q GAIN WILD-TYPE 463  12
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               16               475 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                12 
$`5Q GAIN MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD 
       20.58        20.48         5.72         8.71        54.21        57.01 
TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ 
       10.65         6.05        17.59        17.46        13.51        12.26 
TCGA-ET-A39N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       98.56        33.63         1.64         0.99 

$`5Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         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-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        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-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
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-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       13.32        11.87        26.86        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       18.05        19.79        19.46        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       16.44        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ 
       12.07        17.59        17.46        17.29        14.60        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-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       16.41        15.62        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
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-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       54.05        22.09        16.08        29.19        19.76         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-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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       68.22       102.90        66.77        81.34        39.95        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.15        17.82         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.99              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            98.56            158.83 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           15.485            16.570 
[1] "1.0 - 98.6 (15.5)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "5.2"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  5Q GAIN MUTATED         5        5         5        1         0         0
  5Q GAIN WILD-TYPE     275       46       104        1        45         6
D7V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 5               275
  STAGE II                5                46
  STAGE III               5               104
  STAGE IV                1                 1
  STAGE IVA               0                45
  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
  5Q GAIN MUTATED     3   6   6   1
  5Q GAIN WILD-TYPE 137 160 159  20
D7V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               3               137
  T2               6               160
  T3               6               159
  T4               1                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"
D7V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    11   1
  5Q GAIN WILD-TYPE 212 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11    1
  5Q GAIN WILD-TYPE  212  221
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              11               212
  1               1               221
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5Q GAIN MUTATED     1   0  15
  5Q GAIN WILD-TYPE 272   9 197
D7V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               1               272
  M1               0                 9
  MX              15               197
[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
  5Q GAIN MUTATED    11   5
  5Q GAIN WILD-TYPE 353 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11    5
  5Q GAIN WILD-TYPE  353  126
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              11               353
  MALE                 5               126
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  5Q GAIN MUTATED                0
  5Q GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  5Q GAIN MUTATED                                               8
  5Q GAIN WILD-TYPE                                           345
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  5Q GAIN MUTATED                                                                        8
  5Q GAIN WILD-TYPE                                                                     90
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  5Q GAIN MUTATED                                                                     0
  5Q GAIN WILD-TYPE                                                                  35
D7V8, multiclass
                                                                        clus
vv                                                                       5Q GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       5Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        345
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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
  5Q GAIN MUTATED     1  15
  5Q GAIN WILD-TYPE  13 466
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   15
  5Q GAIN WILD-TYPE   13  466
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                1                13
  YES              15               466
[1] 2 2
[1] FALSE
D7V10, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    15   0
  5Q GAIN WILD-TYPE 402  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     15    0
  5Q GAIN WILD-TYPE  402   17
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               15               402
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  5Q GAIN MUTATED              2                       0   13
  5Q GAIN WILD-TYPE          128                      16  315
                   vv
clus                VERY ADVANCED (T4B)
  5Q GAIN MUTATED                     1
  5Q GAIN WILD-TYPE                   0
D7V11, multiclass
                         clus
vv                        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  MINIMAL (T3)                          2               128
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                 13               315
  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
  5Q GAIN MUTATED    12   2   0   2
  5Q GAIN WILD-TYPE 366  49   4  28
D7V12, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              12               366
  R1               2                49
  R2               0                 4
  RX               2                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"
D7V13, continuous
D7V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     8   8
  5Q GAIN WILD-TYPE 216 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8    8
  5Q GAIN WILD-TYPE  216  253
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  MULTIFOCAL               8               216
  UNIFOCAL                 8               253
[1] 2 2
[1] FALSE
D7V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     0
  5Q GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           0     9
  5Q GAIN WILD-TYPE                        26   312
D7V16, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          9               312
[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"
D7V17, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0   9
  5Q GAIN WILD-TYPE  38 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    9
  5Q GAIN WILD-TYPE   38  341
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               9               341
[1] 2 2
[1] FALSE

Clustering(8) Variable = 7P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    16   1
  7P GAIN WILD-TYPE 461  13
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               17               474 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                1                13 
$`7P GAIN MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DJ-A2Q0 TCGA-EL-A3T9 TCGA-EM-A1YC 
       20.58        20.48         0.03         8.12         5.72        54.21 
TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 
       57.01        10.65         6.05        17.59        17.46         9.24 
TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 TCGA-FY-A3NM 
       13.51        12.26        98.56         1.64         0.99 

$`7P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        6.48         3.45         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
        0.23        11.38        10.68         0.10         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-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12         4.27 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
        3.22         2.76        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-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-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        12.76        25.02        20.22        30.61        14.56 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20         9.83        21.27        20.48        11.93        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       21.01        18.97         7.76         8.32        17.36        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       27.62        18.21        10.78        10.98        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-A3X7 TCGA-E8-A413 
       30.31        14.04         1.15        22.29        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 
       14.27        13.81        14.07        14.27         3.02        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        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-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29        95.38        66.90        82.82        77.36 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       78.97        31.50        50.33        53.06        47.38        52.50 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       45.53        48.16         7.07        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        19.59        30.51        33.60 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       28.73        41.13        37.78        29.95        13.32        11.87 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
        8.71        26.86        18.18        20.91        12.36        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        11.74        11.15        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       17.88        13.18        23.51         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        12.07 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        17.29        14.60        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        21.01        12.07        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-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
       12.53        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        39.95        33.63        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82         1.51         0.76         0.03         4.67        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
       86.70         6.02        12.43         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        0.72        16.64        32.45         8.71        10.98         5.19 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.03              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            98.56            158.83 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           12.260            16.685 
[1] "0.0 - 98.6 (12.3)"  "0.0 - 158.8 (16.7)"
[1] "hr=" "2.6"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  7P GAIN MUTATED         7        6         3        1         0         0
  7P GAIN WILD-TYPE     273       45       106        1        45         6
D8V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 7               273
  STAGE II                6                45
  STAGE III               3               106
  STAGE IV                1                 1
  STAGE IVA               0                45
  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
  7P GAIN MUTATED     4   7   5   1
  7P GAIN WILD-TYPE 136 159 160  20
D8V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               4               136
  T2               7               159
  T3               5               160
  T4               1                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"
D8V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    12   1
  7P GAIN WILD-TYPE 211 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     12    1
  7P GAIN WILD-TYPE  211  221
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              12               211
  1               1               221
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7P GAIN MUTATED     3   0  14
  7P GAIN WILD-TYPE 270   9 198
D8V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0               3               270
  M1               0                 9
  MX              14               198
[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
  7P GAIN MUTATED    13   4
  7P GAIN WILD-TYPE 351 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     13    4
  7P GAIN WILD-TYPE  351  127
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              13               351
  MALE                 4               127
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  7P GAIN MUTATED                0
  7P GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  7P GAIN MUTATED                                               8
  7P GAIN WILD-TYPE                                           345
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  7P GAIN MUTATED                                                                        9
  7P GAIN WILD-TYPE                                                                     89
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  7P GAIN MUTATED                                                                     0
  7P GAIN WILD-TYPE                                                                  35
D8V8, multiclass
                                                                        clus
vv                                                                       7P GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       7P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        345
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                89
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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
  7P GAIN MUTATED     0  17
  7P GAIN WILD-TYPE  14 464
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      0   17
  7P GAIN WILD-TYPE   14  464
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                0                14
  YES              17               464
[1] 2 2
[1] FALSE
D8V10, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    15   0
  7P GAIN WILD-TYPE 402  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     15    0
  7P GAIN WILD-TYPE  402   17
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               15               402
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  7P GAIN MUTATED              1                       0   14
  7P GAIN WILD-TYPE          129                      16  314
                   vv
clus                VERY ADVANCED (T4B)
  7P GAIN MUTATED                     1
  7P GAIN WILD-TYPE                   0
D8V11, multiclass
                         clus
vv                        7P GAIN MUTATED 7P GAIN WILD-TYPE
  MINIMAL (T3)                          1               129
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                 14               314
  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
  7P GAIN MUTATED    12   2   0   2
  7P GAIN WILD-TYPE 366  49   4  28
D8V12, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              12               366
  R1               2                49
  R2               0                 4
  RX               2                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"
D8V13, continuous
D8V14, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     8   9
  7P GAIN WILD-TYPE 216 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8    9
  7P GAIN WILD-TYPE  216  252
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  MULTIFOCAL               8               216
  UNIFOCAL                 9               252
[1] 2 2
[1] FALSE
D8V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  0     0
  7P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           0     9
  7P GAIN WILD-TYPE                        26   312
D8V16, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          9               312
[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"
D8V17, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     0   9
  7P GAIN WILD-TYPE  38 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      0    9
  7P GAIN WILD-TYPE   38  341
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               9               341
[1] 2 2
[1] FALSE

Clustering(9) Variable = 7Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    18   1
  7Q GAIN WILD-TYPE 459  13
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19               472 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                13 
$`7Q GAIN MUTATED`
TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DJ-A2Q0 TCGA-EL-A3T9 
       20.58         8.09        20.48         0.03         8.12         5.72 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CJ TCGA-EM-A2CO TCGA-EM-A2OY 
       54.21        57.01        10.65        16.44         6.05        17.59 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       17.46         9.24        13.51        12.26        98.56         1.64 
TCGA-FY-A3NM 
        0.99 

$`7Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S 
       17.69        23.34        20.71         4.83         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       22.88        18.38        16.57        18.97         7.04        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D 
       13.94        15.48        23.31        18.64         5.75         6.48 
TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K 
        3.45         6.35         7.82         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-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ 
       11.38        10.68         0.10         0.39         0.10        20.22 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       15.42        36.46         5.98        15.85        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12         4.27         3.22 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        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-A2Q1 
        8.28         7.69         5.52         8.78         8.42         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-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       12.76        25.02        20.22        30.61        14.56        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
        9.83        21.27        20.48        11.93        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        17.36        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       18.21        10.78        10.98        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-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       14.04         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 
       13.81        14.07        14.27         3.02        14.43        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        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-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29        95.38        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        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-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       19.46        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL 
       14.53        11.74        11.15        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        11.15         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10        91.17         1.25         1.15        17.82         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            98.56            158.83 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            12.26             16.75 
[1] "0.0 - 98.6 (12.3)"  "0.0 - 158.8 (16.8)"
[1] "hr=" "2.5"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  7Q GAIN MUTATED         8        6         4        1         0         0
  7Q GAIN WILD-TYPE     272       45       105        1        45         6
D9V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 8               272
  STAGE II                6                45
  STAGE III               4               105
  STAGE IV                1                 1
  STAGE IVA               0                45
  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
  7Q GAIN MUTATED     5   7   6   1
  7Q GAIN WILD-TYPE 135 159 159  20
D9V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               5               135
  T2               7               159
  T3               6               159
  T4               1                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"
D9V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    12   1
  7Q GAIN WILD-TYPE 211 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     12    1
  7Q GAIN WILD-TYPE  211  221
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              12               211
  1               1               221
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7Q GAIN MUTATED     4   0  15
  7Q GAIN WILD-TYPE 269   9 197
D9V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0               4               269
  M1               0                 9
  MX              15               197
[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
  7Q GAIN MUTATED    15   4
  7Q GAIN WILD-TYPE 349 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     15    4
  7Q GAIN WILD-TYPE  349  127
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              15               349
  MALE                 4               127
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  7Q GAIN MUTATED                0
  7Q GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  7Q GAIN MUTATED                                               9
  7Q GAIN WILD-TYPE                                           344
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  7Q GAIN MUTATED                                                                       10
  7Q GAIN WILD-TYPE                                                                     88
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  7Q GAIN MUTATED                                                                     0
  7Q GAIN WILD-TYPE                                                                  35
D9V8, multiclass
                                                                        clus
vv                                                                       7Q GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       7Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                88
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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
  7Q GAIN MUTATED     0  19
  7Q GAIN WILD-TYPE  14 462
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0   19
  7Q GAIN WILD-TYPE   14  462
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                0                14
  YES              19               462
[1] 2 2
[1] FALSE
D9V10, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    17   0
  7Q GAIN WILD-TYPE 400  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     17    0
  7Q GAIN WILD-TYPE  400   17
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               17               400
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  7Q GAIN MUTATED              2                       0   15
  7Q GAIN WILD-TYPE          128                      16  313
                   vv
clus                VERY ADVANCED (T4B)
  7Q GAIN MUTATED                     1
  7Q GAIN WILD-TYPE                   0
D9V11, multiclass
                         clus
vv                        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  MINIMAL (T3)                          2               128
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                 15               313
  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
  7Q GAIN MUTATED    13   2   0   3
  7Q GAIN WILD-TYPE 365  49   4  27
D9V12, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              13               365
  R1               2                49
  R2               0                 4
  RX               3                27
[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
  7Q GAIN MUTATED     9  10
  7Q GAIN WILD-TYPE 215 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      9   10
  7Q GAIN WILD-TYPE  215  251
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  MULTIFOCAL               9               215
  UNIFOCAL                10               251
[1] 2 2
[1] FALSE
D9V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     0
  7Q GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           0    10
  7Q GAIN WILD-TYPE                        26   311
D9V16, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                         10               311
[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"
D9V17, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     0   9
  7Q GAIN WILD-TYPE  38 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0    9
  7Q GAIN WILD-TYPE   38  341
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               9               341
[1] 2 2
[1] FALSE

Clustering(10) Variable = 8P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED     6   0
  8P GAIN WILD-TYPE 471  14
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6               485 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                14 
$`8P GAIN MUTATED`
TCGA-EM-A2CO TCGA-ET-A2MZ TCGA-ET-A39N TCGA-ET-A3BV TCGA-FY-A3I5 TCGA-L6-A4EP 
        6.05        12.26        98.56        42.25         1.64        33.40 

$`8P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        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-A2CP 
       14.24        16.44        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        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-A3BW TCGA-ET-A3BX 
        2.43         5.56        24.72        38.30         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-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99         1.51         0.76         0.03         4.67        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
       86.70         6.02        12.43         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       84.72        35.28        33.24        40.37        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.64              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            98.56            158.83 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            22.83             16.57 
[1] "1.6 - 98.6 (22.8)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  8P GAIN MUTATED         3        1         2        0         0         0
  8P GAIN WILD-TYPE     277       50       107        2        45         6
D10V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 3               277
  STAGE II                1                50
  STAGE III               2               107
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  8P GAIN MUTATED     1   3   2   0
  8P GAIN WILD-TYPE 139 163 163  21
D10V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               1               139
  T2               3               163
  T3               2               163
  T4               0                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"
D10V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3   1
  8P GAIN WILD-TYPE 220 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3    1
  8P GAIN WILD-TYPE  220  221
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               3               220
  1               1               221
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8P GAIN MUTATED     1   0   5
  8P GAIN WILD-TYPE 272   9 207
D10V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               1               272
  M1               0                 9
  MX               5               207
[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
  8P GAIN MUTATED     5   1
  8P GAIN WILD-TYPE 359 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    1
  8P GAIN WILD-TYPE  359  130
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               5               359
  MALE                 1               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  8P GAIN MUTATED                0
  8P GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  8P GAIN MUTATED                                               4
  8P GAIN WILD-TYPE                                           349
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  8P GAIN MUTATED                                                                        2
  8P GAIN WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8P GAIN MUTATED                                                                     0
  8P GAIN WILD-TYPE                                                                  35
D10V8, multiclass
                                                                        clus
vv                                                                       8P GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       8P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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
  8P GAIN MUTATED     0   6
  8P GAIN WILD-TYPE  14 475
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0    6
  8P GAIN WILD-TYPE   14  475
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                0                14
  YES               6               475
[1] 2 2
[1] FALSE
D10V10, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     5   0
  8P GAIN WILD-TYPE 412  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    0
  8P GAIN WILD-TYPE  412   17
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                5               412
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  8P GAIN MUTATED              0                       0    6
  8P GAIN WILD-TYPE          130                      16  322
                   vv
clus                VERY ADVANCED (T4B)
  8P GAIN MUTATED                     0
  8P GAIN WILD-TYPE                   1
D10V11, multiclass
                         clus
vv                        8P GAIN MUTATED 8P GAIN WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  6               322
  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
  8P GAIN MUTATED     5   0   0   1
  8P GAIN WILD-TYPE 373  51   4  29
D10V12, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0               5               373
  R1               0                51
  R2               0                 4
  RX               1                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"
D10V13, continuous
D10V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1   5
  8P GAIN WILD-TYPE 223 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1    5
  8P GAIN WILD-TYPE  223  256
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  MULTIFOCAL               1               223
  UNIFOCAL                 5               256
[1] 2 2
[1] FALSE
D10V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     1
  8P GAIN WILD-TYPE                                1    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           0     4
  8P GAIN WILD-TYPE                        26   317
D10V16, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                48
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          4               317
[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"
D10V17, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0   5
  8P GAIN WILD-TYPE  38 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0    5
  8P GAIN WILD-TYPE   38  345
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               5               345
[1] 2 2
[1] FALSE

Clustering(11) Variable = 8Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED     6   1
  8Q GAIN WILD-TYPE 471  13
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7               484 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                13 
$`8Q GAIN MUTATED`
TCGA-EL-A3T9 TCGA-EM-A2CO TCGA-ET-A2MZ TCGA-ET-A39N TCGA-ET-A3BV TCGA-FY-A3I5 
        5.72         6.05        12.26        98.56        42.25         1.64 
TCGA-L6-A4EP 
       33.40 

$`8Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
       95.38        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-A2CP TCGA-EM-A2CQ 
       16.44        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       27.09        18.38        29.49        54.05        22.09        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        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-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.56        24.72        38.30         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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.24        40.37        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             1.64              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            98.56            158.83 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           12.260            16.605 
[1] "1.6 - 98.6 (12.3)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "4.4"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  8Q GAIN MUTATED         3        1         2        1         0         0
  8Q GAIN WILD-TYPE     277       50       107        1        45         6
D11V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 3               277
  STAGE II                1                50
  STAGE III               2               107
  STAGE IV                1                 1
  STAGE IVA               0                45
  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
  8Q GAIN MUTATED     1   3   2   1
  8Q GAIN WILD-TYPE 139 163 163  20
D11V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               1               139
  T2               3               163
  T3               2               163
  T4               1                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"
D11V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3   2
  8Q GAIN WILD-TYPE 220 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3    2
  8Q GAIN WILD-TYPE  220  220
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               3               220
  1               2               220
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8Q GAIN MUTATED     1   0   6
  8Q GAIN WILD-TYPE 272   9 206
D11V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               1               272
  M1               0                 9
  MX               6               206
[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
  8Q GAIN MUTATED     6   1
  8Q GAIN WILD-TYPE 358 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    1
  8Q GAIN WILD-TYPE  358  130
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               6               358
  MALE                 1               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  8Q GAIN MUTATED                0
  8Q GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  8Q GAIN MUTATED                                               5
  8Q GAIN WILD-TYPE                                           348
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  8Q GAIN MUTATED                                                                        2
  8Q GAIN WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8Q GAIN MUTATED                                                                     0
  8Q GAIN WILD-TYPE                                                                  35
D11V8, multiclass
                                                                        clus
vv                                                                       8Q GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       8Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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
  8Q GAIN MUTATED     0   7
  8Q GAIN WILD-TYPE  14 474
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      0    7
  8Q GAIN WILD-TYPE   14  474
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                0                14
  YES               7               474
[1] 2 2
[1] FALSE
D11V10, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     6   0
  8Q GAIN WILD-TYPE 411  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    0
  8Q GAIN WILD-TYPE  411   17
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                6               411
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  8Q GAIN MUTATED              0                       0    6
  8Q GAIN WILD-TYPE          130                      16  322
                   vv
clus                VERY ADVANCED (T4B)
  8Q GAIN MUTATED                     1
  8Q GAIN WILD-TYPE                   0
D11V11, multiclass
                         clus
vv                        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  6               322
  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
  8Q GAIN MUTATED     5   1   0   1
  8Q GAIN WILD-TYPE 373  50   4  29
D11V12, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0               5               373
  R1               1                50
  R2               0                 4
  RX               1                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"
D11V13, continuous
D11V14, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1   6
  8Q GAIN WILD-TYPE 223 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1    6
  8Q GAIN WILD-TYPE  223  255
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  MULTIFOCAL               1               223
  UNIFOCAL                 6               255
[1] 2 2
[1] FALSE
D11V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     1
  8Q GAIN WILD-TYPE                                1    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           0     5
  8Q GAIN WILD-TYPE                        26   316
D11V16, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                48
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          5               316
[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"
D11V17, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     0   6
  8Q GAIN WILD-TYPE  38 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      0    6
  8Q GAIN WILD-TYPE   38  344
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               6               344
[1] 2 2
[1] FALSE

Clustering(12) Variable = 9P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     3   0
  9P GAIN WILD-TYPE 474  14
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               488 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                14 
$`9P GAIN MUTATED`
TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-FY-A3I5 
       37.78        57.01         1.64 

$`9P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       41.13        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-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         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-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
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-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.64              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            57.01            158.83 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            37.78             16.57 
[1] "1.6 - 57.0 (37.8)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9100000"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  9P GAIN MUTATED         0        2         1        0         0         0
  9P GAIN WILD-TYPE     280       49       108        2        45         6
D12V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0               280
  STAGE II                2                49
  STAGE III               1               108
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  9P GAIN MUTATED     0   2   1   0
  9P GAIN WILD-TYPE 140 164 164  21
D12V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               0               140
  T2               2               164
  T3               1               164
  T4               0                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"
D12V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3   0
  9P GAIN WILD-TYPE 220 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    0
  9P GAIN WILD-TYPE  220  222
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               3               220
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED     1   0   2
  9P GAIN WILD-TYPE 272   9 210
D12V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               1               272
  M1               0                 9
  MX               2               210
[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"
D12V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2   1
  9P GAIN WILD-TYPE 362 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE  362  130
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2               362
  MALE                 1               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  9P GAIN MUTATED                0
  9P GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  9P GAIN MUTATED                                               1
  9P GAIN WILD-TYPE                                           352
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  9P GAIN MUTATED                                                                        2
  9P GAIN WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9P GAIN MUTATED                                                                     0
  9P GAIN WILD-TYPE                                                                  35
D12V8, multiclass
                                                                        clus
vv                                                                       9P GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       9P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D12V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0   3
  9P GAIN WILD-TYPE  14 478
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    3
  9P GAIN WILD-TYPE   14  478
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                0                14
  YES               3               478
[1] 2 2
[1] FALSE
D12V10, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2   0
  9P GAIN WILD-TYPE 415  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    0
  9P GAIN WILD-TYPE  415   17
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2               415
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  9P GAIN MUTATED              1                       0    2
  9P GAIN WILD-TYPE          129                      16  326
                   vv
clus                VERY ADVANCED (T4B)
  9P GAIN MUTATED                     0
  9P GAIN WILD-TYPE                   1
D12V11, multiclass
                         clus
vv                        9P GAIN MUTATED 9P GAIN WILD-TYPE
  MINIMAL (T3)                          1               129
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  2               326
  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
  9P GAIN MUTATED     3   0   0   0
  9P GAIN WILD-TYPE 375  51   4  30
D12V12, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               3               375
  R1               0                51
  R2               0                 4
  RX               0                30
[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"
D12V13, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2               389 
       TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZB        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ        TCGA-BJ-A18Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191        TCGA-BJ-A28R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD        TCGA-DE-A0XZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB        TCGA-EL-A3ZH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZP        TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CT        TCGA-EM-A2CU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OW        TCGA-EM-A2OX        TCGA-EM-A2OY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2OZ        TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A2P3        TCGA-EM-A3AJ        TCGA-EM-A3AK        TCGA-EM-A3AL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AQ        TCGA-EM-A3AR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FL        TCGA-EM-A3FM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O7        TCGA-EM-A3O8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SY        TCGA-EM-A3SZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A4FF        TCGA-EM-A4FH        TCGA-EM-A4FK        TCGA-EM-A4FM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EM-A4FU        TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-QD-A8IV 
"9P GAIN WILD-TYPE" 
D12V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2   1
  9P GAIN WILD-TYPE 222 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE  222  260
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  MULTIFOCAL               2               222
  UNIFOCAL                 1               260
[1] 2 2
[1] FALSE
D12V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0     2
  9P GAIN WILD-TYPE                        26   319
D12V16, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2               395 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4        TCGA-BJ-A3EZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT        TCGA-BJ-A3PU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BJ-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A13U        TCGA-DJ-A13W        TCGA-DJ-A1QD        TCGA-DJ-A1QE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QF        TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A1QM        TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PO        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3US 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UT        TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3UY        TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A415        TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A418 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A419        TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-E8-A44M        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3T0        TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3T3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3T6        TCGA-EL-A3T7        TCGA-EL-A3T8        TCGA-EL-A3T9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3TA        TCGA-EL-A3TB        TCGA-EL-A3ZG        TCGA-EL-A3ZH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZP        TCGA-EL-A3ZQ        TCGA-EL-A3ZR        TCGA-EL-A3ZS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A3ZT        TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4KD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-ET-A25G 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A25R        TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3DO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FK-A3SB        TCGA-FK-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR        TCGA-FY-A40K 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-FY-A76V        TCGA-GE-A2C6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-L6-A4ET        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-MK-A84Z        TCGA-QD-A8IV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D12V17, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0   2
  9P GAIN WILD-TYPE  38 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    2
  9P GAIN WILD-TYPE   38  348
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               348
[1] 2 2
[1] FALSE

Clustering(13) Variable = 9Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     4   0
  9Q GAIN WILD-TYPE 473  14
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               487 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                14 
$`9Q GAIN MUTATED`
TCGA-DJ-A2PW TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-FY-A3I5 
        7.69        37.78        57.01         1.64 

$`9Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PX 
       10.45         1.51         9.60        12.56         8.28         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
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-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-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        39.95        33.63        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.64              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            57.01            158.83 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           22.735            16.570 
[1] "1.6 - 57.0 (22.7)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9100000"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  9Q GAIN MUTATED         0        2         2        0         0         0
  9Q GAIN WILD-TYPE     280       49       107        2        45         6
D13V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 0               280
  STAGE II                2                49
  STAGE III               2               107
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  9Q GAIN MUTATED     0   2   2   0
  9Q GAIN WILD-TYPE 140 164 163  21
D13V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               0               140
  T2               2               164
  T3               2               163
  T4               0                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"
D13V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3   1
  9Q GAIN WILD-TYPE 220 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    1
  9Q GAIN WILD-TYPE  220  221
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               3               220
  1               1               221
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9Q GAIN MUTATED     2   0   2
  9Q GAIN WILD-TYPE 271   9 210
D13V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               2               271
  M1               0                 9
  MX               2               210
[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"
D13V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2   2
  9Q GAIN WILD-TYPE 362 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    2
  9Q GAIN WILD-TYPE  362  129
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2               362
  MALE                 2               129
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  9Q GAIN MUTATED                0
  9Q GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  9Q GAIN MUTATED                                               2
  9Q GAIN WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  9Q GAIN MUTATED                                                                        2
  9Q GAIN WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9Q GAIN MUTATED                                                                     0
  9Q GAIN WILD-TYPE                                                                  35
D13V8, multiclass
                                                                        clus
vv                                                                       9Q GAIN 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                                                                       9Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D13V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0   4
  9Q GAIN WILD-TYPE  14 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    4
  9Q GAIN WILD-TYPE   14  477
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                14
  YES               4               477
[1] 2 2
[1] FALSE
D13V10, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3   0
  9Q GAIN WILD-TYPE 414  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    0
  9Q GAIN WILD-TYPE  414   17
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                3               414
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  9Q GAIN MUTATED              1                       0    3
  9Q GAIN WILD-TYPE          129                      16  325
                   vv
clus                VERY ADVANCED (T4B)
  9Q GAIN MUTATED                     0
  9Q GAIN WILD-TYPE                   1
D13V11, multiclass
                         clus
vv                        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  MINIMAL (T3)                          1               129
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  3               325
  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
  9Q GAIN MUTATED     4   0   0   0
  9Q GAIN WILD-TYPE 374  51   4  30
D13V12, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               4               374
  R1               0                51
  R2               0                 4
  RX               0                30
[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"
D13V13, continuous
D13V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3   1
  9Q GAIN WILD-TYPE 221 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    1
  9Q GAIN WILD-TYPE  221  260
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  MULTIFOCAL               3               221
  UNIFOCAL                 1               260
[1] 2 2
[1] FALSE
D13V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     0
  9Q GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           0     3
  9Q GAIN WILD-TYPE                        26   318
D13V16, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          3               318
[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"
D13V17, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0   3
  9Q GAIN WILD-TYPE  38 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    3
  9Q GAIN WILD-TYPE   38  347
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               347
[1] 2 2
[1] FALSE

Clustering(14) Variable = 11P GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     6   0
  11P GAIN WILD-TYPE 471  14
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                485 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                 14 
$`11P GAIN MUTATED`
TCGA-EL-A3ZR TCGA-EM-A1YC TCGA-EM-A2P2 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       48.16        54.21        17.29        13.51        12.26        98.56 

$`11P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AI 
       17.59        12.07        17.59        17.46        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
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-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        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-A238 
       24.69        68.22       102.90        66.77        81.34        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       91.17         1.25         1.15        17.82         1.64         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             12.26               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             98.56             158.83 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            32.725             16.570 
[1] "12.3 - 98.6 (32.7)" "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D14V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  11P GAIN MUTATED         3        1         2        0         0         0
  11P GAIN WILD-TYPE     277       50       107        2        45         6
D14V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  3                277
  STAGE II                 1                 50
  STAGE III                2                107
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  11P GAIN MUTATED     2   1   3   0
  11P GAIN WILD-TYPE 138 165 162  21
D14V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                2                138
  T2                1                165
  T3                3                162
  T4                0                 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"
D14V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     4   0
  11P GAIN WILD-TYPE 219 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    0
  11P GAIN WILD-TYPE  219  222
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                4                219
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11P GAIN MUTATED     1   0   5
  11P GAIN WILD-TYPE 272   9 207
D14V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                1                272
  M1                0                  9
  MX                5                207
[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"
D14V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     3   3
  11P GAIN WILD-TYPE 361 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    3
  11P GAIN WILD-TYPE  361  128
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                3                361
  MALE                  3                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  11P GAIN MUTATED                0
  11P GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  11P GAIN MUTATED                                               3
  11P GAIN WILD-TYPE                                           350
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  11P GAIN MUTATED                                                                        3
  11P GAIN WILD-TYPE                                                                     95
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11P GAIN MUTATED                                                                     0
  11P GAIN WILD-TYPE                                                                  35
D14V8, multiclass
                                                                        clus
vv                                                                       11P GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       11P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D14V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0   6
  11P GAIN WILD-TYPE  14 475
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    6
  11P GAIN WILD-TYPE   14  475
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 0                 14
  YES                6                475
[1] 2 2
[1] FALSE
D14V10, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6   0
  11P GAIN WILD-TYPE 411  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6    0
  11P GAIN WILD-TYPE  411   17
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 6                411
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  11P GAIN MUTATED              0                       0    6
  11P GAIN WILD-TYPE          130                      16  322
                    vv
clus                 VERY ADVANCED (T4B)
  11P GAIN MUTATED                     0
  11P GAIN WILD-TYPE                   1
D14V11, multiclass
                         clus
vv                        11P GAIN MUTATED 11P GAIN WILD-TYPE
  MINIMAL (T3)                           0                130
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   6                322
  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
  11P GAIN MUTATED     5   0   0   1
  11P GAIN WILD-TYPE 373  51   4  29
D14V12, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                5                373
  R1                0                 51
  R2                0                  4
  RX                1                 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"
D14V13, continuous
D14V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1   5
  11P GAIN WILD-TYPE 223 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    5
  11P GAIN WILD-TYPE  223  256
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  MULTIFOCAL                1                223
  UNIFOCAL                  5                256
[1] 2 2
[1] FALSE
D14V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           0     3
  11P GAIN WILD-TYPE                        26   318
D14V16, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           3                318
[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"
D14V17, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0   3
  11P GAIN WILD-TYPE  38 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    3
  11P GAIN WILD-TYPE   38  347
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                3                347
[1] 2 2
[1] FALSE

Clustering(15) Variable = 11Q GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     5   0
  11Q GAIN WILD-TYPE 472  14
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                486 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                 14 
$`11Q GAIN MUTATED`
TCGA-EL-A3ZR TCGA-EM-A1YC TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       48.16        54.21        13.51        12.26        98.56 

$`11Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10        91.17         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-A3R9 
        0.99         1.51         0.76         0.03         4.67        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
       86.70         6.02        12.43         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        0.72        16.64        32.45         8.71        10.98         5.19 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             12.26               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             98.56             158.83 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             48.16              16.57 
[1] "12.3 - 98.6 (48.2)" "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D15V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  11Q GAIN MUTATED         3        1         1        0         0         0
  11Q GAIN WILD-TYPE     277       50       108        2        45         6
D15V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  3                277
  STAGE II                 1                 50
  STAGE III                1                108
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  11Q GAIN MUTATED     2   1   2   0
  11Q GAIN WILD-TYPE 138 165 163  21
D15V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                138
  T2                1                165
  T3                2                163
  T4                0                 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"
D15V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3   0
  11Q GAIN WILD-TYPE 220 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    0
  11Q GAIN WILD-TYPE  220  222
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                3                220
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11Q GAIN MUTATED     1   0   4
  11Q GAIN WILD-TYPE 272   9 208
D15V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                1                272
  M1                0                  9
  MX                4                208
[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"
D15V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3   2
  11Q GAIN WILD-TYPE 361 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    2
  11Q GAIN WILD-TYPE  361  129
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                361
  MALE                  2                129
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  11Q GAIN MUTATED                0
  11Q GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  11Q GAIN MUTATED                                               3
  11Q GAIN WILD-TYPE                                           350
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  11Q GAIN MUTATED                                                                        2
  11Q GAIN WILD-TYPE                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11Q GAIN MUTATED                                                                     0
  11Q GAIN WILD-TYPE                                                                  35
D15V8, multiclass
                                                                        clus
vv                                                                       11Q GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       11Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D15V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   5
  11Q GAIN WILD-TYPE  14 476
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    5
  11Q GAIN WILD-TYPE   14  476
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                 14
  YES                5                476
[1] 2 2
[1] FALSE
D15V10, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     5   0
  11Q GAIN WILD-TYPE 412  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    0
  11Q GAIN WILD-TYPE  412   17
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 5                412
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  11Q GAIN MUTATED              0                       0    5
  11Q GAIN WILD-TYPE          130                      16  323
                    vv
clus                 VERY ADVANCED (T4B)
  11Q GAIN MUTATED                     0
  11Q GAIN WILD-TYPE                   1
D15V11, multiclass
                         clus
vv                        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  MINIMAL (T3)                           0                130
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   5                323
  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
  11Q GAIN MUTATED     4   0   0   1
  11Q GAIN WILD-TYPE 374  51   4  29
D15V12, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                4                374
  R1                0                 51
  R2                0                  4
  RX                1                 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"
D15V13, continuous
D15V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   5
  11Q GAIN WILD-TYPE 224 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    5
  11Q GAIN WILD-TYPE  224  256
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  MULTIFOCAL                0                224
  UNIFOCAL                  5                256
[1] 2 2
[1] FALSE
D15V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           0     3
  11Q GAIN WILD-TYPE                        26   318
D15V16, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           3                318
[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"
D15V17, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   3
  11Q GAIN WILD-TYPE  38 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    3
  11Q GAIN WILD-TYPE   38  347
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                3                347
[1] 2 2
[1] FALSE

Clustering(16) Variable = 12P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    14   0
  12P GAIN WILD-TYPE 463  14
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                477 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                 14 
$`12P GAIN MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       20.58        20.48        54.21        57.01        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-ET-A3DS 
       17.59        17.46        13.51        12.26        98.56         0.30 
TCGA-FY-A3I5 TCGA-FY-A3NM 
        1.64         0.99 

$`12P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         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-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        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-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
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-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A1YE 
       20.91        12.36        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        12.07        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       69.24        59.87        43.50        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        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-A238 
       24.69        68.22       102.90        66.77        81.34        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
       91.17         1.25         1.15        17.82         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       10.26        16.90         9.80         9.63         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.30               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             98.56             158.83 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            15.485             16.570 
[1] "0.3 - 98.6 (15.5)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "2.5e+07"
D16V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  12P GAIN MUTATED         6        5         3        0         0         0
  12P GAIN WILD-TYPE     274       46       106        2        45         6
D16V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  6                274
  STAGE II                 5                 46
  STAGE III                3                106
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  12P GAIN MUTATED     4   6   4   0
  12P GAIN WILD-TYPE 136 160 161  21
D16V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                4                136
  T2                6                160
  T3                4                161
  T4                0                 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"
D16V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    10   0
  12P GAIN WILD-TYPE 213 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     10    0
  12P GAIN WILD-TYPE  213  222
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               10                213
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12P GAIN MUTATED     1   0  13
  12P GAIN WILD-TYPE 272   9 199
D16V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                1                272
  M1                0                  9
  MX               13                199
[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"
D16V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    11   3
  12P GAIN WILD-TYPE 353 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     11    3
  12P GAIN WILD-TYPE  353  128
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               11                353
  MALE                  3                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  12P GAIN MUTATED                0
  12P GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  12P GAIN MUTATED                                               6
  12P GAIN WILD-TYPE                                           347
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  12P GAIN MUTATED                                                                        8
  12P GAIN WILD-TYPE                                                                     90
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  12P GAIN MUTATED                                                                     0
  12P GAIN WILD-TYPE                                                                  35
D16V8, multiclass
                                                                        clus
vv                                                                       12P GAIN 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                                                                       12P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D16V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  14
  12P GAIN WILD-TYPE  14 467
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   14
  12P GAIN WILD-TYPE   14  467
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 0                 14
  YES               14                467
[1] 2 2
[1] FALSE
D16V10, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    13   0
  12P GAIN WILD-TYPE 404  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     13    0
  12P GAIN WILD-TYPE  404   17
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                13                404
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  12P GAIN MUTATED              1                       0   13
  12P GAIN WILD-TYPE          129                      16  315
                    vv
clus                 VERY ADVANCED (T4B)
  12P GAIN MUTATED                     0
  12P GAIN WILD-TYPE                   1
D16V11, multiclass
                         clus
vv                        12P GAIN MUTATED 12P GAIN WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                  13                315
  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
  12P GAIN MUTATED    11   1   0   2
  12P GAIN WILD-TYPE 367  50   4  28
D16V12, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               11                367
  R1                1                 50
  R2                0                  4
  RX                2                 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"
D16V13, continuous
D16V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     7   7
  12P GAIN WILD-TYPE 217 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7    7
  12P GAIN WILD-TYPE  217  254
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  MULTIFOCAL                7                217
  UNIFOCAL                  7                254
[1] 2 2
[1] FALSE
D16V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     0
  12P GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           0     7
  12P GAIN WILD-TYPE                        26   314
D16V16, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           7                314
[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"
D16V17, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0   7
  12P GAIN WILD-TYPE  38 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0    7
  12P GAIN WILD-TYPE   38  343
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                7                343
[1] 2 2
[1] FALSE

Clustering(17) Variable = 12Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    15   0
  12Q GAIN WILD-TYPE 462  14
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                476 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                 14 
$`12Q GAIN MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       20.58        20.48        54.21        57.01        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-ET-A3DS 
       17.59        17.46        13.51        12.26        98.56         0.30 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA 
        1.64         0.99        17.06 

$`12Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         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-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        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-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
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-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A1YE 
       20.91        12.36        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        12.07        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       69.24        59.87        43.50        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        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-A238 
       24.69        68.22       102.90        66.77        81.34        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
       91.17         1.25         1.15        17.82         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        16.57        18.08         0.30         0.76 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.30               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             98.56             158.83 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             17.06              16.57 
[1] "0.3 - 98.6 (17.1)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "2.5e+07"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  12Q GAIN MUTATED         7        5         3        0         0         0
  12Q GAIN WILD-TYPE     273       46       106        2        45         6
D17V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  7                273
  STAGE II                 5                 46
  STAGE III                3                106
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  12Q GAIN MUTATED     5   6   4   0
  12Q GAIN WILD-TYPE 135 160 161  21
D17V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                5                135
  T2                6                160
  T3                4                161
  T4                0                 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"
D17V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    10   0
  12Q GAIN WILD-TYPE 213 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     10    0
  12Q GAIN WILD-TYPE  213  222
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               10                213
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12Q GAIN MUTATED     1   0  14
  12Q GAIN WILD-TYPE 272   9 198
D17V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                1                272
  M1                0                  9
  MX               14                198
[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"
D17V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    12   3
  12Q GAIN WILD-TYPE 352 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12    3
  12Q GAIN WILD-TYPE  352  128
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               12                352
  MALE                  3                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  12Q GAIN MUTATED                0
  12Q GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  12Q GAIN MUTATED                                               6
  12Q GAIN WILD-TYPE                                           347
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  12Q GAIN MUTATED                                                                        9
  12Q GAIN WILD-TYPE                                                                     89
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  12Q GAIN MUTATED                                                                     0
  12Q GAIN WILD-TYPE                                                                  35
D17V8, multiclass
                                                                        clus
vv                                                                       12Q GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       12Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 89
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D17V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  15
  12Q GAIN WILD-TYPE  14 466
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   15
  12Q GAIN WILD-TYPE   14  466
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 0                 14
  YES               15                466
[1] 2 2
[1] FALSE
D17V10, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    14   0
  12Q GAIN WILD-TYPE 403  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     14    0
  12Q GAIN WILD-TYPE  403   17
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                14                403
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  12Q GAIN MUTATED              1                       0   14
  12Q GAIN WILD-TYPE          129                      16  314
                    vv
clus                 VERY ADVANCED (T4B)
  12Q GAIN MUTATED                     0
  12Q GAIN WILD-TYPE                   1
D17V11, multiclass
                         clus
vv                        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                  14                314
  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
  12Q GAIN MUTATED    12   1   0   2
  12Q GAIN WILD-TYPE 366  50   4  28
D17V12, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               12                366
  R1                1                 50
  R2                0                  4
  RX                2                 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"
D17V13, continuous
D17V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     7   8
  12Q GAIN WILD-TYPE 217 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7    8
  12Q GAIN WILD-TYPE  217  253
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  MULTIFOCAL                7                217
  UNIFOCAL                  8                253
[1] 2 2
[1] FALSE
D17V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     0
  12Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           0     8
  12Q GAIN WILD-TYPE                        26   313
D17V16, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           8                313
[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"
D17V17, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0   8
  12Q GAIN WILD-TYPE  38 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0    8
  12Q GAIN WILD-TYPE   38  342
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                8                342
[1] 2 2
[1] FALSE

Clustering(18) Variable = 13Q GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     5   0
  13Q GAIN WILD-TYPE 472  14
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                486 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                 14 
$`13Q GAIN MUTATED`
TCGA-BJ-A45E TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
        0.03         8.71        57.01         6.05        17.59 

$`13Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       13.18        23.51         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        19.73        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-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        21.01        12.07        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-A3ST TCGA-EM-A3SU 
       12.53         9.24        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        13.51        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
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-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10        91.17         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-A3R9 
        0.99         1.51         0.76         0.03         4.67        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
       86.70         6.02        12.43         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        0.72        16.64        32.45         8.71        10.98         5.19 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.03               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             57.01             158.83 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             8.710             16.605 
[1] "0.0 - 57.0 (8.7)"   "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  13Q GAIN MUTATED         1        3         1        0         0         0
  13Q GAIN WILD-TYPE     279       48       108        2        45         6
D18V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                279
  STAGE II                 3                 48
  STAGE III                1                108
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  13Q GAIN MUTATED     1   3   1   0
  13Q GAIN WILD-TYPE 139 163 164  21
D18V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                1                139
  T2                3                163
  T3                1                164
  T4                0                 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"
D18V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 219 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE  219  222
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                4                219
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  13Q GAIN MUTATED     1   0   4
  13Q GAIN WILD-TYPE 272   9 208
D18V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                1                272
  M1                0                  9
  MX                4                208
[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"
D18V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   1
  13Q GAIN WILD-TYPE 360 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    1
  13Q GAIN WILD-TYPE  360  130
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                360
  MALE                  1                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  13Q GAIN MUTATED                0
  13Q GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  13Q GAIN MUTATED                                               2
  13Q GAIN WILD-TYPE                                           351
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  13Q GAIN MUTATED                                                                        3
  13Q GAIN WILD-TYPE                                                                     95
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  13Q GAIN MUTATED                                                                     0
  13Q GAIN WILD-TYPE                                                                  35
D18V8, multiclass
                                                                        clus
vv                                                                       13Q GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       13Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D18V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   5
  13Q GAIN WILD-TYPE  14 476
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    5
  13Q GAIN WILD-TYPE   14  476
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 0                 14
  YES                5                476
[1] 2 2
[1] FALSE
D18V10, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE  413   17
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 4                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  13Q GAIN MUTATED              1                       0    3
  13Q GAIN WILD-TYPE          129                      16  325
                    vv
clus                 VERY ADVANCED (T4B)
  13Q GAIN MUTATED                     0
  13Q GAIN WILD-TYPE                   1
D18V11, multiclass
                         clus
vv                        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   3                325
  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
  13Q GAIN MUTATED     4   0   0   0
  13Q GAIN WILD-TYPE 374  51   4  30
D18V12, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                4                374
  R1                0                 51
  R2                0                  4
  RX                0                 30
[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"
D18V13, continuous
D18V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     3   2
  13Q GAIN WILD-TYPE 221 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    2
  13Q GAIN WILD-TYPE  221  259
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  MULTIFOCAL                3                221
  UNIFOCAL                  2                259
[1] 2 2
[1] FALSE
D18V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           0     2
  13Q GAIN WILD-TYPE                        26   319
D18V16, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                395 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z2         TCGA-BJ-A0Z3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0Z5         TCGA-BJ-A0Z9         TCGA-BJ-A0ZA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZB         TCGA-BJ-A0ZC         TCGA-BJ-A0ZE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A0ZG         TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28X         TCGA-BJ-A28Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A2N7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A2P4         TCGA-BJ-A3EZ         TCGA-BJ-A3F0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A3PR         TCGA-BJ-A3PT         TCGA-BJ-A3PU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A45G         TCGA-BJ-A45H         TCGA-BJ-A45I 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A45J         TCGA-BJ-A45K         TCGA-BJ-A4O8 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BJ-A4O9         TCGA-CE-A13K         TCGA-CE-A27D 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CE-A3MD         TCGA-CE-A3ME         TCGA-CE-A481 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CE-A482         TCGA-CE-A483         TCGA-CE-A484 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CE-A485         TCGA-DE-A0XZ         TCGA-DE-A0Y2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A0Y3         TCGA-DE-A2OL         TCGA-DE-A3KN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A4M8         TCGA-DE-A4M9         TCGA-DE-A4MA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A4MB         TCGA-DE-A4MC         TCGA-DE-A4MD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DE-A69J         TCGA-DE-A69K         TCGA-DE-A7U5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A13M         TCGA-DJ-A13O         TCGA-DJ-A13P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A13R         TCGA-DJ-A13S         TCGA-DJ-A13T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A13U         TCGA-DJ-A13W         TCGA-DJ-A1QD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QE         TCGA-DJ-A1QF         TCGA-DJ-A1QG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QH         TCGA-DJ-A1QI         TCGA-DJ-A1QM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A1QO         TCGA-DJ-A1QQ         TCGA-DJ-A2PN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PO         TCGA-DJ-A2PQ         TCGA-DJ-A2PR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PT         TCGA-DJ-A2PU         TCGA-DJ-A2PV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PW         TCGA-DJ-A2PX         TCGA-DJ-A2PY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2PZ         TCGA-DJ-A2Q0         TCGA-DJ-A2Q1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q2         TCGA-DJ-A2Q3         TCGA-DJ-A2Q4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UK         TCGA-DJ-A3UM         TCGA-DJ-A3UN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UO         TCGA-DJ-A3UQ         TCGA-DJ-A3UR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3US         TCGA-DJ-A3UT         TCGA-DJ-A3UU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UW         TCGA-DJ-A3UX         TCGA-DJ-A3UY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3UZ         TCGA-DJ-A3V2         TCGA-DJ-A3V3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V4         TCGA-DJ-A3V5         TCGA-DJ-A3V7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3V8         TCGA-DJ-A3V9         TCGA-DJ-A3VD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VE         TCGA-DJ-A3VF         TCGA-DJ-A3VG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A3VJ         TCGA-DJ-A3VL         TCGA-DJ-A3VM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UL         TCGA-DJ-A4UQ         TCGA-DJ-A4UR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A4UT         TCGA-DJ-A4UW         TCGA-DJ-A4V0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DJ-A4V4         TCGA-DJ-A4V5         TCGA-DO-A1JZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-DO-A2HM         TCGA-E3-A3DY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E3-A3DZ         TCGA-E3-A3E0         TCGA-E3-A3E1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E3-A3E2         TCGA-E3-A3E3         TCGA-E3-A3E5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A242         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A3X7         TCGA-E8-A413         TCGA-E8-A414 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A415         TCGA-E8-A416         TCGA-E8-A417 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A418         TCGA-E8-A419         TCGA-E8-A432 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A433         TCGA-E8-A434         TCGA-E8-A436 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A437         TCGA-E8-A438         TCGA-E8-A44K 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-E8-A44M         TCGA-EL-A3CL         TCGA-EL-A3CM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CN         TCGA-EL-A3CO         TCGA-EL-A3CP 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CR         TCGA-EL-A3CS         TCGA-EL-A3CT 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CU         TCGA-EL-A3CV         TCGA-EL-A3CW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3CX         TCGA-EL-A3CY         TCGA-EL-A3CZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3D0         TCGA-EL-A3D1         TCGA-EL-A3D4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3D5         TCGA-EL-A3D6         TCGA-EL-A3GO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3GP         TCGA-EL-A3GQ         TCGA-EL-A3GR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3GS         TCGA-EL-A3GU         TCGA-EL-A3GV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3GW         TCGA-EL-A3GX         TCGA-EL-A3GY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3GZ         TCGA-EL-A3H1         TCGA-EL-A3H2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3H8         TCGA-EL-A3MW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3MX         TCGA-EL-A3MY         TCGA-EL-A3MZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3N2         TCGA-EL-A3N3         TCGA-EL-A3T0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3T3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3T6         TCGA-EL-A3T7         TCGA-EL-A3T8 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3T9         TCGA-EL-A3TA         TCGA-EL-A3TB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZG         TCGA-EL-A3ZH         TCGA-EL-A3ZK 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZL         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZQ         TCGA-EL-A3ZR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A3ZS         TCGA-EL-A3ZT         TCGA-EL-A4JV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4K9         TCGA-EL-A4KD         TCGA-EL-A4KG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EL-A4KH         TCGA-ET-A25G         TCGA-ET-A25I 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A25J         TCGA-ET-A25K         TCGA-ET-A25L 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A25M         TCGA-ET-A25N         TCGA-ET-A25O 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A25P         TCGA-ET-A25R         TCGA-ET-A2MX 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A2MY         TCGA-ET-A2MZ         TCGA-ET-A2N0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A2N1         TCGA-ET-A2N3         TCGA-ET-A2N4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A2N5         TCGA-ET-A39I         TCGA-ET-A39J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A39K         TCGA-ET-A39M         TCGA-ET-A39N 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A39O         TCGA-ET-A39P         TCGA-ET-A39R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A39S         TCGA-ET-A39T         TCGA-ET-A3BN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3BO         TCGA-ET-A3BQ         TCGA-ET-A3BS 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3BT         TCGA-ET-A3BU         TCGA-ET-A3BV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3BW         TCGA-ET-A3DO         TCGA-ET-A3DP 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3DQ         TCGA-ET-A3DR         TCGA-ET-A3DS 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3DT         TCGA-ET-A3DU         TCGA-ET-A3DV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A3DW         TCGA-ET-A40P         TCGA-ET-A40Q 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A40R         TCGA-ET-A40S         TCGA-ET-A40T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ET-A4KN         TCGA-ET-A4KQ         TCGA-FE-A22Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A230         TCGA-FE-A231         TCGA-FE-A232 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A233         TCGA-FE-A234         TCGA-FE-A235 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A236         TCGA-FE-A237         TCGA-FE-A238 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FE-A3PA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FE-A3PB         TCGA-FE-A3PC         TCGA-FE-A3PD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FK-A3S3         TCGA-FK-A3SB         TCGA-FK-A3SD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FK-A3SE         TCGA-FK-A3SG         TCGA-FK-A3SH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FK-A4UB         TCGA-FY-A2QD         TCGA-FY-A3BL 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3I4         TCGA-FY-A3I5         TCGA-FY-A3NM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3ON         TCGA-FY-A3R6         TCGA-FY-A3R7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3R8         TCGA-FY-A3R9         TCGA-FY-A3RA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A3W9         TCGA-FY-A3WA         TCGA-FY-A3YR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A40K         TCGA-FY-A40L         TCGA-FY-A40M 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A40N         TCGA-FY-A4B0         TCGA-FY-A4B3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FY-A4B4         TCGA-FY-A76V         TCGA-GE-A2C6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-H2-A26U         TCGA-H2-A2K9         TCGA-H2-A3RH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-H2-A3RI         TCGA-H2-A421         TCGA-H2-A422 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IM-A3EB         TCGA-IM-A3ED         TCGA-IM-A3U2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IM-A3U3         TCGA-IM-A41Y         TCGA-IM-A41Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IM-A420         TCGA-IM-A4EB         TCGA-J8-A3NZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-J8-A3O0         TCGA-J8-A3O1         TCGA-J8-A3O2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-J8-A3YD         TCGA-J8-A3YE         TCGA-J8-A3YF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-J8-A3YG         TCGA-J8-A3YH         TCGA-J8-A42S 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-J8-A4HW         TCGA-J8-A4HY         TCGA-KS-A41F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A41I         TCGA-KS-A41J         TCGA-KS-A41L 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A4I1         TCGA-KS-A4I3         TCGA-KS-A4I5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A4I7         TCGA-KS-A4I9         TCGA-KS-A4IB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-KS-A4IC         TCGA-KS-A4ID         TCGA-L6-A4EP 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-L6-A4EQ         TCGA-L6-A4ET         TCGA-L6-A4EU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MK-A4N6         TCGA-MK-A4N7         TCGA-MK-A4N9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MK-A84Z         TCGA-QD-A8IV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D18V17, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   2
  13Q GAIN WILD-TYPE  38 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    2
  13Q GAIN WILD-TYPE   38  348
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                2                348
[1] 2 2
[1] FALSE

Clustering(19) Variable = 14Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    11   0
  14Q GAIN WILD-TYPE 466  14
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                480 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                 14 
$`14Q GAIN MUTATED`
TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       48.16         8.71        57.01        10.65         6.05        17.59 
TCGA-EM-A3AI TCGA-ET-A39N TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-J8-A3YG 
       17.46        98.56         1.64         0.99        22.29 

$`14Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        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-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
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-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.15        17.82         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YH 
       27.19        11.24        31.82        27.85        24.69         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
       86.70         6.02        12.43         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        0.72        16.64        32.45         8.71        10.98         5.19 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.99               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             98.56             158.83 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             17.46              16.57 
[1] "1.0 - 98.6 (17.5)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "2.5e+07"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  14Q GAIN MUTATED         2        5         4        0         0         0
  14Q GAIN WILD-TYPE     278       46       105        2        45         6
D19V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  2                278
  STAGE II                 5                 46
  STAGE III                4                105
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  14Q GAIN MUTATED     1   6   4   0
  14Q GAIN WILD-TYPE 139 160 161  21
D19V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                1                139
  T2                6                160
  T3                4                161
  T4                0                 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"
D19V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     7   1
  14Q GAIN WILD-TYPE 216 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      7    1
  14Q GAIN WILD-TYPE  216  221
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                7                216
  1                1                221
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  14Q GAIN MUTATED     2   0   9
  14Q GAIN WILD-TYPE 271   9 203
D19V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                2                271
  M1                0                  9
  MX                9                203
[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"
D19V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    10   1
  14Q GAIN WILD-TYPE 354 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10    1
  14Q GAIN WILD-TYPE  354  130
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               10                354
  MALE                  1                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  14Q GAIN MUTATED                0
  14Q GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  14Q GAIN MUTATED                                               5
  14Q GAIN WILD-TYPE                                           348
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  14Q GAIN MUTATED                                                                        6
  14Q GAIN WILD-TYPE                                                                     92
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  14Q GAIN MUTATED                                                                     0
  14Q GAIN WILD-TYPE                                                                  35
D19V8, multiclass
                                                                        clus
vv                                                                       14Q GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                6
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       14Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D19V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  11
  14Q GAIN WILD-TYPE  14 470
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   11
  14Q GAIN WILD-TYPE   14  470
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 0                 14
  YES               11                470
[1] 2 2
[1] FALSE
D19V10, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    10   0
  14Q GAIN WILD-TYPE 407  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10    0
  14Q GAIN WILD-TYPE  407   17
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                10                407
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  14Q GAIN MUTATED              2                       0    9
  14Q GAIN WILD-TYPE          128                      16  319
                    vv
clus                 VERY ADVANCED (T4B)
  14Q GAIN MUTATED                     0
  14Q GAIN WILD-TYPE                   1
D19V11, multiclass
                         clus
vv                        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  MINIMAL (T3)                           2                128
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   9                319
  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
  14Q GAIN MUTATED    10   0   0   1
  14Q GAIN WILD-TYPE 368  51   4  29
D19V12, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               10                368
  R1                0                 51
  R2                0                  4
  RX                1                 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"
D19V13, continuous
D19V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     8   3
  14Q GAIN WILD-TYPE 216 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      8    3
  14Q GAIN WILD-TYPE  216  258
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  MULTIFOCAL                8                216
  UNIFOCAL                  3                258
[1] 2 2
[1] FALSE
D19V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     0
  14Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           0     6
  14Q GAIN WILD-TYPE                        26   315
D19V16, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           6                315
[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"
D19V17, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0   5
  14Q GAIN WILD-TYPE  38 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    5
  14Q GAIN WILD-TYPE   38  345
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                345
[1] 2 2
[1] FALSE

Clustering(20) Variable = 16P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    14   1
  16P GAIN WILD-TYPE 463  13
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                476 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 13 
$`16P GAIN MUTATED`
TCGA-BJ-A192 TCGA-BJ-A2N9 TCGA-DJ-A2Q0 TCGA-EL-A3T9 TCGA-EM-A1YD TCGA-EM-A22N 
        8.09        20.48         8.12         5.72        57.01        10.65 
TCGA-EM-A2CO TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
        6.05        17.46         9.24        13.51        12.26        98.56 
TCGA-ET-A3DS TCGA-FY-A3I5 TCGA-FY-A3NM 
        0.30         1.64         0.99 

$`16P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A28R 
       17.69        23.34        20.71        20.58         4.83         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         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-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        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-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42         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-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        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-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
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-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        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-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB 
      116.91        98.24        41.29        95.38        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
       77.36        78.97        31.50        50.33        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        45.53        48.16         7.07        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       19.30        45.96        37.94        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       33.60        28.73        41.13        37.78        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-A1YE TCGA-EM-A22I 
       18.05        19.79        19.46        54.21        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P 
       14.50        15.75        10.45        14.53        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        16.44        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-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-A3OA TCGA-EM-A3OB 
       14.50        11.15         7.33        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
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-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        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-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       59.87        43.50        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25         1.15        17.82         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.30               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             98.56             158.83 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             9.240             16.785 
[1] "0.3 - 98.6 (9.2)"   "0.0 - 158.8 (16.8)"
[1] "hr=" "3.4"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  16P GAIN MUTATED         7        4         3        1         0         0
  16P GAIN WILD-TYPE     273       47       106        1        45         6
D20V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  7                273
  STAGE II                 4                 47
  STAGE III                3                106
  STAGE IV                 1                  1
  STAGE IVA                0                 45
  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
  16P GAIN MUTATED     4   5   5   1
  16P GAIN WILD-TYPE 136 161 160  20
D20V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                4                136
  T2                5                161
  T3                5                160
  T4                1                 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"
D20V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     9   1
  16P GAIN WILD-TYPE 214 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    1
  16P GAIN WILD-TYPE  214  221
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                9                214
  1                1                221
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED     3   0  12
  16P GAIN WILD-TYPE 270   9 200
D20V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                3                270
  M1                0                  9
  MX               12                200
[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"
D20V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    12   3
  16P GAIN WILD-TYPE 352 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     12    3
  16P GAIN WILD-TYPE  352  128
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               12                352
  MALE                  3                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  16P GAIN MUTATED                0
  16P GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  16P GAIN MUTATED                                               8
  16P GAIN WILD-TYPE                                           345
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  16P GAIN MUTATED                                                                        7
  16P GAIN WILD-TYPE                                                                     91
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  16P GAIN MUTATED                                                                     0
  16P GAIN WILD-TYPE                                                                  35
D20V8, multiclass
                                                                        clus
vv                                                                       16P GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       16P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         345
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D20V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  15
  16P GAIN WILD-TYPE  14 466
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   15
  16P GAIN WILD-TYPE   14  466
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 0                 14
  YES               15                466
[1] 2 2
[1] FALSE
D20V10, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    14   0
  16P GAIN WILD-TYPE 403  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     14    0
  16P GAIN WILD-TYPE  403   17
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                14                403
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  16P GAIN MUTATED              2                       0   12
  16P GAIN WILD-TYPE          128                      16  316
                    vv
clus                 VERY ADVANCED (T4B)
  16P GAIN MUTATED                     1
  16P GAIN WILD-TYPE                   0
D20V11, multiclass
                         clus
vv                        16P GAIN MUTATED 16P GAIN WILD-TYPE
  MINIMAL (T3)                           2                128
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                  12                316
  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
  16P GAIN MUTATED    10   2   0   3
  16P GAIN WILD-TYPE 368  49   4  27
D20V12, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               10                368
  R1                2                 49
  R2                0                  4
  RX                3                 27
[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"
D20V13, continuous
D20V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     6   9
  16P GAIN WILD-TYPE 218 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6    9
  16P GAIN WILD-TYPE  218  252
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  MULTIFOCAL                6                218
  UNIFOCAL                  9                252
[1] 2 2
[1] FALSE
D20V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     0
  16P GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           0     9
  16P GAIN WILD-TYPE                        26   312
D20V16, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           9                312
[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"
D20V17, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0   8
  16P GAIN WILD-TYPE  38 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0    8
  16P GAIN WILD-TYPE   38  342
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                8                342
[1] 2 2
[1] FALSE

Clustering(21) Variable = 16Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    12   1
  16Q GAIN WILD-TYPE 465  13
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                478 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 13 
$`16Q GAIN MUTATED`
TCGA-BJ-A2N9 TCGA-DJ-A2Q0 TCGA-EL-A3T9 TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       20.48         8.12         5.72        57.01        10.65         6.05 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       17.46         9.24        13.51        12.26        98.56         1.64 
TCGA-FY-A3NM 
        0.99 

$`16Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         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-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
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-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        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-A1YE 
       12.36        18.05        19.79        19.46        54.21        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-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-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        11.15         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10        91.17         1.25         1.15        17.82         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.99               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             98.56             158.83 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             10.65              16.75 
[1] "1.0 - 98.6 (10.7)"  "0.0 - 158.8 (16.8)"
[1] "hr=" "3.5"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  16Q GAIN MUTATED         6        4         2        1         0         0
  16Q GAIN WILD-TYPE     274       47       107        1        45         6
D21V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  6                274
  STAGE II                 4                 47
  STAGE III                2                107
  STAGE IV                 1                  1
  STAGE IVA                0                 45
  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
  16Q GAIN MUTATED     3   5   4   1
  16Q GAIN WILD-TYPE 137 161 161  20
D21V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                3                137
  T2                5                161
  T3                4                161
  T4                1                 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"
D21V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     8   1
  16Q GAIN WILD-TYPE 215 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      8    1
  16Q GAIN WILD-TYPE  215  221
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                8                215
  1                1                221
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED     2   0  11
  16Q GAIN WILD-TYPE 271   9 201
D21V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                2                271
  M1                0                  9
  MX               11                201
[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"
D21V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    10   3
  16Q GAIN WILD-TYPE 354 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    3
  16Q GAIN WILD-TYPE  354  128
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               10                354
  MALE                  3                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  16Q GAIN MUTATED                0
  16Q GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  16Q GAIN MUTATED                                               6
  16Q GAIN WILD-TYPE                                           347
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  16Q GAIN MUTATED                                                                        7
  16Q GAIN WILD-TYPE                                                                     91
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  16Q GAIN MUTATED                                                                     0
  16Q GAIN WILD-TYPE                                                                  35
D21V8, multiclass
                                                                        clus
vv                                                                       16Q GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       16Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D21V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  13
  16Q GAIN WILD-TYPE  14 468
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   13
  16Q GAIN WILD-TYPE   14  468
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 0                 14
  YES               13                468
[1] 2 2
[1] FALSE
D21V10, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    12   0
  16Q GAIN WILD-TYPE 405  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     12    0
  16Q GAIN WILD-TYPE  405   17
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                12                405
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  16Q GAIN MUTATED              1                       0   11
  16Q GAIN WILD-TYPE          129                      16  317
                    vv
clus                 VERY ADVANCED (T4B)
  16Q GAIN MUTATED                     1
  16Q GAIN WILD-TYPE                   0
D21V11, multiclass
                         clus
vv                        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                  11                317
  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
  16Q GAIN MUTATED     9   2   0   2
  16Q GAIN WILD-TYPE 369  49   4  28
D21V12, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                9                369
  R1                2                 49
  R2                0                  4
  RX                2                 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"
D21V13, continuous
D21V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     6   7
  16Q GAIN WILD-TYPE 218 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6    7
  16Q GAIN WILD-TYPE  218  254
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  MULTIFOCAL                6                218
  UNIFOCAL                  7                254
[1] 2 2
[1] FALSE
D21V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           0     7
  16Q GAIN WILD-TYPE                        26   314
D21V16, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           7                314
[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"
D21V17, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0   7
  16Q GAIN WILD-TYPE  38 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    7
  16Q GAIN WILD-TYPE   38  343
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                7                343
[1] 2 2
[1] FALSE

Clustering(22) Variable = 17P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    16   0
  17P GAIN WILD-TYPE 461  14
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                475 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                 14 
$`17P GAIN MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YC 
        8.12        78.97        48.16        28.73         8.71        54.21 
TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY 
       57.01        10.65         6.05        17.59        17.46        13.51 
TCGA-ET-A25P TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       18.38        12.26        98.56         1.64 

$`17P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZK TCGA-EL-A3ZL 
        5.72        66.90        82.82        77.36        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT 
       53.06        47.38        52.50        45.53         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       30.51        33.60        41.13        37.78        29.95        13.32 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       11.87        26.86        18.18        20.91        12.36        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        11.74        11.15        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       17.88        13.18        23.51         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        12.07 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        17.29        14.60        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        21.01        12.07        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-A3ST TCGA-EM-A3SU 
       12.53         9.24        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       15.62        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       12.33        14.79        27.09        29.49        54.05        22.09 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        39.95        33.63        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.64               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             98.56             158.83 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            17.525             16.570 
[1] "1.6 - 98.6 (17.5)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "2.6e+07"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  17P GAIN MUTATED         6        6         3        1         0         0
  17P GAIN WILD-TYPE     274       45       106        1        45         6
D22V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  6                274
  STAGE II                 6                 45
  STAGE III                3                106
  STAGE IV                 1                  1
  STAGE IVA                0                 45
  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
  17P GAIN MUTATED     4   6   5   1
  17P GAIN WILD-TYPE 136 160 160  20
D22V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                4                136
  T2                6                160
  T3                5                160
  T4                1                 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"
D22V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    10   2
  17P GAIN WILD-TYPE 213 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     10    2
  17P GAIN WILD-TYPE  213  220
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               10                213
  1                2                220
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17P GAIN MUTATED     3   0  13
  17P GAIN WILD-TYPE 270   9 199
D22V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                3                270
  M1                0                  9
  MX               13                199
[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"
D22V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    12   4
  17P GAIN WILD-TYPE 352 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     12    4
  17P GAIN WILD-TYPE  352  127
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               12                352
  MALE                  4                127
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  17P GAIN MUTATED                0
  17P GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  17P GAIN MUTATED                                               8
  17P GAIN WILD-TYPE                                           345
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  17P GAIN MUTATED                                                                        8
  17P GAIN WILD-TYPE                                                                     90
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17P GAIN MUTATED                                                                     0
  17P GAIN WILD-TYPE                                                                  35
D22V8, multiclass
                                                                        clus
vv                                                                       17P GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       17P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         345
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D22V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  16
  17P GAIN WILD-TYPE  14 465
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   16
  17P GAIN WILD-TYPE   14  465
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                 14
  YES               16                465
[1] 2 2
[1] FALSE
D22V10, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    15   0
  17P GAIN WILD-TYPE 402  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     15    0
  17P GAIN WILD-TYPE  402   17
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                15                402
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  17P GAIN MUTATED              3                       0   13
  17P GAIN WILD-TYPE          127                      16  315
                    vv
clus                 VERY ADVANCED (T4B)
  17P GAIN MUTATED                     0
  17P GAIN WILD-TYPE                   1
D22V11, multiclass
                         clus
vv                        17P GAIN MUTATED 17P GAIN WILD-TYPE
  MINIMAL (T3)                           3                127
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                  13                315
  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
  17P GAIN MUTATED    14   0   0   2
  17P GAIN WILD-TYPE 364  51   4  28
D22V12, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               14                364
  R1                0                 51
  R2                0                  4
  RX                2                 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"
D22V13, continuous
D22V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     7   9
  17P GAIN WILD-TYPE 217 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7    9
  17P GAIN WILD-TYPE  217  252
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  MULTIFOCAL                7                217
  UNIFOCAL                  9                252
[1] 2 2
[1] FALSE
D22V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     1
  17P GAIN WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           0     8
  17P GAIN WILD-TYPE                        26   313
D22V16, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 48
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           8                313
[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"
D22V17, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0   9
  17P GAIN WILD-TYPE  38 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    9
  17P GAIN WILD-TYPE   38  341
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                9                341
[1] 2 2
[1] FALSE

Clustering(23) Variable = 17Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    17   0
  17Q GAIN WILD-TYPE 460  14
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                474 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                 14 
$`17Q GAIN MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3ZH TCGA-EL-A3ZR TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YC 
        8.12        78.97        48.16        28.73         8.71        54.21 
TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY 
       57.01        10.65         6.05        17.59        17.46        13.51 
TCGA-ET-A25P TCGA-ET-A2MZ TCGA-ET-A39N TCGA-ET-A3DS TCGA-FY-A3I5 
       18.38        12.26        98.56         0.30         1.64 

$`17Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZK TCGA-EL-A3ZL 
        5.72        66.90        82.82        77.36        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT 
       53.06        47.38        52.50        45.53         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       30.51        33.60        41.13        37.78        29.95        13.32 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       11.87        26.86        18.18        20.91        12.36        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        11.74        11.15        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       17.88        13.18        23.51         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        12.07 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        17.29        14.60        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        21.01        12.07        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-A3ST TCGA-EM-A3SU 
       12.53         9.24        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       15.62        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       12.33        14.79        27.09        29.49        54.05        22.09 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        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-A3DT 
        4.50        80.81        69.24        59.87        43.50        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99         1.51         0.76         0.03         4.67        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
       86.70         6.02        12.43         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        0.72        16.64        32.45         8.71        10.98         5.19 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.30               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             98.56             158.83 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             17.46              16.57 
[1] "0.3 - 98.6 (17.5)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "2.6e+07"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  17Q GAIN MUTATED         7        6         3        1         0         0
  17Q GAIN WILD-TYPE     273       45       106        1        45         6
D23V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  7                273
  STAGE II                 6                 45
  STAGE III                3                106
  STAGE IV                 1                  1
  STAGE IVA                0                 45
  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
  17Q GAIN MUTATED     5   6   5   1
  17Q GAIN WILD-TYPE 135 160 160  20
D23V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                5                135
  T2                6                160
  T3                5                160
  T4                1                 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"
D23V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    11   2
  17Q GAIN WILD-TYPE 212 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     11    2
  17Q GAIN WILD-TYPE  212  220
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               11                212
  1                2                220
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17Q GAIN MUTATED     3   0  14
  17Q GAIN WILD-TYPE 270   9 198
D23V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                3                270
  M1                0                  9
  MX               14                198
[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"
D23V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    13   4
  17Q GAIN WILD-TYPE 351 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     13    4
  17Q GAIN WILD-TYPE  351  127
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               13                351
  MALE                  4                127
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  17Q GAIN MUTATED                0
  17Q GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  17Q GAIN MUTATED                                               9
  17Q GAIN WILD-TYPE                                           344
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  17Q GAIN MUTATED                                                                        8
  17Q GAIN WILD-TYPE                                                                     90
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17Q GAIN MUTATED                                                                     0
  17Q GAIN WILD-TYPE                                                                  35
D23V8, multiclass
                                                                        clus
vv                                                                       17Q GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       17Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D23V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  17
  17Q GAIN WILD-TYPE  14 464
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   17
  17Q GAIN WILD-TYPE   14  464
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                 14
  YES               17                464
[1] 2 2
[1] FALSE
D23V10, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    16   0
  17Q GAIN WILD-TYPE 401  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     16    0
  17Q GAIN WILD-TYPE  401   17
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                16                401
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  17Q GAIN MUTATED              3                       0   14
  17Q GAIN WILD-TYPE          127                      16  314
                    vv
clus                 VERY ADVANCED (T4B)
  17Q GAIN MUTATED                     0
  17Q GAIN WILD-TYPE                   1
D23V11, multiclass
                         clus
vv                        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  MINIMAL (T3)                           3                127
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                  14                314
  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
  17Q GAIN MUTATED    15   0   0   2
  17Q GAIN WILD-TYPE 363  51   4  28
D23V12, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               15                363
  R1                0                 51
  R2                0                  4
  RX                2                 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"
D23V13, continuous
D23V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     7  10
  17Q GAIN WILD-TYPE 217 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7   10
  17Q GAIN WILD-TYPE  217  251
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  MULTIFOCAL                7                217
  UNIFOCAL                 10                251
[1] 2 2
[1] FALSE
D23V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     1
  17Q GAIN WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           0     9
  17Q GAIN WILD-TYPE                        26   312
D23V16, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 48
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           9                312
[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"
D23V17, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  10
  17Q GAIN WILD-TYPE  38 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   10
  17Q GAIN WILD-TYPE   38  340
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO               10                340
[1] 2 2
[1] FALSE

Clustering(24) Variable = 18P GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     6   0
  18P GAIN WILD-TYPE 471  14
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                485 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                 14 
$`18P GAIN MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
        0.03        48.16         8.71        12.26        98.56         1.64 

$`18P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       50.33        53.06        47.38        52.50        45.53         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       29.95        13.32        11.87        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-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.03               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             98.56             158.83 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            10.485             16.640 
[1] "0.0 - 98.6 (10.5)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  18P GAIN MUTATED         3        1         2        0         0         0
  18P GAIN WILD-TYPE     277       50       107        2        45         6
D24V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  3                277
  STAGE II                 1                 50
  STAGE III                2                107
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  18P GAIN MUTATED     2   1   3   0
  18P GAIN WILD-TYPE 138 165 162  21
D24V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                2                138
  T2                1                165
  T3                3                162
  T4                0                 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"
D24V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     5   0
  18P GAIN WILD-TYPE 218 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    0
  18P GAIN WILD-TYPE  218  222
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                5                218
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18P GAIN MUTATED     2   0   4
  18P GAIN WILD-TYPE 271   9 208
D24V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                2                271
  M1                0                  9
  MX                4                208
[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"
D24V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4   2
  18P GAIN WILD-TYPE 360 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    2
  18P GAIN WILD-TYPE  360  129
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                4                360
  MALE                  2                129
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  18P GAIN MUTATED                0
  18P GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  18P GAIN MUTATED                                               5
  18P GAIN WILD-TYPE                                           348
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  18P GAIN MUTATED                                                                        1
  18P GAIN WILD-TYPE                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18P GAIN MUTATED                                                                     0
  18P GAIN WILD-TYPE                                                                  35
D24V8, multiclass
                                                                        clus
vv                                                                       18P GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       18P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D24V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0   6
  18P GAIN WILD-TYPE  14 475
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0    6
  18P GAIN WILD-TYPE   14  475
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 0                 14
  YES                6                475
[1] 2 2
[1] FALSE
D24V10, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4   0
  18P GAIN WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    0
  18P GAIN WILD-TYPE  413   17
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 4                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  18P GAIN MUTATED              1                       0    4
  18P GAIN WILD-TYPE          129                      16  324
                    vv
clus                 VERY ADVANCED (T4B)
  18P GAIN MUTATED                     0
  18P GAIN WILD-TYPE                   1
D24V11, multiclass
                         clus
vv                        18P GAIN MUTATED 18P GAIN WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   4                324
  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
  18P GAIN MUTATED     4   0   0   1
  18P GAIN WILD-TYPE 374  51   4  29
D24V12, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                4                374
  R1                0                 51
  R2                0                  4
  RX                1                 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"
D24V13, continuous
D24V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2   4
  18P GAIN WILD-TYPE 222 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    4
  18P GAIN WILD-TYPE  222  257
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  MULTIFOCAL                2                222
  UNIFOCAL                  4                257
[1] 2 2
[1] FALSE
D24V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           0     6
  18P GAIN WILD-TYPE                        26   315
D24V16, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           6                315
[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"
D24V17, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0   6
  18P GAIN WILD-TYPE  38 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0    6
  18P GAIN WILD-TYPE   38  344
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                344
[1] 2 2
[1] FALSE

Clustering(25) Variable = 18Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     6   0
  18Q GAIN WILD-TYPE 471  14
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                485 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                 14 
$`18Q GAIN MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
        0.03        48.16         8.71        12.26        98.56         1.64 

$`18Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       50.33        53.06        47.38        52.50        45.53         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       29.95        13.32        11.87        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-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.03               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             98.56             158.83 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            10.485             16.640 
[1] "0.0 - 98.6 (10.5)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  18Q GAIN MUTATED         3        1         2        0         0         0
  18Q GAIN WILD-TYPE     277       50       107        2        45         6
D25V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  3                277
  STAGE II                 1                 50
  STAGE III                2                107
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  18Q GAIN MUTATED     2   1   3   0
  18Q GAIN WILD-TYPE 138 165 162  21
D25V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                2                138
  T2                1                165
  T3                3                162
  T4                0                 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"
D25V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5   0
  18Q GAIN WILD-TYPE 218 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    0
  18Q GAIN WILD-TYPE  218  222
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                5                218
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED     2   0   4
  18Q GAIN WILD-TYPE 271   9 208
D25V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                2                271
  M1                0                  9
  MX                4                208
[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"
D25V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4   2
  18Q GAIN WILD-TYPE 360 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    2
  18Q GAIN WILD-TYPE  360  129
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                360
  MALE                  2                129
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  18Q GAIN MUTATED                0
  18Q GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  18Q GAIN MUTATED                                               5
  18Q GAIN WILD-TYPE                                           348
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  18Q GAIN MUTATED                                                                        1
  18Q GAIN WILD-TYPE                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18Q GAIN MUTATED                                                                     0
  18Q GAIN WILD-TYPE                                                                  35
D25V8, multiclass
                                                                        clus
vv                                                                       18Q GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       18Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D25V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   6
  18Q GAIN WILD-TYPE  14 475
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    6
  18Q GAIN WILD-TYPE   14  475
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 0                 14
  YES                6                475
[1] 2 2
[1] FALSE
D25V10, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4   0
  18Q GAIN WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE  413   17
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 4                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  18Q GAIN MUTATED              1                       0    4
  18Q GAIN WILD-TYPE          129                      16  324
                    vv
clus                 VERY ADVANCED (T4B)
  18Q GAIN MUTATED                     0
  18Q GAIN WILD-TYPE                   1
D25V11, multiclass
                         clus
vv                        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   4                324
  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
  18Q GAIN MUTATED     4   0   0   1
  18Q GAIN WILD-TYPE 374  51   4  29
D25V12, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                4                374
  R1                0                 51
  R2                0                  4
  RX                1                 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"
D25V13, continuous
D25V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2   4
  18Q GAIN WILD-TYPE 222 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    4
  18Q GAIN WILD-TYPE  222  257
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  MULTIFOCAL                2                222
  UNIFOCAL                  4                257
[1] 2 2
[1] FALSE
D25V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           0     6
  18Q GAIN WILD-TYPE                        26   315
D25V16, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           6                315
[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"
D25V17, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   6
  18Q GAIN WILD-TYPE  38 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    6
  18Q GAIN WILD-TYPE   38  344
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                344
[1] 2 2
[1] FALSE

Clustering(26) Variable = 19P GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     7   0
  19P GAIN WILD-TYPE 470  14
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                484 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                 14 
$`19P GAIN MUTATED`
TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A22N TCGA-EM-A2OY TCGA-EM-A3O9 TCGA-EM-A3SY 
        8.71        54.21        10.65        17.59         9.24        13.51 
TCGA-FY-A3I5 
        1.64 

$`19P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       41.13        37.78        29.95        13.32        11.87        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-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-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        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-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        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-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        7.33        12.53        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       15.62        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        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-A238 
       24.69        68.22       102.90        66.77        81.34        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.64               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             54.21             158.83 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            10.650             16.685 
[1] "1.6 - 54.2 (10.7)"  "0.0 - 158.8 (16.7)"
[1] "hr="     "3300000"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  19P GAIN MUTATED         4        1         3        0         0         0
  19P GAIN WILD-TYPE     276       50       106        2        45         6
D26V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  4                276
  STAGE II                 1                 50
  STAGE III                3                106
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  19P GAIN MUTATED     3   1   4   0
  19P GAIN WILD-TYPE 137 165 161  21
D26V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                3                137
  T2                1                165
  T3                4                161
  T4                0                 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"
D26V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6   0
  19P GAIN WILD-TYPE 217 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6    0
  19P GAIN WILD-TYPE  217  222
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                6                217
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19P GAIN MUTATED     0   0   8
  19P GAIN WILD-TYPE 273   9 204
D26V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                0                273
  M1                0                  9
  MX                8                204
[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"
D26V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     4   4
  19P GAIN WILD-TYPE 360 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4    4
  19P GAIN WILD-TYPE  360  127
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                4                360
  MALE                  4                127
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  19P GAIN MUTATED                0
  19P GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  19P GAIN MUTATED                                               2
  19P GAIN WILD-TYPE                                           351
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  19P GAIN MUTATED                                                                        6
  19P GAIN WILD-TYPE                                                                     92
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  19P GAIN MUTATED                                                                     0
  19P GAIN WILD-TYPE                                                                  35
D26V8, multiclass
                                                                        clus
vv                                                                       19P GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                6
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       19P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D26V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0   8
  19P GAIN WILD-TYPE  14 473
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    8
  19P GAIN WILD-TYPE   14  473
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 0                 14
  YES                8                473
[1] 2 2
[1] FALSE
D26V10, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     7   0
  19P GAIN WILD-TYPE 410  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7    0
  19P GAIN WILD-TYPE  410   17
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 7                410
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  19P GAIN MUTATED              1                       0    7
  19P GAIN WILD-TYPE          129                      16  321
                    vv
clus                 VERY ADVANCED (T4B)
  19P GAIN MUTATED                     0
  19P GAIN WILD-TYPE                   1
D26V11, multiclass
                         clus
vv                        19P GAIN MUTATED 19P GAIN WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   7                321
  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
  19P GAIN MUTATED     6   1   0   1
  19P GAIN WILD-TYPE 372  50   4  29
D26V12, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                6                372
  R1                1                 50
  R2                0                  4
  RX                1                 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"
D26V13, continuous
D26V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6   2
  19P GAIN WILD-TYPE 218 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6    2
  19P GAIN WILD-TYPE  218  259
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  MULTIFOCAL                6                218
  UNIFOCAL                  2                259
[1] 2 2
[1] FALSE
D26V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     0
  19P GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           0     3
  19P GAIN WILD-TYPE                        26   318
D26V16, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           3                318
[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"
D26V17, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0   3
  19P GAIN WILD-TYPE  38 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    3
  19P GAIN WILD-TYPE   38  347
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                3                347
[1] 2 2
[1] FALSE

Clustering(27) Variable = 19Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED     8   1
  19Q GAIN WILD-TYPE 469  13
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                482 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 13 
$`19Q GAIN MUTATED`
TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A22N TCGA-EM-A2OY TCGA-EM-A3O9 TCGA-EM-A3SY 
        8.71        54.21        10.65        17.59         9.24        13.51 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3WA 
       33.63         1.64        17.06 

$`19Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       41.13        37.78        29.95        13.32        11.87        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-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-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        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-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        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-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        7.33        12.53        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       15.62        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        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-A238 
       24.69        68.22       102.90        66.77        81.34        39.95 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         0.99         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        16.57        18.08         0.30         0.76 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.64               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             54.21             158.83 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            13.510             16.605 
[1] "1.6 - 54.2 (13.5)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "7.2"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  19Q GAIN MUTATED         5        1         4        0         0         0
  19Q GAIN WILD-TYPE     275       50       105        2        45         6
D27V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  5                275
  STAGE II                 1                 50
  STAGE III                4                105
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  19Q GAIN MUTATED     4   1   5   0
  19Q GAIN WILD-TYPE 136 165 160  21
D27V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                4                136
  T2                1                165
  T3                5                160
  T4                0                 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"
D27V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     7   0
  19Q GAIN WILD-TYPE 216 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      7    0
  19Q GAIN WILD-TYPE  216  222
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                7                216
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19Q GAIN MUTATED     0   0  10
  19Q GAIN WILD-TYPE 273   9 202
D27V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                0                273
  M1                0                  9
  MX               10                202
[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"
D27V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     5   5
  19Q GAIN WILD-TYPE 359 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5    5
  19Q GAIN WILD-TYPE  359  126
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                5                359
  MALE                  5                126
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  19Q GAIN MUTATED                0
  19Q GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  19Q GAIN MUTATED                                               3
  19Q GAIN WILD-TYPE                                           350
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  19Q GAIN MUTATED                                                                        7
  19Q GAIN WILD-TYPE                                                                     91
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  19Q GAIN MUTATED                                                                     0
  19Q GAIN WILD-TYPE                                                                  35
D27V8, multiclass
                                                                        clus
vv                                                                       19Q GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       19Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D27V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1   9
  19Q GAIN WILD-TYPE  13 472
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    9
  19Q GAIN WILD-TYPE   13  472
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                 13
  YES                9                472
[1] 2 2
[1] FALSE
D27V10, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     9   0
  19Q GAIN WILD-TYPE 408  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9    0
  19Q GAIN WILD-TYPE  408   17
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 9                408
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  19Q GAIN MUTATED              1                       0    9
  19Q GAIN WILD-TYPE          129                      16  319
                    vv
clus                 VERY ADVANCED (T4B)
  19Q GAIN MUTATED                     0
  19Q GAIN WILD-TYPE                   1
D27V11, multiclass
                         clus
vv                        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   9                319
  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
  19Q GAIN MUTATED     8   1   0   1
  19Q GAIN WILD-TYPE 370  50   4  29
D27V12, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                8                370
  R1                1                 50
  R2                0                  4
  RX                1                 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"
D27V13, continuous
D27V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     6   4
  19Q GAIN WILD-TYPE 218 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6    4
  19Q GAIN WILD-TYPE  218  257
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  MULTIFOCAL                6                218
  UNIFOCAL                  4                257
[1] 2 2
[1] FALSE
D27V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     0
  19Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           0     5
  19Q GAIN WILD-TYPE                        26   316
D27V16, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           5                316
[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"
D27V17, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0   5
  19Q GAIN WILD-TYPE  38 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    5
  19Q GAIN WILD-TYPE   38  345
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                345
[1] 2 2
[1] FALSE

Clustering(28) Variable = 20P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    11   1
  20P GAIN WILD-TYPE 466  13
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                479 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                 13 
$`20P GAIN MUTATED`
TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
        5.72         8.71        54.21        57.01         6.05        17.59 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       17.46         9.24        13.51        12.26        98.56         1.64 

$`20P GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
       95.38        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        12.36        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        11.15         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              1.64               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             98.56             158.83 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            12.885             16.640 
[1] "1.6 - 98.6 (12.9)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "2.8"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  20P GAIN MUTATED         4        4         3        1         0         0
  20P GAIN WILD-TYPE     276       47       106        1        45         6
D28V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  4                276
  STAGE II                 4                 47
  STAGE III                3                106
  STAGE IV                 1                  1
  STAGE IVA                0                 45
  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
  20P GAIN MUTATED     2   4   5   1
  20P GAIN WILD-TYPE 138 162 160  20
D28V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                2                138
  T2                4                162
  T3                5                160
  T4                1                 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"
D28V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     7   1
  20P GAIN WILD-TYPE 216 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7    1
  20P GAIN WILD-TYPE  216  221
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                7                216
  1                1                221
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20P GAIN MUTATED     0   0  12
  20P GAIN WILD-TYPE 273   9 200
D28V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                0                273
  M1                0                  9
  MX               12                200
[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"
D28V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     8   4
  20P GAIN WILD-TYPE 356 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      8    4
  20P GAIN WILD-TYPE  356  127
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                8                356
  MALE                  4                127
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  20P GAIN MUTATED                0
  20P GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  20P GAIN MUTATED                                               4
  20P GAIN WILD-TYPE                                           349
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  20P GAIN MUTATED                                                                        8
  20P GAIN WILD-TYPE                                                                     90
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  20P GAIN MUTATED                                                                     0
  20P GAIN WILD-TYPE                                                                  35
D28V8, multiclass
                                                                        clus
vv                                                                       20P GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       20P GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D28V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     0  12
  20P GAIN WILD-TYPE  14 469
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0   12
  20P GAIN WILD-TYPE   14  469
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 0                 14
  YES               12                469
[1] 2 2
[1] FALSE
D28V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    11   0
  20P GAIN WILD-TYPE 406  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     11    0
  20P GAIN WILD-TYPE  406   17
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                11                406
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  20P GAIN MUTATED              1                       0   10
  20P GAIN WILD-TYPE          129                      16  318
                    vv
clus                 VERY ADVANCED (T4B)
  20P GAIN MUTATED                     1
  20P GAIN WILD-TYPE                   0
D28V11, multiclass
                         clus
vv                        20P GAIN MUTATED 20P GAIN WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                  10                318
  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
  20P GAIN MUTATED    10   1   0   1
  20P GAIN WILD-TYPE 368  50   4  29
D28V12, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               10                368
  R1                1                 50
  R2                0                  4
  RX                1                 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"
D28V13, continuous
D28V14, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     6   6
  20P GAIN WILD-TYPE 218 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      6    6
  20P GAIN WILD-TYPE  218  255
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  MULTIFOCAL                6                218
  UNIFOCAL                  6                255
[1] 2 2
[1] FALSE
D28V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     0
  20P GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           0     5
  20P GAIN WILD-TYPE                        26   316
D28V16, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           5                316
[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"
D28V17, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     0   5
  20P GAIN WILD-TYPE  38 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0    5
  20P GAIN WILD-TYPE   38  345
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                345
[1] 2 2
[1] FALSE

Clustering(29) Variable = 20Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    11   1
  20Q GAIN WILD-TYPE 466  13
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                479 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                 13 
$`20Q GAIN MUTATED`
TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
        5.72         8.71        54.21        57.01         6.05        17.59 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       17.46         9.24        13.51        12.26        98.56         1.64 

$`20Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
       95.38        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        12.36        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        11.15         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1.64               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             98.56             158.83 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            12.885             16.640 
[1] "1.6 - 98.6 (12.9)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "2.8"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  20Q GAIN MUTATED         4        4         3        1         0         0
  20Q GAIN WILD-TYPE     276       47       106        1        45         6
D29V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  4                276
  STAGE II                 4                 47
  STAGE III                3                106
  STAGE IV                 1                  1
  STAGE IVA                0                 45
  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
  20Q GAIN MUTATED     2   4   5   1
  20Q GAIN WILD-TYPE 138 162 160  20
D29V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                2                138
  T2                4                162
  T3                5                160
  T4                1                 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"
D29V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     7   1
  20Q GAIN WILD-TYPE 216 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      7    1
  20Q GAIN WILD-TYPE  216  221
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0                7                216
  1                1                221
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20Q GAIN MUTATED     0   0  12
  20Q GAIN WILD-TYPE 273   9 200
D29V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0                0                273
  M1                0                  9
  MX               12                200
[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"
D29V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     8   4
  20Q GAIN WILD-TYPE 356 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8    4
  20Q GAIN WILD-TYPE  356  127
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                8                356
  MALE                  4                127
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  20Q GAIN MUTATED                0
  20Q GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  20Q GAIN MUTATED                                               4
  20Q GAIN WILD-TYPE                                           349
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  20Q GAIN MUTATED                                                                        8
  20Q GAIN WILD-TYPE                                                                     90
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  20Q GAIN MUTATED                                                                     0
  20Q GAIN WILD-TYPE                                                                  35
D29V8, multiclass
                                                                        clus
vv                                                                       20Q GAIN MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       20Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D29V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     0  12
  20Q GAIN WILD-TYPE  14 469
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0   12
  20Q GAIN WILD-TYPE   14  469
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 0                 14
  YES               12                469
[1] 2 2
[1] FALSE
D29V10, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    11   0
  20Q GAIN WILD-TYPE 406  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11    0
  20Q GAIN WILD-TYPE  406   17
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                11                406
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  20Q GAIN MUTATED              1                       0   10
  20Q GAIN WILD-TYPE          129                      16  318
                    vv
clus                 VERY ADVANCED (T4B)
  20Q GAIN MUTATED                     1
  20Q GAIN WILD-TYPE                   0
D29V11, multiclass
                         clus
vv                        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                  10                318
  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
  20Q GAIN MUTATED    10   1   0   1
  20Q GAIN WILD-TYPE 368  50   4  29
D29V12, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               10                368
  R1                1                 50
  R2                0                  4
  RX                1                 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"
D29V13, continuous
D29V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     6   6
  20Q GAIN WILD-TYPE 218 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6    6
  20Q GAIN WILD-TYPE  218  255
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  MULTIFOCAL                6                218
  UNIFOCAL                  6                255
[1] 2 2
[1] FALSE
D29V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     0
  20Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           0     5
  20Q GAIN WILD-TYPE                        26   316
D29V16, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           5                316
[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"
D29V17, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     0   5
  20Q GAIN WILD-TYPE  38 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0    5
  20Q GAIN WILD-TYPE   38  345
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                345
[1] 2 2
[1] FALSE

Clustering(30) Variable = 21Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED     5   0
  21Q GAIN WILD-TYPE 472  14
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                486 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                 14 
$`21Q GAIN MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
        0.03        48.16        13.51        12.26        98.56 

$`21Q GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       50.33        53.06        47.38        52.50        45.53         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10        91.17         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-A3R9 
        0.99         1.51         0.76         0.03         4.67        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
       86.70         6.02        12.43         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        0.72        16.64        32.45         8.71        10.98         5.19 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.03               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             98.56             158.83 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            13.510             16.605 
[1] "0.0 - 98.6 (13.5)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  21Q GAIN MUTATED         4        1         0        0         0         0
  21Q GAIN WILD-TYPE     276       50       109        2        45         6
D30V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  4                276
  STAGE II                 1                 50
  STAGE III                0                109
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  21Q GAIN MUTATED     3   1   1   0
  21Q GAIN WILD-TYPE 137 165 164  21
D30V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                137
  T2                1                165
  T3                1                164
  T4                0                 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"
D30V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3   0
  21Q GAIN WILD-TYPE 220 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    0
  21Q GAIN WILD-TYPE  220  222
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                3                220
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  21Q GAIN MUTATED     2   0   3
  21Q GAIN WILD-TYPE 271   9 209
D30V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                2                271
  M1                0                  9
  MX                3                209
[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"
D30V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3   2
  21Q GAIN WILD-TYPE 361 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    2
  21Q GAIN WILD-TYPE  361  129
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                361
  MALE                  2                129
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  21Q GAIN MUTATED                0
  21Q GAIN WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  21Q GAIN MUTATED                                               4
  21Q GAIN WILD-TYPE                                           349
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  21Q GAIN MUTATED                                                                        1
  21Q GAIN WILD-TYPE                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  21Q GAIN MUTATED                                                                     0
  21Q GAIN WILD-TYPE                                                                  35
D30V8, multiclass
                                                                        clus
vv                                                                       21Q GAIN 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                                                                       21Q GAIN WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D30V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0   5
  21Q GAIN WILD-TYPE  14 476
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    5
  21Q GAIN WILD-TYPE   14  476
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                 14
  YES                5                476
[1] 2 2
[1] FALSE
D30V10, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4   0
  21Q GAIN WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    0
  21Q GAIN WILD-TYPE  413   17
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 4                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  21Q GAIN MUTATED              0                       0    4
  21Q GAIN WILD-TYPE          130                      16  324
                    vv
clus                 VERY ADVANCED (T4B)
  21Q GAIN MUTATED                     0
  21Q GAIN WILD-TYPE                   1
D30V11, multiclass
                         clus
vv                        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  MINIMAL (T3)                           0                130
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   4                324
  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
  21Q GAIN MUTATED     3   0   0   1
  21Q GAIN WILD-TYPE 375  51   4  29
D30V12, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                3                375
  R1                0                 51
  R2                0                  4
  RX                1                 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"
D30V13, continuous
D30V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0   5
  21Q GAIN WILD-TYPE 224 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    5
  21Q GAIN WILD-TYPE  224  256
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  MULTIFOCAL                0                224
  UNIFOCAL                  5                256
[1] 2 2
[1] FALSE
D30V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     0
  21Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           0     4
  21Q GAIN WILD-TYPE                        26   317
D30V16, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           4                317
[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"
D30V17, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0   4
  21Q GAIN WILD-TYPE  38 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    4
  21Q GAIN WILD-TYPE   38  346
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                4                346
[1] 2 2
[1] FALSE

Clustering(31) Variable = XQ GAIN MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     8   1
  XQ GAIN WILD-TYPE 469  13
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9               482 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                13 
$`XQ GAIN MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI 
       20.48         5.72        54.21        57.01        10.65        17.46 
TCGA-EM-A3FK TCGA-ET-A40S TCGA-FY-A3NM 
       23.77         5.03         0.99 

$`XQ GAIN WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A1YE 
       20.91        12.36        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        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-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.46        17.29        14.60        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-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        3.22         7.17         4.80         2.14         4.01         1.94 
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-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         1.64         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.99              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            57.01            158.83 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            17.46             16.57 
[1] "1.0 - 57.0 (17.5)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "5.3"
D31V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  XQ GAIN MUTATED         3        3         2        1         0         0
  XQ GAIN WILD-TYPE     277       48       107        1        45         6
D31V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 3               277
  STAGE II                3                48
  STAGE III               2               107
  STAGE IV                1                 1
  STAGE IVA               0                45
  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
  XQ GAIN MUTATED     2   4   2   1
  XQ GAIN WILD-TYPE 138 162 163  20
D31V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               2               138
  T2               4               162
  T3               2               163
  T4               1                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"
D31V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     6   2
  XQ GAIN WILD-TYPE 217 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6    2
  XQ GAIN WILD-TYPE  217  220
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               6               217
  1               2               220
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  XQ GAIN MUTATED     1   0   8
  XQ GAIN WILD-TYPE 272   9 204
D31V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               1               272
  M1               0                 9
  MX               8               204
[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"
D31V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     8   1
  XQ GAIN WILD-TYPE 356 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8    1
  XQ GAIN WILD-TYPE  356  130
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               8               356
  MALE                 1               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  XQ GAIN MUTATED                0
  XQ GAIN WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  XQ GAIN MUTATED                                               5
  XQ GAIN WILD-TYPE                                           348
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  XQ GAIN MUTATED                                                                        4
  XQ GAIN WILD-TYPE                                                                     94
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  XQ GAIN MUTATED                                                                     0
  XQ GAIN WILD-TYPE                                                                  35
D31V8, multiclass
                                                                        clus
vv                                                                       XQ GAIN MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       XQ GAIN WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                94
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D31V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0   9
  XQ GAIN WILD-TYPE  14 472
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    9
  XQ GAIN WILD-TYPE   14  472
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                14
  YES               9               472
[1] 2 2
[1] FALSE
D31V10, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     8   1
  XQ GAIN WILD-TYPE 409  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8    1
  XQ GAIN WILD-TYPE  409   16
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                8               409
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  XQ GAIN MUTATED              1                       0    7
  XQ GAIN WILD-TYPE          129                      16  321
                   vv
clus                VERY ADVANCED (T4B)
  XQ GAIN MUTATED                     1
  XQ GAIN WILD-TYPE                   0
D31V11, multiclass
                         clus
vv                        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  MINIMAL (T3)                          1               129
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  7               321
  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
  XQ GAIN MUTATED     5   2   0   2
  XQ GAIN WILD-TYPE 373  49   4  28
D31V12, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               5               373
  R1               2                49
  R2               0                 4
  RX               2                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"
D31V13, continuous
D31V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     6   3
  XQ GAIN WILD-TYPE 218 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6    3
  XQ GAIN WILD-TYPE  218  258
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  MULTIFOCAL               6               218
  UNIFOCAL                 3               258
[1] 2 2
[1] FALSE
D31V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     0
  XQ GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           0     4
  XQ GAIN WILD-TYPE                        26   317
D31V16, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          4               317
[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"
D31V17, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0   4
  XQ GAIN WILD-TYPE  38 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    4
  XQ GAIN WILD-TYPE   38  346
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               346
[1] 2 2
[1] FALSE

Clustering(32) Variable = 1P LOSS MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     4   0
  1P LOSS WILD-TYPE 473  14
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               487 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                14 
$`1P LOSS MUTATED`
TCGA-E8-A432 TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       14.43        54.08        98.56         1.64 

$`1P LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.07        14.27         3.02        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        57.01        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        39.95        33.63        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1.64              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            98.56            158.83 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           34.255            16.570 
[1] "1.6 - 98.6 (34.3)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D32V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  1P LOSS MUTATED         1        2         1        0         0         0
  1P LOSS WILD-TYPE     279       49       108        2        45         6
D32V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 1               279
  STAGE II                2                49
  STAGE III               1               108
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  1P LOSS MUTATED     0   2   2   0
  1P LOSS WILD-TYPE 140 164 163  21
D32V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               0               140
  T2               2               164
  T3               2               163
  T4               0                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"
D32V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3   0
  1P LOSS WILD-TYPE 220 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    0
  1P LOSS WILD-TYPE  220  222
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               3               220
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1P LOSS MUTATED     1   0   3
  1P LOSS WILD-TYPE 272   9 209
D32V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               1               272
  M1               0                 9
  MX               3               209
[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"
D32V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     4   0
  1P LOSS WILD-TYPE 360 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    0
  1P LOSS WILD-TYPE  360  131
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               4               360
  MALE                 0               131
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  1P LOSS MUTATED                0
  1P LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  1P LOSS MUTATED                                               2
  1P LOSS WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  1P LOSS MUTATED                                                                        2
  1P LOSS WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1P LOSS MUTATED                                                                     0
  1P LOSS WILD-TYPE                                                                  35
D32V8, multiclass
                                                                        clus
vv                                                                       1P LOSS 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                                                                       1P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D32V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0   4
  1P LOSS WILD-TYPE  14 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    4
  1P LOSS WILD-TYPE   14  477
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                0                14
  YES               4               477
[1] 2 2
[1] FALSE
D32V10, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3   0
  1P LOSS WILD-TYPE 414  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    0
  1P LOSS WILD-TYPE  414   17
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3               414
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  1P LOSS MUTATED              0                       0    4
  1P LOSS WILD-TYPE          130                      16  324
                   vv
clus                VERY ADVANCED (T4B)
  1P LOSS MUTATED                     0
  1P LOSS WILD-TYPE                   1
D32V11, multiclass
                         clus
vv                        1P LOSS MUTATED 1P LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  4               324
  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
  1P LOSS MUTATED     4   0   0   0
  1P LOSS WILD-TYPE 374  51   4  30
D32V12, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0               4               374
  R1               0                51
  R2               0                 4
  RX               0                30
[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"
D32V13, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               389 
       TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZB        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ        TCGA-BJ-A18Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191        TCGA-BJ-A28R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD        TCGA-DE-A0XZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB        TCGA-EL-A3ZH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A3ZP        TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CT        TCGA-EM-A2CU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OW        TCGA-EM-A2OX        TCGA-EM-A2OY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2OZ        TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A2P3        TCGA-EM-A3AJ        TCGA-EM-A3AK        TCGA-EM-A3AL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AQ        TCGA-EM-A3AR 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FL        TCGA-EM-A3FM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O7        TCGA-EM-A3O8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SY        TCGA-EM-A3SZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A4FF        TCGA-EM-A4FH        TCGA-EM-A4FK        TCGA-EM-A4FM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EM-A4FU        TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-QD-A8IV 
"1P LOSS WILD-TYPE" 
D32V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1   3
  1P LOSS WILD-TYPE 223 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    3
  1P LOSS WILD-TYPE  223  258
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  MULTIFOCAL               1               223
  UNIFOCAL                 3               258
[1] 2 2
[1] FALSE
D32V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                1    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           0     2
  1P LOSS WILD-TYPE                        26   319
D32V16, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                48
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          2               319
[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"
D32V17, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0   3
  1P LOSS WILD-TYPE  38 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    3
  1P LOSS WILD-TYPE   38  347
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               347
[1] 2 2
[1] FALSE

Clustering(33) Variable = 1Q LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     3   0
  1Q LOSS WILD-TYPE 474  14
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3               488 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                14 
$`1Q LOSS MUTATED`
TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       54.08        98.56         1.64 

$`1Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        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-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        54.21        57.01        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-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        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-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
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-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.64              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            98.56            158.83 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            54.08             16.57 
[1] "1.6 - 98.6 (54.1)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D33V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  1Q LOSS MUTATED         1        1         1        0         0         0
  1Q LOSS WILD-TYPE     279       50       108        2        45         6
D33V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 1               279
  STAGE II                1                50
  STAGE III               1               108
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  1Q LOSS MUTATED     0   1   2   0
  1Q LOSS WILD-TYPE 140 165 163  21
D33V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0               140
  T2               1               165
  T3               2               163
  T4               0                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"
D33V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2   0
  1Q LOSS WILD-TYPE 221 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    0
  1Q LOSS WILD-TYPE  221  222
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               2               221
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1Q LOSS MUTATED     0   0   3
  1Q LOSS WILD-TYPE 273   9 209
D33V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               0               273
  M1               0                 9
  MX               3               209
[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"
D33V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3   0
  1Q LOSS WILD-TYPE 361 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    0
  1Q LOSS WILD-TYPE  361  131
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               3               361
  MALE                 0               131
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  1Q LOSS MUTATED                0
  1Q LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  1Q LOSS MUTATED                                               1
  1Q LOSS WILD-TYPE                                           352
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  1Q LOSS MUTATED                                                                        2
  1Q LOSS WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  1Q LOSS MUTATED                                                                     0
  1Q LOSS WILD-TYPE                                                                  35
D33V8, multiclass
                                                                        clus
vv                                                                       1Q LOSS MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       1Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D33V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   3
  1Q LOSS WILD-TYPE  14 478
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    3
  1Q LOSS WILD-TYPE   14  478
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                0                14
  YES               3               478
[1] 2 2
[1] FALSE
D33V10, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2   0
  1Q LOSS WILD-TYPE 415  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    0
  1Q LOSS WILD-TYPE  415   17
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                2               415
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  1Q LOSS MUTATED              0                       0    3
  1Q LOSS WILD-TYPE          130                      16  325
                   vv
clus                VERY ADVANCED (T4B)
  1Q LOSS MUTATED                     0
  1Q LOSS WILD-TYPE                   1
D33V11, multiclass
                         clus
vv                        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  3               325
  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
  1Q LOSS MUTATED     3   0   0   0
  1Q LOSS WILD-TYPE 375  51   4  30
D33V12, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               3               375
  R1               0                51
  R2               0                 4
  RX               0                30
[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"
D33V13, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               389 
       TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZB        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ        TCGA-BJ-A18Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191        TCGA-BJ-A28R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD        TCGA-DE-A0XZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB        TCGA-EL-A3ZH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZP        TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CT        TCGA-EM-A2CU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OW        TCGA-EM-A2OX        TCGA-EM-A2OY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2OZ        TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A2P3        TCGA-EM-A3AJ        TCGA-EM-A3AK        TCGA-EM-A3AL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AQ        TCGA-EM-A3AR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FL        TCGA-EM-A3FM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O7        TCGA-EM-A3O8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SY        TCGA-EM-A3SZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A4FF        TCGA-EM-A4FH        TCGA-EM-A4FK        TCGA-EM-A4FM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EM-A4FU        TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-QD-A8IV 
"1Q LOSS WILD-TYPE" 
D33V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1   2
  1Q LOSS WILD-TYPE 223 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    2
  1Q LOSS WILD-TYPE  223  259
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  MULTIFOCAL               1               223
  UNIFOCAL                 2               259
[1] 2 2
[1] FALSE
D33V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     0
  1Q LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           0     2
  1Q LOSS WILD-TYPE                        26   319
D33V16, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               395 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A2N9        TCGA-BJ-A2NA        TCGA-BJ-A2P4        TCGA-BJ-A3EZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A3F0        TCGA-BJ-A3PR        TCGA-BJ-A3PT        TCGA-BJ-A3PU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45G        TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BJ-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CE-A27D        TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CE-A482        TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A0XZ        TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A13U        TCGA-DJ-A13W        TCGA-DJ-A1QD        TCGA-DJ-A1QE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QF        TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QM        TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PO        TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3US 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UT        TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UY        TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UW        TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DO-A1JZ        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A415        TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A418 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A419        TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A436        TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-E8-A44M        TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3T0        TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3T3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3T6        TCGA-EL-A3T7        TCGA-EL-A3T8        TCGA-EL-A3T9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3TA        TCGA-EL-A3TB        TCGA-EL-A3ZG        TCGA-EL-A3ZH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZP        TCGA-EL-A3ZQ        TCGA-EL-A3ZR        TCGA-EL-A3ZS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZT        TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4K9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KH        TCGA-EL-A4KI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A25P        TCGA-ET-A25R        TCGA-ET-A2MX        TCGA-ET-A2MY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39K        TCGA-ET-A39M        TCGA-ET-A39O        TCGA-ET-A39P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3DO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FK-A3SB        TCGA-FK-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR        TCGA-FY-A40K 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-FY-A76V        TCGA-GE-A2C6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-L6-A4ET        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-MK-A84Z        TCGA-QD-A8IV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D33V17, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   2
  1Q LOSS WILD-TYPE  38 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    2
  1Q LOSS WILD-TYPE   38  348
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               348
[1] 2 2
[1] FALSE

Clustering(34) Variable = 2P LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    10   0
  2P LOSS WILD-TYPE 467  14
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               481 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                14 
$`2P LOSS MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       20.58         8.12        54.08        10.65         6.05        17.59 
TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A3DS TCGA-FY-A3I5 
        9.24        13.51         0.30         1.64 

$`2P LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         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-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
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-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        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-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       13.91         7.82        11.51        16.41        15.62        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         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-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        39.95        33.63        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.30              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            54.08            158.83 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            9.945            16.730 
[1] "0.3 - 54.1 (9.9)"   "0.0 - 158.8 (16.7)"
[1] "hr="     "3300000"
D34V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  2P LOSS MUTATED         4        5         1        0         0         0
  2P LOSS WILD-TYPE     276       46       108        2        45         6
D34V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 4               276
  STAGE II                5                46
  STAGE III               1               108
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  2P LOSS MUTATED     3   5   2   0
  2P LOSS WILD-TYPE 137 161 163  21
D34V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               3               137
  T2               5               161
  T3               2               163
  T4               0                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"
D34V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     8   0
  2P LOSS WILD-TYPE 215 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      8    0
  2P LOSS WILD-TYPE  215  222
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               8               215
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2P LOSS MUTATED     1   0   9
  2P LOSS WILD-TYPE 272   9 203
D34V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               1               272
  M1               0                 9
  MX               9               203
[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"
D34V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7   3
  2P LOSS WILD-TYPE 357 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7    3
  2P LOSS WILD-TYPE  357  128
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               357
  MALE                 3               128
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  2P LOSS MUTATED                0
  2P LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  2P LOSS MUTATED                                               3
  2P LOSS WILD-TYPE                                           350
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  2P LOSS MUTATED                                                                        7
  2P LOSS WILD-TYPE                                                                     91
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  2P LOSS MUTATED                                                                     0
  2P LOSS WILD-TYPE                                                                  35
D34V8, multiclass
                                                                        clus
vv                                                                       2P LOSS MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       2P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D34V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  10
  2P LOSS WILD-TYPE  14 471
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   10
  2P LOSS WILD-TYPE   14  471
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                0                14
  YES              10               471
[1] 2 2
[1] FALSE
D34V10, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9   0
  2P LOSS WILD-TYPE 408  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    0
  2P LOSS WILD-TYPE  408   17
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                9               408
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  2P LOSS MUTATED              0                       0   10
  2P LOSS WILD-TYPE          130                      16  318
                   vv
clus                VERY ADVANCED (T4B)
  2P LOSS MUTATED                     0
  2P LOSS WILD-TYPE                   1
D34V11, multiclass
                         clus
vv                        2P LOSS MUTATED 2P LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                 10               318
  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
  2P LOSS MUTATED     9   0   0   1
  2P LOSS WILD-TYPE 369  51   4  29
D34V12, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               9               369
  R1               0                51
  R2               0                 4
  RX               1                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"
D34V13, continuous
D34V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     5   5
  2P LOSS WILD-TYPE 219 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    5
  2P LOSS WILD-TYPE  219  256
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  MULTIFOCAL               5               219
  UNIFOCAL                 5               256
[1] 2 2
[1] FALSE
D34V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           0     4
  2P LOSS WILD-TYPE                        26   317
D34V16, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          4               317
[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"
D34V17, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0   4
  2P LOSS WILD-TYPE  38 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    4
  2P LOSS WILD-TYPE   38  346
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               346
[1] 2 2
[1] FALSE

Clustering(35) Variable = 2Q LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    10   0
  2Q LOSS WILD-TYPE 467  14
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               481 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                14 
$`2Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       20.58         8.12        54.08        10.65         6.05        17.59 
TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FY-A3I5 
        9.24        13.51        98.56         1.64 

$`2Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         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-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
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-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        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-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       13.91         7.82        11.51        16.41        15.62        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        39.95        33.63        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             1.64              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            98.56            158.83 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            12.08             16.64 
[1] "1.6 - 98.6 (12.1)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D35V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  2Q LOSS MUTATED         4        5         1        0         0         0
  2Q LOSS WILD-TYPE     276       46       108        2        45         6
D35V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 4               276
  STAGE II                5                46
  STAGE III               1               108
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  2Q LOSS MUTATED     2   5   3   0
  2Q LOSS WILD-TYPE 138 161 162  21
D35V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               2               138
  T2               5               161
  T3               3               162
  T4               0                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"
D35V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   0
  2Q LOSS WILD-TYPE 216 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    0
  2Q LOSS WILD-TYPE  216  222
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               7               216
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2Q LOSS MUTATED     1   0   9
  2Q LOSS WILD-TYPE 272   9 203
D35V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               1               272
  M1               0                 9
  MX               9               203
[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"
D35V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   3
  2Q LOSS WILD-TYPE 357 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    3
  2Q LOSS WILD-TYPE  357  128
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               7               357
  MALE                 3               128
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  2Q LOSS MUTATED                0
  2Q LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  2Q LOSS MUTATED                                               3
  2Q LOSS WILD-TYPE                                           350
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  2Q LOSS MUTATED                                                                        7
  2Q LOSS WILD-TYPE                                                                     91
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  2Q LOSS MUTATED                                                                     0
  2Q LOSS WILD-TYPE                                                                  35
D35V8, multiclass
                                                                        clus
vv                                                                       2Q LOSS MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       2Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D35V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  10
  2Q LOSS WILD-TYPE  14 471
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   10
  2Q LOSS WILD-TYPE   14  471
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                0                14
  YES              10               471
[1] 2 2
[1] FALSE
D35V10, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     9   0
  2Q LOSS WILD-TYPE 408  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9    0
  2Q LOSS WILD-TYPE  408   17
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                9               408
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  2Q LOSS MUTATED              0                       0   10
  2Q LOSS WILD-TYPE          130                      16  318
                   vv
clus                VERY ADVANCED (T4B)
  2Q LOSS MUTATED                     0
  2Q LOSS WILD-TYPE                   1
D35V11, multiclass
                         clus
vv                        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                 10               318
  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
  2Q LOSS MUTATED     9   0   0   1
  2Q LOSS WILD-TYPE 369  51   4  29
D35V12, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               9               369
  R1               0                51
  R2               0                 4
  RX               1                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"
D35V13, continuous
D35V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     5   5
  2Q LOSS WILD-TYPE 219 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    5
  2Q LOSS WILD-TYPE  219  256
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  MULTIFOCAL               5               219
  UNIFOCAL                 5               256
[1] 2 2
[1] FALSE
D35V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     0
  2Q LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           0     4
  2Q LOSS WILD-TYPE                        26   317
D35V16, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          4               317
[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"
D35V17, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   4
  2Q LOSS WILD-TYPE  38 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    4
  2Q LOSS WILD-TYPE   38  346
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               346
[1] 2 2
[1] FALSE

Clustering(36) Variable = 3P LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED     3   0
  3P LOSS WILD-TYPE 474  14
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               488 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                14 
$`3P LOSS MUTATED`
TCGA-BJ-A190 TCGA-ET-A39N TCGA-FY-A3I5 
       20.58        98.56         1.64 

$`3P LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        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-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
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-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.64              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            98.56            158.83 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            20.58             16.57 
[1] "1.6 - 98.6 (20.6)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D36V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  3P LOSS MUTATED         1        1         1        0         0         0
  3P LOSS WILD-TYPE     279       50       108        2        45         6
D36V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 1               279
  STAGE II                1                50
  STAGE III               1               108
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  3P LOSS MUTATED     0   1   2   0
  3P LOSS WILD-TYPE 140 165 163  21
D36V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               0               140
  T2               1               165
  T3               2               163
  T4               0                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"
D36V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2   0
  3P LOSS WILD-TYPE 221 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    0
  3P LOSS WILD-TYPE  221  222
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               2               221
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3P LOSS MUTATED     0   0   3
  3P LOSS WILD-TYPE 273   9 209
D36V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               0               273
  M1               0                 9
  MX               3               209
[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"
D36V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2   1
  3P LOSS WILD-TYPE 362 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    1
  3P LOSS WILD-TYPE  362  130
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               2               362
  MALE                 1               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  3P LOSS MUTATED                0
  3P LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  3P LOSS MUTATED                                               2
  3P LOSS WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  3P LOSS MUTATED                                                                        1
  3P LOSS WILD-TYPE                                                                     97
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  3P LOSS MUTATED                                                                     0
  3P LOSS WILD-TYPE                                                                  35
D36V8, multiclass
                                                                        clus
vv                                                                       3P LOSS 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                                                                       3P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D36V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   3
  3P LOSS WILD-TYPE  14 478
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    3
  3P LOSS WILD-TYPE   14  478
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                0                14
  YES               3               478
[1] 2 2
[1] FALSE
D36V10, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2   0
  3P LOSS WILD-TYPE 415  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    0
  3P LOSS WILD-TYPE  415   17
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                2               415
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  3P LOSS MUTATED              0                       0    3
  3P LOSS WILD-TYPE          130                      16  325
                   vv
clus                VERY ADVANCED (T4B)
  3P LOSS MUTATED                     0
  3P LOSS WILD-TYPE                   1
D36V11, multiclass
                         clus
vv                        3P LOSS MUTATED 3P LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  3               325
  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
  3P LOSS MUTATED     3   0   0   0
  3P LOSS WILD-TYPE 375  51   4  30
D36V12, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               3               375
  R1               0                51
  R2               0                 4
  RX               0                30
[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"
D36V13, continuous
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2               389 
       TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZB        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ        TCGA-BJ-A18Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A28R        TCGA-BJ-A28T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A290 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N8        TCGA-BJ-A2N9        TCGA-BJ-A2NA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU        TCGA-BJ-A45C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G        TCGA-BJ-A45I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8        TCGA-BJ-A4O9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CE-A13K        TCGA-CE-A3MD        TCGA-DE-A0XZ        TCGA-DE-A0Y2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8        TCGA-DE-A4MA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69K 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13U        TCGA-DJ-A13V 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG        TCGA-DJ-A1QH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9        TCGA-DJ-A2QA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ        TCGA-DJ-A3UR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD        TCGA-DJ-A3VF 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A4UL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW        TCGA-DJ-A4V2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415        TCGA-E8-A417 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436        TCGA-E8-A438 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0        TCGA-EL-A3T1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3T2        TCGA-EL-A3TB        TCGA-EL-A3ZH        TCGA-EL-A3ZK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4KD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS        TCGA-EM-A1CT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW        TCGA-EM-A1YA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD        TCGA-EM-A1YE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN        TCGA-EM-A2CP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CT        TCGA-EM-A2CU 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2OV        TCGA-EM-A2OW        TCGA-EM-A2OX        TCGA-EM-A2OY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2OZ        TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A2P3        TCGA-EM-A3AJ        TCGA-EM-A3AK        TCGA-EM-A3AL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AQ        TCGA-EM-A3AR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FL        TCGA-EM-A3FM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O7        TCGA-EM-A3O8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SY        TCGA-EM-A3SZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A4FF        TCGA-EM-A4FH        TCGA-EM-A4FK        TCGA-EM-A4FM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ        TCGA-EM-A4FR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EM-A4FU        TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A2N4        TCGA-ET-A39K        TCGA-ET-A39L        TCGA-ET-A39O 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-QD-A8IV 
"3P LOSS WILD-TYPE" 
D36V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2   1
  3P LOSS WILD-TYPE 222 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    1
  3P LOSS WILD-TYPE  222  260
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  MULTIFOCAL               2               222
  UNIFOCAL                 1               260
[1] 2 2
[1] FALSE
D36V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     0
  3P LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           0     3
  3P LOSS WILD-TYPE                        26   318
D36V16, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          3               318
[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"
D36V17, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   3
  3P LOSS WILD-TYPE  38 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    3
  3P LOSS WILD-TYPE   38  347
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               347
[1] 2 2
[1] FALSE

Clustering(37) Variable = 3Q LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     4   0
  3Q LOSS WILD-TYPE 473  14
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               487 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                14 
$`3Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       20.58        54.08        98.56         1.64 

$`3Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        57.01        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        39.95        33.63        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.64              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            98.56            158.83 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            37.33             16.57 
[1] "1.6 - 98.6 (37.3)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D37V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  3Q LOSS MUTATED         1        2         1        0         0         0
  3Q LOSS WILD-TYPE     279       49       108        2        45         6
D37V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 1               279
  STAGE II                2                49
  STAGE III               1               108
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  3Q LOSS MUTATED     0   2   2   0
  3Q LOSS WILD-TYPE 140 164 163  21
D37V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0               140
  T2               2               164
  T3               2               163
  T4               0                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"
D37V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   0
  3Q LOSS WILD-TYPE 220 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    0
  3Q LOSS WILD-TYPE  220  222
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               3               220
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED     0   0   4
  3Q LOSS WILD-TYPE 273   9 208
D37V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               0               273
  M1               0                 9
  MX               4               208
[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"
D37V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   1
  3Q LOSS WILD-TYPE 361 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    1
  3Q LOSS WILD-TYPE  361  130
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               3               361
  MALE                 1               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  3Q LOSS MUTATED                0
  3Q LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  3Q LOSS MUTATED                                               2
  3Q LOSS WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  3Q LOSS MUTATED                                                                        2
  3Q LOSS WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  3Q LOSS MUTATED                                                                     0
  3Q LOSS WILD-TYPE                                                                  35
D37V8, multiclass
                                                                        clus
vv                                                                       3Q LOSS 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                                                                       3Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D37V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   4
  3Q LOSS WILD-TYPE  14 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    4
  3Q LOSS WILD-TYPE   14  477
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                14
  YES               4               477
[1] 2 2
[1] FALSE
D37V10, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   0
  3Q LOSS WILD-TYPE 414  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    0
  3Q LOSS WILD-TYPE  414   17
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                3               414
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  3Q LOSS MUTATED              0                       0    4
  3Q LOSS WILD-TYPE          130                      16  324
                   vv
clus                VERY ADVANCED (T4B)
  3Q LOSS MUTATED                     0
  3Q LOSS WILD-TYPE                   1
D37V11, multiclass
                         clus
vv                        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  4               324
  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
  3Q LOSS MUTATED     4   0   0   0
  3Q LOSS WILD-TYPE 374  51   4  30
D37V12, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               4               374
  R1               0                51
  R2               0                 4
  RX               0                30
[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"
D37V13, continuous
D37V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2   2
  3Q LOSS WILD-TYPE 222 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    2
  3Q LOSS WILD-TYPE  222  259
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  MULTIFOCAL               2               222
  UNIFOCAL                 2               259
[1] 2 2
[1] FALSE
D37V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           0     3
  3Q LOSS WILD-TYPE                        26   318
D37V16, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          3               318
[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"
D37V17, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   3
  3Q LOSS WILD-TYPE  38 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    3
  3Q LOSS WILD-TYPE   38  347
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               3               347
[1] 2 2
[1] FALSE

Clustering(38) Variable = 6P LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED     3   0
  6P LOSS WILD-TYPE 474  14
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                3               488 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                0                14 
$`6P LOSS MUTATED`
TCGA-ET-A39N TCGA-ET-A3BV TCGA-FY-A3I5 
       98.56        42.25         1.64 

$`6P LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         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-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-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-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
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-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             1.64              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            98.56            158.83 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            42.25             16.57 
[1] "1.6 - 98.6 (42.2)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D38V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  6P LOSS MUTATED         2        0         2        0         0         0
  6P LOSS WILD-TYPE     278       51       107        2        45         6
D38V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 2               278
  STAGE II                0                51
  STAGE III               2               107
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  6P LOSS MUTATED     1   1   2   0
  6P LOSS WILD-TYPE 139 165 163  21
D38V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               1               139
  T2               1               165
  T3               2               163
  T4               0                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"
D38V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1   1
  6P LOSS WILD-TYPE 222 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    1
  6P LOSS WILD-TYPE  222  221
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               1               222
  1               1               221
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6P LOSS MUTATED     0   0   4
  6P LOSS WILD-TYPE 273   9 208
D38V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               0               273
  M1               0                 9
  MX               4               208
[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"
D38V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     3   1
  6P LOSS WILD-TYPE 361 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    1
  6P LOSS WILD-TYPE  361  130
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               3               361
  MALE                 1               130
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  6P LOSS MUTATED                0
  6P LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  6P LOSS MUTATED                                               3
  6P LOSS WILD-TYPE                                           350
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  6P LOSS MUTATED                                                                        1
  6P LOSS WILD-TYPE                                                                     97
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  6P LOSS MUTATED                                                                     0
  6P LOSS WILD-TYPE                                                                  35
D38V8, multiclass
                                                                        clus
vv                                                                       6P LOSS 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                                                                       6P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D38V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0   4
  6P LOSS WILD-TYPE  14 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    4
  6P LOSS WILD-TYPE   14  477
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0                14
  YES               4               477
[1] 2 2
[1] FALSE
D38V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     3   0
  6P LOSS WILD-TYPE 414  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    0
  6P LOSS WILD-TYPE  414   17
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                3               414
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  6P LOSS MUTATED              0                       0    4
  6P LOSS WILD-TYPE          130                      16  324
                   vv
clus                VERY ADVANCED (T4B)
  6P LOSS MUTATED                     0
  6P LOSS WILD-TYPE                   1
D38V11, multiclass
                         clus
vv                        6P LOSS MUTATED 6P LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  4               324
  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
  6P LOSS MUTATED     3   1   0   0
  6P LOSS WILD-TYPE 375  50   4  30
D38V12, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0               3               375
  R1               1                50
  R2               0                 4
  RX               0                30
[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"
D38V13, continuous
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2               389 
       TCGA-BJ-A0Z0        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZB        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ        TCGA-BJ-A18Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A18Z        TCGA-BJ-A190        TCGA-BJ-A191        TCGA-BJ-A28R 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A3EZ        TCGA-BJ-A3PR        TCGA-BJ-A3PU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A45C        TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45G 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A3MD        TCGA-DE-A0XZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A3KN        TCGA-DE-A4M8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC        TCGA-DE-A4MD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DE-A69K        TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A13P        TCGA-DJ-A13R        TCGA-DJ-A13T        TCGA-DJ-A13U 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X        TCGA-DJ-A1QG 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QM        TCGA-DJ-A2PO        TCGA-DJ-A2PP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PS        TCGA-DJ-A2PT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PU        TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8        TCGA-DJ-A2Q9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK        TCGA-DJ-A3UM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP        TCGA-DJ-A3UQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3V4        TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3V9        TCGA-DJ-A3VA        TCGA-DJ-A3VB        TCGA-DJ-A3VD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V5        TCGA-DO-A1K0        TCGA-DO-A2HM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0        TCGA-E3-A3E1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5        TCGA-E8-A242 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A414        TCGA-E8-A415 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A419        TCGA-E8-A433        TCGA-E8-A436 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-EL-A3CM        TCGA-EL-A3CN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CO        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GS        TCGA-EL-A3GU 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GX        TCGA-EL-A3H3        TCGA-EL-A3H4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3MX        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3T0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3TB        TCGA-EL-A3ZH 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3ZK        TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A3ZP        TCGA-EL-A3ZS        TCGA-EL-A4JV        TCGA-EL-A4JW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0        TCGA-EL-A4K1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6        TCGA-EL-A4K7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EL-A4KD        TCGA-EL-A4KG        TCGA-EL-A4KI        TCGA-EM-A1CS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A1YE        TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22L        TCGA-EM-A22M        TCGA-EM-A22N        TCGA-EM-A22O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A22P        TCGA-EM-A22Q        TCGA-EM-A2CK        TCGA-EM-A2CN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS        TCGA-EM-A2CT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2CU        TCGA-EM-A2OV        TCGA-EM-A2OW        TCGA-EM-A2OX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2OZ        TCGA-EM-A2P0        TCGA-EM-A2P1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A2P2        TCGA-EM-A2P3        TCGA-EM-A3AJ        TCGA-EM-A3AK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3AR        TCGA-EM-A3FJ        TCGA-EM-A3FK        TCGA-EM-A3FL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3FM        TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3FQ        TCGA-EM-A3FR        TCGA-EM-A3O3        TCGA-EM-A3O7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3O8        TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3ST        TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A3SZ        TCGA-EM-A4FF        TCGA-EM-A4FH        TCGA-EM-A4FK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A4FM        TCGA-EM-A4FN        TCGA-EM-A4FO        TCGA-EM-A4FQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EM-A4FR        TCGA-EM-A4FU        TCGA-EM-A4FV        TCGA-EM-A4G1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25G        TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25L        TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A25P        TCGA-ET-A2MX        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N4        TCGA-ET-A39K        TCGA-ET-A39L 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39O        TCGA-ET-A39P        TCGA-ET-A39R        TCGA-ET-A39S 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A39T        TCGA-ET-A3BO        TCGA-ET-A3BP        TCGA-ET-A3BQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU        TCGA-ET-A3BX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A231 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FE-A23A        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FK-A3S3        TCGA-FK-A3SB        TCGA-FK-A3SE        TCGA-FK-A3SG 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3I4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3NM        TCGA-FY-A3NN        TCGA-FY-A3ON        TCGA-FY-A3R6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R9        TCGA-FY-A3TY        TCGA-FY-A3W9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A3YR        TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FY-A40N        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-GE-A2C6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7        TCGA-MK-A4N9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-QD-A8IV 
"6P LOSS WILD-TYPE" 
D38V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2   2
  6P LOSS WILD-TYPE 222 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    2
  6P LOSS WILD-TYPE  222  259
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  MULTIFOCAL               2               222
  UNIFOCAL                 2               259
[1] 2 2
[1] FALSE
D38V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     0
  6P LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           0     4
  6P LOSS WILD-TYPE                        26   317
D38V16, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          4               317
[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"
D38V17, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0   4
  6P LOSS WILD-TYPE  38 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    4
  6P LOSS WILD-TYPE   38  346
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               4               346
[1] 2 2
[1] FALSE

Clustering(39) Variable = 6Q LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED     4   2
  6Q LOSS WILD-TYPE 473  12
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6               485 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                12 
$`6Q LOSS MUTATED`
TCGA-EL-A3H2 TCGA-EM-A1YE TCGA-ET-A39N TCGA-ET-A3BV TCGA-FE-A239 TCGA-FY-A3I5 
       33.50        54.08        98.56        42.25        33.63         1.64 

$`6Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        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-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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        57.01        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        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-A3BW TCGA-ET-A3BX 
        2.43         5.56        24.72        38.30         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-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       81.34        39.95        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1.64              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            98.56            158.83 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            37.94             16.44 
[1] "1.6 - 98.6 (37.9)"  "0.0 - 158.8 (16.4)"
[1] "hr=" "6.4"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  6Q LOSS MUTATED         2        2         3        0         0         0
  6Q LOSS WILD-TYPE     278       49       106        2        45         6
D39V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 2               278
  STAGE II                2                49
  STAGE III               3               106
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  6Q LOSS MUTATED     1   3   3   0
  6Q LOSS WILD-TYPE 139 163 162  21
D39V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               1               139
  T2               3               163
  T3               3               162
  T4               0                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"
D39V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     4   1
  6Q LOSS WILD-TYPE 219 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    1
  6Q LOSS WILD-TYPE  219  221
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0               4               219
  1               1               221
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6Q LOSS MUTATED     0   0   7
  6Q LOSS WILD-TYPE 273   9 205
D39V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               0               273
  M1               0                 9
  MX               7               205
[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"
D39V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     4   3
  6Q LOSS WILD-TYPE 360 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    3
  6Q LOSS WILD-TYPE  360  128
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4               360
  MALE                 3               128
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  6Q LOSS MUTATED                0
  6Q LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  6Q LOSS MUTATED                                               5
  6Q LOSS WILD-TYPE                                           348
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  6Q LOSS MUTATED                                                                        2
  6Q LOSS WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  6Q LOSS MUTATED                                                                     0
  6Q LOSS WILD-TYPE                                                                  35
D39V8, multiclass
                                                                        clus
vv                                                                       6Q LOSS MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       6Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D39V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1   6
  6Q LOSS WILD-TYPE  13 475
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1    6
  6Q LOSS WILD-TYPE   13  475
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                1                13
  YES               6               475
[1] 2 2
[1] FALSE
D39V10, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     5   1
  6Q LOSS WILD-TYPE 412  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    1
  6Q LOSS WILD-TYPE  412   16
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                5               412
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  6Q LOSS MUTATED              0                       0    7
  6Q LOSS WILD-TYPE          130                      16  321
                   vv
clus                VERY ADVANCED (T4B)
  6Q LOSS MUTATED                     0
  6Q LOSS WILD-TYPE                   1
D39V11, multiclass
                         clus
vv                        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  7               321
  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
  6Q LOSS MUTATED     6   1   0   0
  6Q LOSS WILD-TYPE 372  50   4  30
D39V12, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0               6               372
  R1               1                50
  R2               0                 4
  RX               0                30
[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"
D39V13, continuous
D39V14, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     2   5
  6Q LOSS WILD-TYPE 222 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2    5
  6Q LOSS WILD-TYPE  222  256
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  MULTIFOCAL               2               222
  UNIFOCAL                 5               256
[1] 2 2
[1] FALSE
D39V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     0
  6Q LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           0     6
  6Q LOSS WILD-TYPE                        26   315
D39V16, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                49
  BLACK OR AFRICAN AMERICAN                      0                26
  WHITE                                          6               315
[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"
D39V17, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0   6
  6Q LOSS WILD-TYPE  38 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0    6
  6Q LOSS WILD-TYPE   38  344
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               6               344
[1] 2 2
[1] FALSE

Clustering(40) Variable = 8P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED     4   0
  8P LOSS WILD-TYPE 473  14
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4               487 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                14 
$`8P LOSS MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58         8.12         9.24        13.51 

$`8P LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         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-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
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-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3OA TCGA-EM-A3OB 
       14.50        11.15         7.33        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         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-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             8.12              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            20.58            158.83 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           11.375            16.640 
[1] "8.1 - 20.6 (11.4)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "1200000"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  8P LOSS MUTATED         2        2         0        0         0         0
  8P LOSS WILD-TYPE     278       49       109        2        45         6
D40V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 2               278
  STAGE II                2                49
  STAGE III               0               109
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  8P LOSS MUTATED     1   2   1   0
  8P LOSS WILD-TYPE 139 164 164  21
D40V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               1               139
  T2               2               164
  T3               1               164
  T4               0                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"
D40V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     3   0
  8P LOSS WILD-TYPE 220 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    0
  8P LOSS WILD-TYPE  220  222
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               3               220
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8P LOSS MUTATED     1   0   3
  8P LOSS WILD-TYPE 272   9 209
D40V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               1               272
  M1               0                 9
  MX               3               209
[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"
D40V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1   3
  8P LOSS WILD-TYPE 363 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    3
  8P LOSS WILD-TYPE  363  128
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               1               363
  MALE                 3               128
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  8P LOSS MUTATED                0
  8P LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  8P LOSS MUTATED                                               2
  8P LOSS WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  8P LOSS MUTATED                                                                        2
  8P LOSS WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8P LOSS MUTATED                                                                     0
  8P LOSS WILD-TYPE                                                                  35
D40V8, multiclass
                                                                        clus
vv                                                                       8P LOSS 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                                                                       8P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D40V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0   4
  8P LOSS WILD-TYPE  14 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    4
  8P LOSS WILD-TYPE   14  477
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                0                14
  YES               4               477
[1] 2 2
[1] FALSE
D40V10, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4   0
  8P LOSS WILD-TYPE 413  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    0
  8P LOSS WILD-TYPE  413   17
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4               413
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  8P LOSS MUTATED              0                       0    4
  8P LOSS WILD-TYPE          130                      16  324
                   vv
clus                VERY ADVANCED (T4B)
  8P LOSS MUTATED                     0
  8P LOSS WILD-TYPE                   1
D40V11, multiclass
                         clus
vv                        8P LOSS MUTATED 8P LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  4               324
  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
  8P LOSS MUTATED     4   0   0   0
  8P LOSS WILD-TYPE 374  51   4  30
D40V12, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0               4               374
  R1               0                51
  R2               0                 4
  RX               0                30
[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"
D40V13, continuous
D40V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     2   2
  8P LOSS WILD-TYPE 222 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2    2
  8P LOSS WILD-TYPE  222  259
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  MULTIFOCAL               2               222
  UNIFOCAL                 2               259
[1] 2 2
[1] FALSE
D40V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     0
  8P LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           0     2
  8P LOSS WILD-TYPE                        26   319
D40V16, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2               395 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A290 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A3PR        TCGA-BJ-A3PT        TCGA-BJ-A3PU        TCGA-BJ-A45C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F        TCGA-BJ-A45G 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A27D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481        TCGA-CE-A482 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0XZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PT        TCGA-DJ-A2PU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3US        TCGA-DJ-A3UT        TCGA-DJ-A3UU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3UZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4        TCGA-DJ-A3V5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL        TCGA-DJ-A4UQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A4UR        TCGA-DJ-A4UT        TCGA-DJ-A4UW        TCGA-DJ-A4V0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ        TCGA-DO-A1K0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A3X7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415        TCGA-E8-A416 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A418        TCGA-E8-A419        TCGA-E8-A432 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A433        TCGA-E8-A434        TCGA-E8-A436        TCGA-E8-A437 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-E8-A44M        TCGA-EL-A3CL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EL-A3T0        TCGA-EL-A3T1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6        TCGA-EL-A3T7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA        TCGA-EL-A3TB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT        TCGA-EL-A4JV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD        TCGA-EL-A4KG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-ET-A25G        TCGA-ET-A25I 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A25R 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4        TCGA-ET-A2N5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K        TCGA-ET-A39M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P        TCGA-ET-A39R 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3DO        TCGA-ET-A3DP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z        TCGA-FE-A230 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA        TCGA-FE-A3PB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3        TCGA-FK-A3SB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FK-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR        TCGA-FY-A40K 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-FY-A76V        TCGA-GE-A2C6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-L6-A4ET        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-MK-A84Z        TCGA-QD-A8IV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D40V17, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0   2
  8P LOSS WILD-TYPE  38 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    2
  8P LOSS WILD-TYPE   38  348
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               348
[1] 2 2
[1] FALSE

Clustering(41) Variable = 8Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     4   0
  8Q LOSS WILD-TYPE 473  14
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               487 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                14 
$`8Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58         8.12         9.24        13.51 

$`8Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         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-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
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-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3OA TCGA-EM-A3OB 
       14.50        11.15         7.33        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         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-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             8.12              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            20.58            158.83 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           11.375            16.640 
[1] "8.1 - 20.6 (11.4)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "1200000"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  8Q LOSS MUTATED         2        2         0        0         0         0
  8Q LOSS WILD-TYPE     278       49       109        2        45         6
D41V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 2               278
  STAGE II                2                49
  STAGE III               0               109
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  8Q LOSS MUTATED     1   2   1   0
  8Q LOSS WILD-TYPE 139 164 164  21
D41V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               1               139
  T2               2               164
  T3               1               164
  T4               0                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"
D41V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     3   0
  8Q LOSS WILD-TYPE 220 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    0
  8Q LOSS WILD-TYPE  220  222
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               3               220
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED     1   0   3
  8Q LOSS WILD-TYPE 272   9 209
D41V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               1               272
  M1               0                 9
  MX               3               209
[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"
D41V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1   3
  8Q LOSS WILD-TYPE 363 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    3
  8Q LOSS WILD-TYPE  363  128
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               1               363
  MALE                 3               128
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  8Q LOSS MUTATED                0
  8Q LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  8Q LOSS MUTATED                                               2
  8Q LOSS WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  8Q LOSS MUTATED                                                                        2
  8Q LOSS WILD-TYPE                                                                     96
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  8Q LOSS MUTATED                                                                     0
  8Q LOSS WILD-TYPE                                                                  35
D41V8, multiclass
                                                                        clus
vv                                                                       8Q LOSS 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                                                                       8Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D41V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0   4
  8Q LOSS WILD-TYPE  14 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    4
  8Q LOSS WILD-TYPE   14  477
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                14
  YES               4               477
[1] 2 2
[1] FALSE
D41V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     4   0
  8Q LOSS WILD-TYPE 413  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4    0
  8Q LOSS WILD-TYPE  413   17
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                4               413
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  8Q LOSS MUTATED              0                       0    4
  8Q LOSS WILD-TYPE          130                      16  324
                   vv
clus                VERY ADVANCED (T4B)
  8Q LOSS MUTATED                     0
  8Q LOSS WILD-TYPE                   1
D41V11, multiclass
                         clus
vv                        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  4               324
  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
  8Q LOSS MUTATED     4   0   0   0
  8Q LOSS WILD-TYPE 374  51   4  30
D41V12, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               4               374
  R1               0                51
  R2               0                 4
  RX               0                30
[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"
D41V13, continuous
D41V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2   2
  8Q LOSS WILD-TYPE 222 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    2
  8Q LOSS WILD-TYPE  222  259
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  MULTIFOCAL               2               222
  UNIFOCAL                 2               259
[1] 2 2
[1] FALSE
D41V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     0
  8Q LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           0     2
  8Q LOSS WILD-TYPE                        26   319
D41V16, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               395 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A290 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A3PR        TCGA-BJ-A3PT        TCGA-BJ-A3PU        TCGA-BJ-A45C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F        TCGA-BJ-A45G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A27D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481        TCGA-CE-A482 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0XZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PT        TCGA-DJ-A2PU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB        TCGA-DJ-A3UK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UR        TCGA-DJ-A3US        TCGA-DJ-A3UT        TCGA-DJ-A3UU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UY        TCGA-DJ-A3UZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4        TCGA-DJ-A3V5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9        TCGA-DJ-A3VD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG        TCGA-DJ-A3VJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL        TCGA-DJ-A4UQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A4UR        TCGA-DJ-A4UT        TCGA-DJ-A4UW        TCGA-DJ-A4V0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ        TCGA-DO-A1K0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ        TCGA-E3-A3E0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3        TCGA-E3-A3E5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A2JQ        TCGA-E8-A3X7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415        TCGA-E8-A416 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A417        TCGA-E8-A418        TCGA-E8-A419        TCGA-E8-A432 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A433        TCGA-E8-A434        TCGA-E8-A436        TCGA-E8-A437 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E8-A438        TCGA-E8-A44K        TCGA-E8-A44M        TCGA-EL-A3CL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2        TCGA-EL-A3H3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7        TCGA-EL-A3H8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY        TCGA-EL-A3MZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EL-A3T0        TCGA-EL-A3T1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6        TCGA-EL-A3T7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA        TCGA-EL-A3TB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK        TCGA-EL-A3ZL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP        TCGA-EL-A3ZQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT        TCGA-EL-A4JV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ        TCGA-EL-A4K0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4        TCGA-EL-A4K6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD        TCGA-EL-A4KG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-ET-A25G        TCGA-ET-A25I 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A25R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4        TCGA-ET-A2N5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K        TCGA-ET-A39M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P        TCGA-ET-A39R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT        TCGA-ET-A3BU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3DO        TCGA-ET-A3DP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS        TCGA-ET-A3DT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW        TCGA-ET-A40P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A40T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z        TCGA-FE-A230 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233        TCGA-FE-A234 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237        TCGA-FE-A238 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA        TCGA-FE-A3PB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3        TCGA-FK-A3SB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FK-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG        TCGA-FK-A3SH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL        TCGA-FY-A3I4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3ON        TCGA-FY-A3R6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9        TCGA-FY-A3RA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR        TCGA-FY-A40K 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N        TCGA-FY-A4B0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-FY-A76V        TCGA-GE-A2C6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH        TCGA-H2-A3RI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB        TCGA-IM-A3ED 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y        TCGA-IM-A41Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ        TCGA-J8-A3O0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD        TCGA-J8-A3YE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH        TCGA-J8-A42S 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F        TCGA-KS-A41I 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1        TCGA-KS-A4I3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-L6-A4ET        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-MK-A84Z        TCGA-QD-A8IV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D41V17, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0   2
  8Q LOSS WILD-TYPE  38 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    2
  8Q LOSS WILD-TYPE   38  348
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               348
[1] 2 2
[1] FALSE

Clustering(42) Variable = 9P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    17   1
  9P LOSS WILD-TYPE 460  13
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               18               473 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                13 
$`9P LOSS MUTATED`
TCGA-BJ-A2N8 TCGA-DJ-A2Q0 TCGA-DO-A2HM TCGA-E8-A432 TCGA-EL-A3GP TCGA-EL-A3MX 
       16.57         8.12         2.33        14.43         1.41        57.63 
TCGA-EL-A3ZK TCGA-EL-A3ZO TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YE TCGA-EM-A2OY 
       31.50        47.38        28.73         8.71        54.08        17.59 
TCGA-EM-A3O3 TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FK-A3SG TCGA-FY-A40M 
       14.50         9.24        13.51        98.56         0.92         4.54 

$`9P LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         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-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
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-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       54.90        21.53        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-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        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-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
       33.47       108.36        39.32        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-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      131.15       108.66        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-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       50.33        53.06        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       19.59        30.51        33.60        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       13.32        11.87        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-A22I 
       18.05        19.79        19.46        54.21        57.01        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        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-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       16.18        15.02        11.15         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        39.95        33.63        81.83       106.36        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-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10        91.17         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-A3R9 
        0.99         1.51         0.76         0.03         4.67        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        6.58         0.89         1.35         1.15         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.92              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            98.56            158.83 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           14.465            16.730 
[1] "0.9 - 98.6 (14.5)"  "0.0 - 158.8 (16.7)"
[1] "hr=" "2.2"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  9P LOSS MUTATED         8        4         4        1         1         1
  9P LOSS WILD-TYPE     272       47       105        1        44         5
D42V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 8               272
  STAGE II                4                47
  STAGE III               4               105
  STAGE IV                1                 1
  STAGE IVA               1                44
  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
  9P LOSS MUTATED     5   7   5   2
  9P LOSS WILD-TYPE 135 159 160  19
D42V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               5               135
  T2               7               159
  T3               5               160
  T4               2                19
[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"
D42V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     8   8
  9P LOSS WILD-TYPE 215 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8    8
  9P LOSS WILD-TYPE  215  214
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               8               215
  1               8               214
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9P LOSS MUTATED     6   1  12
  9P LOSS WILD-TYPE 267   8 200
D42V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               6               267
  M1               1                 8
  MX              12               200
[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"
D42V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    12   7
  9P LOSS WILD-TYPE 352 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     12    7
  9P LOSS WILD-TYPE  352  124
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              12               352
  MALE                 7               124
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  9P LOSS MUTATED                0
  9P LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  9P LOSS MUTATED                                              15
  9P LOSS WILD-TYPE                                           338
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  9P LOSS MUTATED                                                                        4
  9P LOSS WILD-TYPE                                                                     94
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9P LOSS MUTATED                                                                     0
  9P LOSS WILD-TYPE                                                                  35
D42V8, multiclass
                                                                        clus
vv                                                                       9P LOSS MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       15
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       9P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        338
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                94
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D42V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     0  19
  9P LOSS WILD-TYPE  14 462
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   19
  9P LOSS WILD-TYPE   14  462
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                0                14
  YES              19               462
[1] 2 2
[1] FALSE
D42V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    18   0
  9P LOSS WILD-TYPE 399  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     18    0
  9P LOSS WILD-TYPE  399   17
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               18               399
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  9P LOSS MUTATED              4                       0   14
  9P LOSS WILD-TYPE          126                      16  314
                   vv
clus                VERY ADVANCED (T4B)
  9P LOSS MUTATED                     0
  9P LOSS WILD-TYPE                   1
D42V11, multiclass
                         clus
vv                        9P LOSS MUTATED 9P LOSS WILD-TYPE
  MINIMAL (T3)                          4               126
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                 14               314
  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
  9P LOSS MUTATED    15   1   0   2
  9P LOSS WILD-TYPE 363  50   4  28
D42V12, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              15               363
  R1               1                50
  R2               0                 4
  RX               2                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"
D42V13, continuous
D42V14, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     7  12
  9P LOSS WILD-TYPE 217 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7   12
  9P LOSS WILD-TYPE  217  249
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  MULTIFOCAL               7               217
  UNIFOCAL                12               249
[1] 2 2
[1] FALSE
D42V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     1
  9P LOSS WILD-TYPE                                1    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           1    12
  9P LOSS WILD-TYPE                        25   309
D42V16, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                48
  BLACK OR AFRICAN AMERICAN                      1                25
  WHITE                                         12               309
[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"
D42V17, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     0  14
  9P LOSS WILD-TYPE  38 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   14
  9P LOSS WILD-TYPE   38  336
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO              14               336
[1] 2 2
[1] FALSE

Clustering(43) Variable = 9Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    20   2
  9Q LOSS WILD-TYPE 457  12
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22               469 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                12 
$`9Q LOSS MUTATED`
TCGA-BJ-A2N8 TCGA-DE-A4MB TCGA-DJ-A2Q0 TCGA-DO-A2HM TCGA-E8-A432 TCGA-EL-A3GP 
       16.57        11.57         8.12         2.33        14.43         1.41 
TCGA-EL-A3MX TCGA-EL-A3T9 TCGA-EL-A3ZK TCGA-EL-A3ZO TCGA-EL-A4K6 TCGA-EL-A4KI 
       57.63         5.72        31.50        47.38        28.73         8.71 
TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A2OY TCGA-EM-A3O3 TCGA-EM-A3O9 TCGA-EM-A3SY 
       19.46        54.08        17.59        14.50         9.24        13.51 
TCGA-ET-A39N TCGA-FE-A231 TCGA-FK-A3SG TCGA-FY-A40M 
       98.56        31.59         0.92         4.54 

$`9Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD 
       15.85        18.54        18.84        30.12        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        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-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42         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-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
       21.53        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       30.31        14.04         1.15        22.29        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 
       14.27        13.81        14.07        14.27         3.02        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        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-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        39.32        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-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
      108.66        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-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZL TCGA-EL-A3ZN 
       66.90        82.82        77.36        78.97        50.33        53.06 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        45.53        48.16         7.07        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       19.30        45.96        37.94        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       33.60        41.13        37.78        29.95        13.32        11.87 
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-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        57.01        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
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-A3O6 
       12.07        17.49        17.39        16.18        15.02        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        7.33        12.53        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       15.62        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         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-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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
        1.94        73.74        59.70        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
        0.89        22.03        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        6.87         4.14         6.58         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.92              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            98.56            158.83 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           14.465            16.730 
[1] "0.9 - 98.6 (14.5)"  "0.0 - 158.8 (16.7)"
[1] "hr=" "4.4"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  9Q LOSS MUTATED         8        5         4        2         3         1
  9Q LOSS WILD-TYPE     272       46       105        0        42         5
D43V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 8               272
  STAGE II                5                46
  STAGE III               4               105
  STAGE IV                2                 0
  STAGE IVA               3                42
  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
  9Q LOSS MUTATED     5   8   7   3
  9Q LOSS WILD-TYPE 135 158 158  18
D43V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               5               135
  T2               8               158
  T3               7               158
  T4               3                18
[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"
D43V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     8  11
  9Q LOSS WILD-TYPE 215 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   11
  9Q LOSS WILD-TYPE  215  211
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               8               215
  1              11               211
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9Q LOSS MUTATED     7   1  15
  9Q LOSS WILD-TYPE 266   8 197
D43V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               7               266
  M1               1                 8
  MX              15               197
[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"
D43V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    15   8
  9Q LOSS WILD-TYPE 349 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     15    8
  9Q LOSS WILD-TYPE  349  123
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              15               349
  MALE                 8               123
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  9Q LOSS MUTATED                0
  9Q LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  9Q LOSS MUTATED                                              18
  9Q LOSS WILD-TYPE                                           335
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  9Q LOSS MUTATED                                                                        5
  9Q LOSS WILD-TYPE                                                                     93
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  9Q LOSS MUTATED                                                                     0
  9Q LOSS WILD-TYPE                                                                  35
D43V8, multiclass
                                                                        clus
vv                                                                       9Q LOSS MUTATED
  OTHER  SPECIFY                                                                       0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       18
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  0
                                                                        clus
vv                                                                       9Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        335
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D43V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1  22
  9Q LOSS WILD-TYPE  13 459
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   22
  9Q LOSS WILD-TYPE   13  459
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                13
  YES              22               459
[1] 2 2
[1] FALSE
D43V10, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    21   1
  9Q LOSS WILD-TYPE 396  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     21    1
  9Q LOSS WILD-TYPE  396   16
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               21               396
  YES               1                16
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  9Q LOSS MUTATED              5                       0   16
  9Q LOSS WILD-TYPE          125                      16  312
                   vv
clus                VERY ADVANCED (T4B)
  9Q LOSS MUTATED                     1
  9Q LOSS WILD-TYPE                   0
D43V11, multiclass
                         clus
vv                        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  MINIMAL (T3)                          5               125
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                 16               312
  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
  9Q LOSS MUTATED    17   3   0   2
  9Q LOSS WILD-TYPE 361  48   4  28
D43V12, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              17               361
  R1               3                48
  R2               0                 4
  RX               2                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"
D43V13, continuous
D43V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     9  14
  9Q LOSS WILD-TYPE 215 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9   14
  9Q LOSS WILD-TYPE  215  247
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  MULTIFOCAL               9               215
  UNIFOCAL                14               247
[1] 2 2
[1] FALSE
D43V15, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     1
  9Q LOSS WILD-TYPE                                1    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           1    15
  9Q LOSS WILD-TYPE                        25   306
D43V16, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                48
  BLACK OR AFRICAN AMERICAN                      1                25
  WHITE                                         15               306
[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"
D43V17, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1  16
  9Q LOSS WILD-TYPE  37 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   16
  9Q LOSS WILD-TYPE   37  334
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                37
  NOT HISPANIC OR LATINO              16               334
[1] 2 2
[1] FALSE

Clustering(44) Variable = 10P LOSS MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED     7   0
  10P LOSS WILD-TYPE 470  14
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                484 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                 14 
$`10P LOSS MUTATED`
TCGA-BJ-A190 TCGA-E8-A432 TCGA-EL-A4KI TCGA-EM-A1YE TCGA-EM-A3O9 TCGA-ET-A39N 
       20.58        14.43         8.71        54.08         9.24        98.56 
TCGA-FY-A3I5 
        1.64 

$`10P LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       14.27         3.02        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       29.95        13.32        11.87        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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        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-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-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        7.33        12.53        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        13.51        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
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-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
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-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        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-A238 
       24.69        68.22       102.90        66.77        81.34        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.64               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             98.56             158.83 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            14.430             16.605 
[1] "1.6 - 98.6 (14.4)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D44V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  10P LOSS MUTATED         2        3         2        0         0         0
  10P LOSS WILD-TYPE     278       48       107        2        45         6
D44V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  2                278
  STAGE II                 3                 48
  STAGE III                2                107
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  10P LOSS MUTATED     0   3   4   0
  10P LOSS WILD-TYPE 140 163 161  21
D44V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                0                140
  T2                3                163
  T3                4                161
  T4                0                 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"
D44V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     6   0
  10P LOSS WILD-TYPE 217 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    0
  10P LOSS WILD-TYPE  217  222
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                6                217
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10P LOSS MUTATED     1   0   6
  10P LOSS WILD-TYPE 272   9 206
D44V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                1                272
  M1                0                  9
  MX                6                206
[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"
D44V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4   3
  10P LOSS WILD-TYPE 360 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    3
  10P LOSS WILD-TYPE  360  128
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                4                360
  MALE                  3                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  10P LOSS MUTATED                0
  10P LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  10P LOSS MUTATED                                               4
  10P LOSS WILD-TYPE                                           349
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  10P LOSS MUTATED                                                                        3
  10P LOSS WILD-TYPE                                                                     95
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  10P LOSS MUTATED                                                                     0
  10P LOSS WILD-TYPE                                                                  35
D44V8, multiclass
                                                                        clus
vv                                                                       10P LOSS MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       10P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D44V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     0   7
  10P LOSS WILD-TYPE  14 474
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0    7
  10P LOSS WILD-TYPE   14  474
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 0                 14
  YES                7                474
[1] 2 2
[1] FALSE
D44V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     6   0
  10P LOSS WILD-TYPE 411  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    0
  10P LOSS WILD-TYPE  411   17
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 6                411
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  10P LOSS MUTATED              1                       0    6
  10P LOSS WILD-TYPE          129                      16  322
                    vv
clus                 VERY ADVANCED (T4B)
  10P LOSS MUTATED                     0
  10P LOSS WILD-TYPE                   1
D44V11, multiclass
                         clus
vv                        10P LOSS MUTATED 10P LOSS WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   6                322
  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
  10P LOSS MUTATED     7   0   0   0
  10P LOSS WILD-TYPE 371  51   4  30
D44V12, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                7                371
  R1                0                 51
  R2                0                  4
  RX                0                 30
[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"
D44V13, continuous
D44V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4   3
  10P LOSS WILD-TYPE 220 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    3
  10P LOSS WILD-TYPE  220  258
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  MULTIFOCAL                4                220
  UNIFOCAL                  3                258
[1] 2 2
[1] FALSE
D44V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     1
  10P LOSS WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           0     4
  10P LOSS WILD-TYPE                        26   317
D44V16, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 48
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           4                317
[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"
D44V17, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     0   5
  10P LOSS WILD-TYPE  38 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0    5
  10P LOSS WILD-TYPE   38  345
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                345
[1] 2 2
[1] FALSE

Clustering(45) Variable = 10Q LOSS MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED     6   0
  10Q LOSS WILD-TYPE 471  14
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                485 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 0                 14 
$`10Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-E8-A432 TCGA-EL-A4KI TCGA-EM-A3O9 TCGA-ET-A39N TCGA-FY-A3I5 
       20.58        14.43         8.71         9.24        98.56         1.64 

$`10Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       14.27         3.02        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       29.95        13.32        11.87        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-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
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-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       11.15         7.33        12.53        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1.64               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             98.56             158.83 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            11.835             16.640 
[1] "1.6 - 98.6 (11.8)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D45V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  10Q LOSS MUTATED         2        2         2        0         0         0
  10Q LOSS WILD-TYPE     278       49       107        2        45         6
D45V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  2                278
  STAGE II                 2                 49
  STAGE III                2                107
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  10Q LOSS MUTATED     0   2   4   0
  10Q LOSS WILD-TYPE 140 164 161  21
D45V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                0                140
  T2                2                164
  T3                4                161
  T4                0                 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"
D45V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5   0
  10Q LOSS WILD-TYPE 218 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    0
  10Q LOSS WILD-TYPE  218  222
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                5                218
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10Q LOSS MUTATED     1   0   5
  10Q LOSS WILD-TYPE 272   9 207
D45V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                1                272
  M1                0                  9
  MX                5                207
[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"
D45V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3   3
  10Q LOSS WILD-TYPE 361 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    3
  10Q LOSS WILD-TYPE  361  128
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                3                361
  MALE                  3                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  10Q LOSS MUTATED                0
  10Q LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  10Q LOSS MUTATED                                               4
  10Q LOSS WILD-TYPE                                           349
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  10Q LOSS MUTATED                                                                        2
  10Q LOSS WILD-TYPE                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  10Q LOSS MUTATED                                                                     0
  10Q LOSS WILD-TYPE                                                                  35
D45V8, multiclass
                                                                        clus
vv                                                                       10Q LOSS MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       10Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D45V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     0   6
  10Q LOSS WILD-TYPE  14 475
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0    6
  10Q LOSS WILD-TYPE   14  475
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 0                 14
  YES                6                475
[1] 2 2
[1] FALSE
D45V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5   0
  10Q LOSS WILD-TYPE 412  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    0
  10Q LOSS WILD-TYPE  412   17
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 5                412
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  10Q LOSS MUTATED              1                       0    5
  10Q LOSS WILD-TYPE          129                      16  323
                    vv
clus                 VERY ADVANCED (T4B)
  10Q LOSS MUTATED                     0
  10Q LOSS WILD-TYPE                   1
D45V11, multiclass
                         clus
vv                        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   5                323
  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
  10Q LOSS MUTATED     6   0   0   0
  10Q LOSS WILD-TYPE 372  51   4  30
D45V12, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                6                372
  R1                0                 51
  R2                0                  4
  RX                0                 30
[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"
D45V13, continuous
D45V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4   2
  10Q LOSS WILD-TYPE 220 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4    2
  10Q LOSS WILD-TYPE  220  259
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  MULTIFOCAL                4                220
  UNIFOCAL                  2                259
[1] 2 2
[1] FALSE
D45V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     1
  10Q LOSS WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           0     4
  10Q LOSS WILD-TYPE                        26   317
D45V16, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 48
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           4                317
[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"
D45V17, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     0   5
  10Q LOSS WILD-TYPE  38 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0    5
  10Q LOSS WILD-TYPE   38  345
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                345
[1] 2 2
[1] FALSE

Clustering(46) Variable = 11P LOSS MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     6   1
  11P LOSS WILD-TYPE 471  13
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                484 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 13 
$`11P LOSS MUTATED`
TCGA-BJ-A190 TCGA-EL-A3GP TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A22N TCGA-FE-A239 
       20.58         1.41        28.73         8.71        10.65        33.63 
TCGA-FY-A3I5 
        1.64 

$`11P LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       19.59        30.51        33.60        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       13.32        11.87        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-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        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-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        21.01        12.07        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-A3ST TCGA-EM-A3SU 
       12.53         9.24        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        13.51        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
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-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        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-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1.41               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             33.63             158.83 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            10.650             16.605 
[1] "1.4 - 33.6 (10.7)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "15" 
D46V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  11P LOSS MUTATED         1        1         4        1         0         0
  11P LOSS WILD-TYPE     279       50       105        1        45         6
D46V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  1                279
  STAGE II                 1                 50
  STAGE III                4                105
  STAGE IV                 1                  1
  STAGE IVA                0                 45
  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
  11P LOSS MUTATED     1   1   4   1
  11P LOSS WILD-TYPE 139 165 161  20
D46V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                139
  T2                1                165
  T3                4                161
  T4                1                 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"
D46V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5   2
  11P LOSS WILD-TYPE 218 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5    2
  11P LOSS WILD-TYPE  218  220
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                5                218
  1                2                220
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11P LOSS MUTATED     1   0   6
  11P LOSS WILD-TYPE 272   9 206
D46V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                1                272
  M1                0                  9
  MX                6                206
[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"
D46V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2   5
  11P LOSS WILD-TYPE 362 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2    5
  11P LOSS WILD-TYPE  362  126
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                2                362
  MALE                  5                126
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  11P LOSS MUTATED                0
  11P LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  11P LOSS MUTATED                                               5
  11P LOSS WILD-TYPE                                           348
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  11P LOSS MUTATED                                                                        2
  11P LOSS WILD-TYPE                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11P LOSS MUTATED                                                                     0
  11P LOSS WILD-TYPE                                                                  35
D46V8, multiclass
                                                                        clus
vv                                                                       11P LOSS MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       11P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D46V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     1   6
  11P LOSS WILD-TYPE  13 475
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    6
  11P LOSS WILD-TYPE   13  475
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 1                 13
  YES                6                475
[1] 2 2
[1] FALSE
D46V10, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     6   0
  11P LOSS WILD-TYPE 411  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    0
  11P LOSS WILD-TYPE  411   17
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 6                411
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  11P LOSS MUTATED              3                       0    4
  11P LOSS WILD-TYPE          127                      16  324
                    vv
clus                 VERY ADVANCED (T4B)
  11P LOSS MUTATED                     0
  11P LOSS WILD-TYPE                   1
D46V11, multiclass
                         clus
vv                        11P LOSS MUTATED 11P LOSS WILD-TYPE
  MINIMAL (T3)                           3                127
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   4                324
  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
  11P LOSS MUTATED     6   0   0   1
  11P LOSS WILD-TYPE 372  51   4  29
D46V12, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                6                372
  R1                0                 51
  R2                0                  4
  RX                1                 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"
D46V13, continuous
D46V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4   3
  11P LOSS WILD-TYPE 220 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    3
  11P LOSS WILD-TYPE  220  258
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  MULTIFOCAL                4                220
  UNIFOCAL                  3                258
[1] 2 2
[1] FALSE
D46V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           1     5
  11P LOSS WILD-TYPE                        25   316
D46V16, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       1                 25
  WHITE                                           5                316
[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"
D46V17, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0   6
  11P LOSS WILD-TYPE  38 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    6
  11P LOSS WILD-TYPE   38  344
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                6                344
[1] 2 2
[1] FALSE

Clustering(47) Variable = 11Q LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED     8   1
  11Q LOSS WILD-TYPE 469  13
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                482 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 13 
$`11Q LOSS MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-DE-A4MD TCGA-EL-A3GP TCGA-EL-A4K6 TCGA-EL-A4KI 
       13.78        20.58        25.12         1.41        28.73         8.71 
TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 
       10.65        33.63         1.64 

$`11Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        18.21        16.34        14.73         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-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       22.88        18.38        16.57        20.48        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         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-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A69J 
       18.54        18.84        30.12        11.57        30.02         4.27 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
        3.22         2.76        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-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        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-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
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-A3GQ TCGA-EL-A3GR 
       45.40        33.47       108.36        39.32        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
       77.36        78.97        31.50        50.33        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        45.53        48.16         7.07        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       19.30        45.96        37.94        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       33.60        41.13        37.78        29.95        13.32        11.87 
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-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        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-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       68.22       102.90        66.77        81.34        39.95        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1.41               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             33.63             158.83 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            13.780             16.605 
[1] "1.4 - 33.6 (13.8)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "13" 
D47V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  11Q LOSS MUTATED         1        2         4        1         1         0
  11Q LOSS WILD-TYPE     279       49       105        1        44         6
D47V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  1                279
  STAGE II                 2                 49
  STAGE III                4                105
  STAGE IV                 1                  1
  STAGE IVA                1                 44
  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
  11Q LOSS MUTATED     1   2   5   1
  11Q LOSS WILD-TYPE 139 164 160  20
D47V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                1                139
  T2                2                164
  T3                5                160
  T4                1                 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"
D47V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     6   3
  11Q LOSS WILD-TYPE 217 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6    3
  11Q LOSS WILD-TYPE  217  219
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                6                217
  1                3                219
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11Q LOSS MUTATED     2   0   7
  11Q LOSS WILD-TYPE 271   9 205
D47V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                2                271
  M1                0                  9
  MX                7                205
[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"
D47V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2   7
  11Q LOSS WILD-TYPE 362 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    7
  11Q LOSS WILD-TYPE  362  124
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                2                362
  MALE                  7                124
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  11Q LOSS MUTATED                0
  11Q LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  11Q LOSS MUTATED                                               7
  11Q LOSS WILD-TYPE                                           346
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  11Q LOSS MUTATED                                                                        2
  11Q LOSS WILD-TYPE                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  11Q LOSS MUTATED                                                                     0
  11Q LOSS WILD-TYPE                                                                  35
D47V8, multiclass
                                                                        clus
vv                                                                       11Q LOSS MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         7
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       11Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         346
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D47V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1   8
  11Q LOSS WILD-TYPE  13 473
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1    8
  11Q LOSS WILD-TYPE   13  473
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 1                 13
  YES                8                473
[1] 2 2
[1] FALSE
D47V10, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     7   0
  11Q LOSS WILD-TYPE 410  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      7    0
  11Q LOSS WILD-TYPE  410   17
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 7                410
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  11Q LOSS MUTATED              3                       0    6
  11Q LOSS WILD-TYPE          127                      16  322
                    vv
clus                 VERY ADVANCED (T4B)
  11Q LOSS MUTATED                     0
  11Q LOSS WILD-TYPE                   1
D47V11, multiclass
                         clus
vv                        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  MINIMAL (T3)                           3                127
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   6                322
  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
  11Q LOSS MUTATED     8   0   0   1
  11Q LOSS WILD-TYPE 370  51   4  29
D47V12, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                8                370
  R1                0                 51
  R2                0                  4
  RX                1                 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"
D47V13, continuous
D47V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     4   5
  11Q LOSS WILD-TYPE 220 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4    5
  11Q LOSS WILD-TYPE  220  256
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  MULTIFOCAL                4                220
  UNIFOCAL                  5                256
[1] 2 2
[1] FALSE
D47V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     0
  11Q LOSS WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           1     6
  11Q LOSS WILD-TYPE                        25   315
D47V16, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       1                 25
  WHITE                                           6                315
[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"
D47V17, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0   8
  11Q LOSS WILD-TYPE  38 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    8
  11Q LOSS WILD-TYPE   38  342
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                8                342
[1] 2 2
[1] FALSE

Clustering(48) Variable = 13Q LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    12   1
  13Q LOSS WILD-TYPE 465  13
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                13                478 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 13 
$`13Q LOSS MUTATED`
TCGA-BJ-A3F0 TCGA-CE-A13K TCGA-DJ-A13P TCGA-DJ-A1QN TCGA-DJ-A2Q2 TCGA-EM-A1YB 
       13.94         0.53       137.88         8.88         6.77        19.46 
TCGA-EM-A22M TCGA-EM-A22Q TCGA-ET-A39N TCGA-ET-A40S TCGA-FE-A239 TCGA-FY-A3I5 
       14.53        14.24        98.56         5.03        33.63         1.64 
TCGA-FY-A3W9 
        0.76 

$`13Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       18.97         7.04        16.01        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D 
        6.18         5.06         8.98         4.93         5.98         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         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-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13R 
        4.27         3.22         2.76        17.26        14.07         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-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        7.20         1.45         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-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        9.34         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-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       12.76        25.02        20.22        30.61        14.56        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
        9.83        21.27        20.48        11.93        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        17.36        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       18.21        10.78        10.98        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-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       14.04         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 
       13.81        14.07        14.27         3.02        14.43        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        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-A3ZG 
       41.29        95.38         5.72        66.90        82.82        77.36 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       78.97        31.50        50.33        53.06        47.38        52.50 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       45.53        48.16         7.07        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        19.59        30.51        33.60 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       28.73        41.13        37.78        29.95        13.32        11.87 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
        8.71        26.86        18.18        20.91        12.36        18.05 
TCGA-EM-A1YA TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.79        54.21        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ 
       15.75        10.45        10.65        11.74        11.15        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        4.80         2.14         4.01         1.94        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-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       81.34        39.95        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.30        17.06         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.53               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            137.88             158.83 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             13.94              16.75 
[1] "0.5 - 137.9 (13.9)" "0.0 - 158.8 (16.8)"
[1] "hr=" "2.6"
D48V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  13Q LOSS MUTATED         7        3         4        0         0         0
  13Q LOSS WILD-TYPE     273       48       105        2        45         6
D48V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  7                273
  STAGE II                 3                 48
  STAGE III                4                105
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  13Q LOSS MUTATED     4   3   7   0
  13Q LOSS WILD-TYPE 136 163 158  21
D48V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                4                136
  T2                3                163
  T3                7                158
  T4                0                 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"
D48V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    10   1
  13Q LOSS WILD-TYPE 213 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     10    1
  13Q LOSS WILD-TYPE  213  221
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               10                213
  1                1                221
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  13Q LOSS MUTATED     5   0   9
  13Q LOSS WILD-TYPE 268   9 203
D48V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                5                268
  M1                0                  9
  MX                9                203
[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"
D48V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9   5
  13Q LOSS WILD-TYPE 355 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    5
  13Q LOSS WILD-TYPE  355  126
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                355
  MALE                  5                126
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  13Q LOSS MUTATED                0
  13Q LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  13Q LOSS MUTATED                                               9
  13Q LOSS WILD-TYPE                                           344
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  13Q LOSS MUTATED                                                                        5
  13Q LOSS WILD-TYPE                                                                     93
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  13Q LOSS MUTATED                                                                     0
  13Q LOSS WILD-TYPE                                                                  35
D48V8, multiclass
                                                                        clus
vv                                                                       13Q LOSS MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       13Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D48V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  13
  13Q LOSS WILD-TYPE  13 468
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   13
  13Q LOSS WILD-TYPE   13  468
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 1                 13
  YES               13                468
[1] 2 2
[1] FALSE
D48V10, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8   4
  13Q LOSS WILD-TYPE 409  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8    4
  13Q LOSS WILD-TYPE  409   13
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                409
  YES                4                 13
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  13Q LOSS MUTATED              2                       0   12
  13Q LOSS WILD-TYPE          128                      16  316
                    vv
clus                 VERY ADVANCED (T4B)
  13Q LOSS MUTATED                     0
  13Q LOSS WILD-TYPE                   1
D48V11, multiclass
                         clus
vv                        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  MINIMAL (T3)                           2                128
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                  12                316
  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
  13Q LOSS MUTATED    11   2   0   1
  13Q LOSS WILD-TYPE 367  49   4  29
D48V12, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               11                367
  R1                2                 49
  R2                0                  4
  RX                1                 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"
D48V13, continuous
D48V14, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     7   7
  13Q LOSS WILD-TYPE 217 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      7    7
  13Q LOSS WILD-TYPE  217  254
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  MULTIFOCAL                7                217
  UNIFOCAL                  7                254
[1] 2 2
[1] FALSE
D48V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     1
  13Q LOSS WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           0     9
  13Q LOSS WILD-TYPE                        26   312
D48V16, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 48
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           9                312
[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"
D48V17, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     0  10
  13Q LOSS WILD-TYPE  38 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0   10
  13Q LOSS WILD-TYPE   38  340
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO               10                340
[1] 2 2
[1] FALSE

Clustering(49) Variable = 15Q LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED     8   0
  15Q LOSS WILD-TYPE 469  14
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                483 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                 14 
$`15Q LOSS MUTATED`
TCGA-BJ-A3F0 TCGA-DJ-A4UR TCGA-EL-A3GO TCGA-EM-A1YE TCGA-EM-A2OY TCGA-EM-A3O9 
       13.94        10.98        39.32        54.08        17.59         9.24 
TCGA-ET-A39N TCGA-FY-A3I5 
       98.56         1.64 

$`15Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       18.97         7.04        16.01        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
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-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ 
       74.30        45.40        33.47       108.36         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        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-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        19.73        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-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        21.01        12.07        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-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
       12.53        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         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-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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         0.99         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       10.26        16.90         9.80         9.63         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.64               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             98.56             158.83 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            15.765             16.570 
[1] "1.6 - 98.6 (15.8)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D49V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  15Q LOSS MUTATED         4        3         1        0         0         0
  15Q LOSS WILD-TYPE     276       48       108        2        45         6
D49V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  4                276
  STAGE II                 3                 48
  STAGE III                1                108
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  15Q LOSS MUTATED     1   3   4   0
  15Q LOSS WILD-TYPE 139 163 161  21
D49V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                1                139
  T2                3                163
  T3                4                161
  T4                0                 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"
D49V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     6   1
  15Q LOSS WILD-TYPE 217 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6    1
  15Q LOSS WILD-TYPE  217  221
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                6                217
  1                1                221
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  15Q LOSS MUTATED     2   1   5
  15Q LOSS WILD-TYPE 271   8 207
D49V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                2                271
  M1                1                  8
  MX                5                207
[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"
D49V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7   1
  15Q LOSS WILD-TYPE 357 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    1
  15Q LOSS WILD-TYPE  357  130
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                7                357
  MALE                  1                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  15Q LOSS MUTATED                0
  15Q LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  15Q LOSS MUTATED                                               3
  15Q LOSS WILD-TYPE                                           350
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  15Q LOSS MUTATED                                                                        5
  15Q LOSS WILD-TYPE                                                                     93
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  15Q LOSS MUTATED                                                                     0
  15Q LOSS WILD-TYPE                                                                  35
D49V8, multiclass
                                                                        clus
vv                                                                       15Q LOSS MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       15Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D49V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0   8
  15Q LOSS WILD-TYPE  14 473
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0    8
  15Q LOSS WILD-TYPE   14  473
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 0                 14
  YES                8                473
[1] 2 2
[1] FALSE
D49V10, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7   0
  15Q LOSS WILD-TYPE 410  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    0
  15Q LOSS WILD-TYPE  410   17
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 7                410
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  15Q LOSS MUTATED              1                       0    7
  15Q LOSS WILD-TYPE          129                      16  321
                    vv
clus                 VERY ADVANCED (T4B)
  15Q LOSS MUTATED                     0
  15Q LOSS WILD-TYPE                   1
D49V11, multiclass
                         clus
vv                        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   7                321
  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
  15Q LOSS MUTATED     8   0   0   0
  15Q LOSS WILD-TYPE 370  51   4  30
D49V12, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0                8                370
  R1                0                 51
  R2                0                  4
  RX                0                 30
[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"
D49V13, continuous
D49V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3   5
  15Q LOSS WILD-TYPE 221 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    5
  15Q LOSS WILD-TYPE  221  256
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  MULTIFOCAL                3                221
  UNIFOCAL                  5                256
[1] 2 2
[1] FALSE
D49V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     1
  15Q LOSS WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           0     4
  15Q LOSS WILD-TYPE                        26   317
D49V16, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 48
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           4                317
[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"
D49V17, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1   4
  15Q LOSS WILD-TYPE  37 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    4
  15Q LOSS WILD-TYPE   37  346
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 37
  NOT HISPANIC OR LATINO                4                346
[1] 2 2
[1] FALSE

Clustering(50) Variable = 17P LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED     7   0
  17P LOSS WILD-TYPE 470  14
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                484 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                 14 
$`17P LOSS MUTATED`
TCGA-E8-A432 TCGA-EL-A3D5 TCGA-EM-A1YE TCGA-EM-A3O9 TCGA-EM-A3OB TCGA-FE-A22Z 
       14.43        33.47        54.08         9.24         7.82        73.74 
TCGA-FE-A238 
       39.95 

$`17P LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.07        14.27         3.02        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
        1.45        74.30        45.40       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        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-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
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-A3OA TCGA-EM-A3ST TCGA-EM-A3SU 
       11.15         7.33        12.53        13.91        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        13.51        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
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-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        2.14         4.01         1.94        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A239 
       24.69        68.22       102.90        66.77        81.34        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25         1.15        17.82         1.64         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              7.82               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             73.74             158.83 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             33.47              16.57 
[1] "7.8 - 73.7 (33.5)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D50V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  17P LOSS MUTATED         4        2         0        0         1         0
  17P LOSS WILD-TYPE     276       49       109        2        44         6
D50V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  4                276
  STAGE II                 2                 49
  STAGE III                0                109
  STAGE IV                 0                  2
  STAGE IVA                1                 44
  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
  17P LOSS MUTATED     0   3   3   1
  17P LOSS WILD-TYPE 140 163 162  20
D50V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                0                140
  T2                3                163
  T3                3                162
  T4                1                 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"
D50V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     5   2
  17P LOSS WILD-TYPE 218 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5    2
  17P LOSS WILD-TYPE  218  220
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                5                218
  1                2                220
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17P LOSS MUTATED     2   0   5
  17P LOSS WILD-TYPE 271   9 207
D50V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                2                271
  M1                0                  9
  MX                5                207
[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"
D50V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     6   1
  17P LOSS WILD-TYPE 358 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    1
  17P LOSS WILD-TYPE  358  130
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                6                358
  MALE                  1                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  17P LOSS MUTATED                0
  17P LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  17P LOSS MUTATED                                               3
  17P LOSS WILD-TYPE                                           350
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  17P LOSS MUTATED                                                                        4
  17P LOSS WILD-TYPE                                                                     94
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17P LOSS MUTATED                                                                     0
  17P LOSS WILD-TYPE                                                                  35
D50V8, multiclass
                                                                        clus
vv                                                                       17P LOSS MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       17P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 94
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D50V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     2   5
  17P LOSS WILD-TYPE  12 476
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    5
  17P LOSS WILD-TYPE   12  476
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 2                 12
  YES                5                476
[1] 2 2
[1] FALSE
D50V10, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     6   1
  17P LOSS WILD-TYPE 411  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    1
  17P LOSS WILD-TYPE  411   16
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 6                411
  YES                1                 16
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  17P LOSS MUTATED              2                       1    4
  17P LOSS WILD-TYPE          128                      15  324
                    vv
clus                 VERY ADVANCED (T4B)
  17P LOSS MUTATED                     0
  17P LOSS WILD-TYPE                   1
D50V11, multiclass
                         clus
vv                        17P LOSS MUTATED 17P LOSS WILD-TYPE
  MINIMAL (T3)                           2                128
  MODERATE/ADVANCED (T4A)                1                 15
  NONE                                   4                324
  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
  17P LOSS MUTATED     6   1   0   0
  17P LOSS WILD-TYPE 372  50   4  30
D50V12, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0                6                372
  R1                1                 50
  R2                0                  4
  RX                0                 30
[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"
D50V13, continuous
D50V14, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     3   4
  17P LOSS WILD-TYPE 221 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    4
  17P LOSS WILD-TYPE  221  257
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  MULTIFOCAL                3                221
  UNIFOCAL                  4                257
[1] 2 2
[1] FALSE
D50V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     1
  17P LOSS WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           0     3
  17P LOSS WILD-TYPE                        26   318
D50V16, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 48
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           3                318
[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"
D50V17, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     0   4
  17P LOSS WILD-TYPE  38 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0    4
  17P LOSS WILD-TYPE   38  346
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                4                346
[1] 2 2
[1] FALSE

Clustering(51) Variable = 17Q LOSS MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     4   0
  17Q LOSS WILD-TYPE 473  14
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                487 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 0                 14 
$`17Q LOSS MUTATED`
TCGA-E8-A432 TCGA-EM-A3O9 TCGA-EM-A3OB TCGA-FE-A238 
       14.43         9.24         7.82        39.95 

$`17Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.07        14.27         3.02        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        11.15         7.33        12.53        13.91 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77        81.34        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              7.82               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             39.95             158.83 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            11.835             16.640 
[1] "7.8 - 40.0 (11.8)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D51V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  17Q LOSS MUTATED         3        1         0        0         0         0
  17Q LOSS WILD-TYPE     277       50       109        2        45         6
D51V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  3                277
  STAGE II                 1                 50
  STAGE III                0                109
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  17Q LOSS MUTATED     0   2   2   0
  17Q LOSS WILD-TYPE 140 164 163  21
D51V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                140
  T2                2                164
  T3                2                163
  T4                0                 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"
D51V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4   0
  17Q LOSS WILD-TYPE 219 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE  219  222
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                4                219
  1                0                222
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17Q LOSS MUTATED     1   0   3
  17Q LOSS WILD-TYPE 272   9 209
D51V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                1                272
  M1                0                  9
  MX                3                209
[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"
D51V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3   1
  17Q LOSS WILD-TYPE 361 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    1
  17Q LOSS WILD-TYPE  361  130
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                3                361
  MALE                  1                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  17Q LOSS MUTATED                0
  17Q LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  17Q LOSS MUTATED                                               2
  17Q LOSS WILD-TYPE                                           351
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  17Q LOSS MUTATED                                                                        2
  17Q LOSS WILD-TYPE                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  17Q LOSS MUTATED                                                                     0
  17Q LOSS WILD-TYPE                                                                  35
D51V8, multiclass
                                                                        clus
vv                                                                       17Q LOSS 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                                                                       17Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D51V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1   3
  17Q LOSS WILD-TYPE  13 478
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    3
  17Q LOSS WILD-TYPE   13  478
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                 13
  YES                3                478
[1] 2 2
[1] FALSE
D51V10, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4   0
  17Q LOSS WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE  413   17
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 4                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  17Q LOSS MUTATED              1                       0    3
  17Q LOSS WILD-TYPE          129                      16  325
                    vv
clus                 VERY ADVANCED (T4B)
  17Q LOSS MUTATED                     0
  17Q LOSS WILD-TYPE                   1
D51V11, multiclass
                         clus
vv                        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   3                325
  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
  17Q LOSS MUTATED     4   0   0   0
  17Q LOSS WILD-TYPE 374  51   4  30
D51V12, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                4                374
  R1                0                 51
  R2                0                  4
  RX                0                 30
[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"
D51V13, continuous
D51V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2   2
  17Q LOSS WILD-TYPE 222 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    2
  17Q LOSS WILD-TYPE  222  259
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  MULTIFOCAL                2                222
  UNIFOCAL                  2                259
[1] 2 2
[1] FALSE
D51V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     1
  17Q LOSS WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           0     1
  17Q LOSS WILD-TYPE                        26   320
D51V16, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                395 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z2         TCGA-BJ-A0Z3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0Z5         TCGA-BJ-A0Z9         TCGA-BJ-A0ZA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZB         TCGA-BJ-A0ZC         TCGA-BJ-A0ZE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZG         TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28X         TCGA-BJ-A28Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A2N7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A2P4         TCGA-BJ-A3EZ         TCGA-BJ-A3F0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A3PR         TCGA-BJ-A3PT         TCGA-BJ-A3PU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45E 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A45F         TCGA-BJ-A45G         TCGA-BJ-A45H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A45I         TCGA-BJ-A45J         TCGA-BJ-A45K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BJ-A4O8         TCGA-BJ-A4O9         TCGA-CE-A13K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CE-A27D         TCGA-CE-A3MD         TCGA-CE-A3ME 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CE-A481         TCGA-CE-A482         TCGA-CE-A483 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CE-A484         TCGA-CE-A485         TCGA-DE-A0XZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A0Y2         TCGA-DE-A0Y3         TCGA-DE-A2OL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DE-A4M8         TCGA-DE-A4M9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A4MA         TCGA-DE-A4MB         TCGA-DE-A4MC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A4MD         TCGA-DE-A69J         TCGA-DE-A69K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DE-A7U5         TCGA-DJ-A13M         TCGA-DJ-A13O 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A13P         TCGA-DJ-A13R         TCGA-DJ-A13S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A13T         TCGA-DJ-A13U         TCGA-DJ-A13W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QH         TCGA-DJ-A1QI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QO         TCGA-DJ-A1QQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PR         TCGA-DJ-A2PT         TCGA-DJ-A2PU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PV         TCGA-DJ-A2PW         TCGA-DJ-A2PX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q1         TCGA-DJ-A2Q2         TCGA-DJ-A2Q3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q4         TCGA-DJ-A2Q5         TCGA-DJ-A2Q6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q7         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A3UK         TCGA-DJ-A3UM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UN         TCGA-DJ-A3UO         TCGA-DJ-A3UQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UR         TCGA-DJ-A3US         TCGA-DJ-A3UT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UU         TCGA-DJ-A3UW         TCGA-DJ-A3UX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UY         TCGA-DJ-A3UZ         TCGA-DJ-A3V2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V3         TCGA-DJ-A3V4         TCGA-DJ-A3V5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V7         TCGA-DJ-A3V8         TCGA-DJ-A3V9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3VD         TCGA-DJ-A3VE         TCGA-DJ-A3VF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3VG         TCGA-DJ-A3VJ         TCGA-DJ-A3VL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A3VM         TCGA-DJ-A4UL         TCGA-DJ-A4UQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A4UR         TCGA-DJ-A4UT         TCGA-DJ-A4UW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DJ-A4V0         TCGA-DJ-A4V4         TCGA-DJ-A4V5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DO-A1JZ         TCGA-DO-A1K0         TCGA-DO-A2HM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E3-A3DY         TCGA-E3-A3DZ         TCGA-E3-A3E0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E3-A3E1         TCGA-E3-A3E2         TCGA-E3-A3E3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E3-A3E5         TCGA-E8-A242         TCGA-E8-A2EA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A2JQ         TCGA-E8-A3X7         TCGA-E8-A413 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A414         TCGA-E8-A415         TCGA-E8-A416 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A417         TCGA-E8-A418         TCGA-E8-A419 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A433         TCGA-E8-A434         TCGA-E8-A436 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A437         TCGA-E8-A438         TCGA-E8-A44K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E8-A44M         TCGA-EL-A3CL         TCGA-EL-A3CM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CN         TCGA-EL-A3CO         TCGA-EL-A3CP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CR         TCGA-EL-A3CS         TCGA-EL-A3CT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CU         TCGA-EL-A3CV         TCGA-EL-A3CW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3CX         TCGA-EL-A3CY         TCGA-EL-A3CZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3D0         TCGA-EL-A3D1         TCGA-EL-A3D4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3D5         TCGA-EL-A3D6         TCGA-EL-A3GO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3GP         TCGA-EL-A3GQ         TCGA-EL-A3GR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3GS         TCGA-EL-A3GU         TCGA-EL-A3GV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3GW         TCGA-EL-A3GX         TCGA-EL-A3GY 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3GZ         TCGA-EL-A3H1         TCGA-EL-A3H2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3H8         TCGA-EL-A3MW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3MX         TCGA-EL-A3MY         TCGA-EL-A3MZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3N2         TCGA-EL-A3N3         TCGA-EL-A3T0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3T3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3T6         TCGA-EL-A3T7         TCGA-EL-A3T8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3T9         TCGA-EL-A3TA         TCGA-EL-A3TB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZG         TCGA-EL-A3ZH         TCGA-EL-A3ZK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZL         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZQ         TCGA-EL-A3ZR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZS         TCGA-EL-A3ZT         TCGA-EL-A4JV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4K9         TCGA-EL-A4KD         TCGA-EL-A4KG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EL-A4KH         TCGA-EL-A4KI         TCGA-ET-A25G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A25I         TCGA-ET-A25J         TCGA-ET-A25K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A25L         TCGA-ET-A25M         TCGA-ET-A25N 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A25P         TCGA-ET-A25R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A2MX         TCGA-ET-A2MY         TCGA-ET-A2MZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A2N4         TCGA-ET-A2N5         TCGA-ET-A39I 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A39J         TCGA-ET-A39K         TCGA-ET-A39M 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A39N         TCGA-ET-A39O         TCGA-ET-A39P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39S         TCGA-ET-A39T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3BN         TCGA-ET-A3BO         TCGA-ET-A3BQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3DO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3DP         TCGA-ET-A3DQ         TCGA-ET-A3DR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A3DV         TCGA-ET-A3DW         TCGA-ET-A40P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A40Q         TCGA-ET-A40R         TCGA-ET-A40S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ET-A40T         TCGA-ET-A4KN         TCGA-ET-A4KQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FE-A3PA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FE-A3PB         TCGA-FE-A3PC         TCGA-FE-A3PD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FK-A3S3         TCGA-FK-A3SB         TCGA-FK-A3SD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FK-A3SE         TCGA-FK-A3SG         TCGA-FK-A3SH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FK-A4UB         TCGA-FY-A2QD         TCGA-FY-A3BL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3I4         TCGA-FY-A3I5         TCGA-FY-A3NM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3ON         TCGA-FY-A3R6         TCGA-FY-A3R7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3R8         TCGA-FY-A3R9         TCGA-FY-A3RA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A3W9         TCGA-FY-A3WA         TCGA-FY-A3YR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A40K         TCGA-FY-A40L         TCGA-FY-A40M 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A40N         TCGA-FY-A4B0         TCGA-FY-A4B3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FY-A4B4         TCGA-FY-A76V         TCGA-GE-A2C6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-H2-A26U         TCGA-H2-A2K9         TCGA-H2-A3RH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-H2-A3RI         TCGA-H2-A421         TCGA-H2-A422 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IM-A3EB         TCGA-IM-A3ED         TCGA-IM-A3U2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IM-A3U3         TCGA-IM-A41Y         TCGA-IM-A41Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IM-A420         TCGA-IM-A4EB         TCGA-J8-A3NZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-J8-A3O0         TCGA-J8-A3O1         TCGA-J8-A3O2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-J8-A3YD         TCGA-J8-A3YE         TCGA-J8-A3YF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-J8-A3YG         TCGA-J8-A3YH         TCGA-J8-A42S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-J8-A4HW         TCGA-J8-A4HY         TCGA-KS-A41F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A41I         TCGA-KS-A41J         TCGA-KS-A41L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A4I1         TCGA-KS-A4I3         TCGA-KS-A4I5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A4I7         TCGA-KS-A4I9         TCGA-KS-A4IB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-KS-A4IC         TCGA-KS-A4ID         TCGA-L6-A4EP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-L6-A4EQ         TCGA-L6-A4ET         TCGA-L6-A4EU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MK-A4N6         TCGA-MK-A4N7         TCGA-MK-A4N9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MK-A84Z         TCGA-QD-A8IV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D51V17, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0   2
  17Q LOSS WILD-TYPE  38 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0    2
  17Q LOSS WILD-TYPE   38  348
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                2                348
[1] 2 2
[1] FALSE

Clustering(52) Variable = 18P LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED     4   0
  18P LOSS WILD-TYPE 473  14
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                487 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 0                 14 
$`18P LOSS MUTATED`
TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A3SY TCGA-ET-A3BP 
        8.12        54.08        13.51         4.18 

$`18P LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        57.01        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         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-A3BQ 
       57.11        55.10        59.15        28.24         5.85         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-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              4.18               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             54.08             158.83 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            10.815             16.640 
[1] "4.2 - 54.1 (10.8)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D52V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  18P LOSS MUTATED         2        2         0        0         0         0
  18P LOSS WILD-TYPE     278       49       109        2        45         6
D52V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  2                278
  STAGE II                 2                 49
  STAGE III                0                109
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  18P LOSS MUTATED     1   3   0   0
  18P LOSS WILD-TYPE 139 163 165  21
D52V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                1                139
  T2                3                163
  T3                0                165
  T4                0                 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"
D52V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     2   1
  18P LOSS WILD-TYPE 221 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    1
  18P LOSS WILD-TYPE  221  221
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                2                221
  1                1                221
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18P LOSS MUTATED     1   0   3
  18P LOSS WILD-TYPE 272   9 209
D52V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                1                272
  M1                0                  9
  MX                3                209
[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"
D52V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3   1
  18P LOSS WILD-TYPE 361 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    1
  18P LOSS WILD-TYPE  361  130
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                3                361
  MALE                  1                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  18P LOSS MUTATED                0
  18P LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  18P LOSS MUTATED                                               2
  18P LOSS WILD-TYPE                                           351
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  18P LOSS MUTATED                                                                        2
  18P LOSS WILD-TYPE                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18P LOSS MUTATED                                                                     0
  18P LOSS WILD-TYPE                                                                  35
D52V8, multiclass
                                                                        clus
vv                                                                       18P LOSS 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                                                                       18P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D52V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     0   4
  18P LOSS WILD-TYPE  14 477
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0    4
  18P LOSS WILD-TYPE   14  477
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 0                 14
  YES                4                477
[1] 2 2
[1] FALSE
D52V10, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     4   0
  18P LOSS WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    0
  18P LOSS WILD-TYPE  413   17
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 4                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  18P LOSS MUTATED              0                       0    4
  18P LOSS WILD-TYPE          130                      16  324
                    vv
clus                 VERY ADVANCED (T4B)
  18P LOSS MUTATED                     0
  18P LOSS WILD-TYPE                   1
D52V11, multiclass
                         clus
vv                        18P LOSS MUTATED 18P LOSS WILD-TYPE
  MINIMAL (T3)                           0                130
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   4                324
  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
  18P LOSS MUTATED     4   0   0   0
  18P LOSS WILD-TYPE 374  51   4  30
D52V12, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0                4                374
  R1                0                 51
  R2                0                  4
  RX                0                 30
[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"
D52V13, continuous
D52V14, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1   3
  18P LOSS WILD-TYPE 223 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    3
  18P LOSS WILD-TYPE  223  258
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  MULTIFOCAL                1                223
  UNIFOCAL                  3                258
[1] 2 2
[1] FALSE
D52V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     0
  18P LOSS WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           0     1
  18P LOSS WILD-TYPE                        26   320
D52V16, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                396 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z2         TCGA-BJ-A0Z3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0Z5         TCGA-BJ-A0Z9         TCGA-BJ-A0ZA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0ZB         TCGA-BJ-A0ZC         TCGA-BJ-A0ZE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A0ZG         TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28X         TCGA-BJ-A28Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A2N7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A2P4         TCGA-BJ-A3EZ         TCGA-BJ-A3F0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A3PR         TCGA-BJ-A3PT         TCGA-BJ-A3PU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45E 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A45F         TCGA-BJ-A45G         TCGA-BJ-A45H 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A45I         TCGA-BJ-A45J         TCGA-BJ-A45K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BJ-A4O8         TCGA-BJ-A4O9         TCGA-CE-A13K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CE-A27D         TCGA-CE-A3MD         TCGA-CE-A3ME 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CE-A481         TCGA-CE-A482         TCGA-CE-A483 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CE-A484         TCGA-CE-A485         TCGA-DE-A0XZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A0Y2         TCGA-DE-A0Y3         TCGA-DE-A2OL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DE-A4M8         TCGA-DE-A4M9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A4MA         TCGA-DE-A4MB         TCGA-DE-A4MC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A4MD         TCGA-DE-A69J         TCGA-DE-A69K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DE-A7U5         TCGA-DJ-A13M         TCGA-DJ-A13O 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A13P         TCGA-DJ-A13R         TCGA-DJ-A13S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A13T         TCGA-DJ-A13U         TCGA-DJ-A13W 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QH         TCGA-DJ-A1QI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QO         TCGA-DJ-A1QQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2PR         TCGA-DJ-A2PT         TCGA-DJ-A2PU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2PV         TCGA-DJ-A2PW         TCGA-DJ-A2PX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q2         TCGA-DJ-A2Q3         TCGA-DJ-A2Q4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3UK         TCGA-DJ-A3UM         TCGA-DJ-A3UN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3UO         TCGA-DJ-A3UQ         TCGA-DJ-A3UR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3US         TCGA-DJ-A3UT         TCGA-DJ-A3UU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3UW         TCGA-DJ-A3UX         TCGA-DJ-A3UY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3UZ         TCGA-DJ-A3V2         TCGA-DJ-A3V3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3V4         TCGA-DJ-A3V5         TCGA-DJ-A3V7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3V8         TCGA-DJ-A3V9         TCGA-DJ-A3VD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3VE         TCGA-DJ-A3VF         TCGA-DJ-A3VG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A3VJ         TCGA-DJ-A3VL         TCGA-DJ-A3VM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A4UL         TCGA-DJ-A4UQ         TCGA-DJ-A4UR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A4UT         TCGA-DJ-A4UW         TCGA-DJ-A4V0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DJ-A4V4         TCGA-DJ-A4V5         TCGA-DO-A1JZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-DO-A2HM         TCGA-E3-A3DY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E3-A3DZ         TCGA-E3-A3E0         TCGA-E3-A3E1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E3-A3E2         TCGA-E3-A3E3         TCGA-E3-A3E5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A242         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A3X7         TCGA-E8-A413         TCGA-E8-A414 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A415         TCGA-E8-A416         TCGA-E8-A417 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A418         TCGA-E8-A419         TCGA-E8-A432 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A433         TCGA-E8-A434         TCGA-E8-A436 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A437         TCGA-E8-A438         TCGA-E8-A44K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-E8-A44M         TCGA-EL-A3CL         TCGA-EL-A3CM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CN         TCGA-EL-A3CO         TCGA-EL-A3CP 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CR         TCGA-EL-A3CS         TCGA-EL-A3CT 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CU         TCGA-EL-A3CV         TCGA-EL-A3CW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3CX         TCGA-EL-A3CY         TCGA-EL-A3CZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3D0         TCGA-EL-A3D1         TCGA-EL-A3D4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3D5         TCGA-EL-A3D6         TCGA-EL-A3GO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3GP         TCGA-EL-A3GQ         TCGA-EL-A3GR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3GS         TCGA-EL-A3GU         TCGA-EL-A3GV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3GW         TCGA-EL-A3GX         TCGA-EL-A3GY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3GZ         TCGA-EL-A3H1         TCGA-EL-A3H2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3H8         TCGA-EL-A3MW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3MX         TCGA-EL-A3MY         TCGA-EL-A3MZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3N2         TCGA-EL-A3N3         TCGA-EL-A3T0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3T3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3T6         TCGA-EL-A3T7         TCGA-EL-A3T8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3T9         TCGA-EL-A3TA         TCGA-EL-A3TB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZG         TCGA-EL-A3ZH         TCGA-EL-A3ZK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZL         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZQ         TCGA-EL-A3ZR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A3ZS         TCGA-EL-A3ZT         TCGA-EL-A4JV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4K9         TCGA-EL-A4KD         TCGA-EL-A4KG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EL-A4KH         TCGA-EL-A4KI         TCGA-ET-A25G 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A25I         TCGA-ET-A25J         TCGA-ET-A25K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A25L         TCGA-ET-A25M         TCGA-ET-A25N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A25P         TCGA-ET-A25R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A2MX         TCGA-ET-A2MY         TCGA-ET-A2MZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A2N4         TCGA-ET-A2N5         TCGA-ET-A39I 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A39J         TCGA-ET-A39K         TCGA-ET-A39M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A39N         TCGA-ET-A39O         TCGA-ET-A39P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39S         TCGA-ET-A39T 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3BN         TCGA-ET-A3BO         TCGA-ET-A3BQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3DO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3DP         TCGA-ET-A3DQ         TCGA-ET-A3DR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A3DV         TCGA-ET-A3DW         TCGA-ET-A40P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A40Q         TCGA-ET-A40R         TCGA-ET-A40S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ET-A40T         TCGA-ET-A4KN         TCGA-ET-A4KQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A238         TCGA-FE-A239         TCGA-FE-A23A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A3PA         TCGA-FE-A3PB         TCGA-FE-A3PC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FE-A3PD         TCGA-FK-A3S3         TCGA-FK-A3SB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FK-A3SD         TCGA-FK-A3SE         TCGA-FK-A3SG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FK-A3SH         TCGA-FK-A4UB         TCGA-FY-A2QD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3I4         TCGA-FY-A3I5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A3NM         TCGA-FY-A3ON         TCGA-FY-A3R6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A3R7         TCGA-FY-A3R8         TCGA-FY-A3R9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A3RA         TCGA-FY-A3W9         TCGA-FY-A3WA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A3YR         TCGA-FY-A40K         TCGA-FY-A40L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A40M         TCGA-FY-A40N         TCGA-FY-A4B0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FY-A4B3         TCGA-FY-A4B4         TCGA-FY-A76V 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A26U         TCGA-H2-A2K9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-H2-A3RH         TCGA-H2-A3RI         TCGA-H2-A421 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-H2-A422         TCGA-IM-A3EB         TCGA-IM-A3ED 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IM-A3U2         TCGA-IM-A3U3         TCGA-IM-A41Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IM-A41Z         TCGA-IM-A420         TCGA-IM-A4EB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A3O2         TCGA-J8-A3YD         TCGA-J8-A3YE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A3YF         TCGA-J8-A3YG         TCGA-J8-A3YH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-J8-A42S         TCGA-J8-A4HW         TCGA-J8-A4HY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A41F         TCGA-KS-A41I         TCGA-KS-A41J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A41L         TCGA-KS-A4I1         TCGA-KS-A4I3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A4I5         TCGA-KS-A4I7         TCGA-KS-A4I9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KS-A4IB         TCGA-KS-A4IC         TCGA-KS-A4ID 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L6-A4EP         TCGA-L6-A4EQ         TCGA-L6-A4ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-L6-A4EU         TCGA-MK-A4N6         TCGA-MK-A4N7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MK-A4N9         TCGA-MK-A84Z         TCGA-QD-A8IV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D52V17, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1   1
  18P LOSS WILD-TYPE  37 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    1
  18P LOSS WILD-TYPE   37  349
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 37
  NOT HISPANIC OR LATINO                1                349
[1] 2 2
[1] FALSE

Clustering(53) Variable = 18Q LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED     4   0
  18Q LOSS WILD-TYPE 473  14
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                487 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 0                 14 
$`18Q LOSS MUTATED`
TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A3SY TCGA-ET-A3BP 
        8.12        54.08        13.51         4.18 

$`18Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         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-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        57.01        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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         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-A3BQ 
       57.11        55.10        59.15        28.24         5.85         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-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68        86.70         6.02        12.43         6.74        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              4.18               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             54.08             158.83 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            10.815             16.640 
[1] "4.2 - 54.1 (10.8)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D53V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  18Q LOSS MUTATED         2        2         0        0         0         0
  18Q LOSS WILD-TYPE     278       49       109        2        45         6
D53V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  2                278
  STAGE II                 2                 49
  STAGE III                0                109
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  18Q LOSS MUTATED     1   3   0   0
  18Q LOSS WILD-TYPE 139 163 165  21
D53V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                1                139
  T2                3                163
  T3                0                165
  T4                0                 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"
D53V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     2   1
  18Q LOSS WILD-TYPE 221 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    1
  18Q LOSS WILD-TYPE  221  221
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0                2                221
  1                1                221
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18Q LOSS MUTATED     1   0   3
  18Q LOSS WILD-TYPE 272   9 209
D53V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                1                272
  M1                0                  9
  MX                3                209
[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"
D53V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3   1
  18Q LOSS WILD-TYPE 361 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    1
  18Q LOSS WILD-TYPE  361  130
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                3                361
  MALE                  1                130
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  18Q LOSS MUTATED                0
  18Q LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  18Q LOSS MUTATED                                               2
  18Q LOSS WILD-TYPE                                           351
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  18Q LOSS MUTATED                                                                        2
  18Q LOSS WILD-TYPE                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  18Q LOSS MUTATED                                                                     0
  18Q LOSS WILD-TYPE                                                                  35
D53V8, multiclass
                                                                        clus
vv                                                                       18Q LOSS 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                                                                       18Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D53V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     0   4
  18Q LOSS WILD-TYPE  14 477
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0    4
  18Q LOSS WILD-TYPE   14  477
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 0                 14
  YES                4                477
[1] 2 2
[1] FALSE
D53V10, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4   0
  18Q LOSS WILD-TYPE 413  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    0
  18Q LOSS WILD-TYPE  413   17
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 4                413
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  18Q LOSS MUTATED              0                       0    4
  18Q LOSS WILD-TYPE          130                      16  324
                    vv
clus                 VERY ADVANCED (T4B)
  18Q LOSS MUTATED                     0
  18Q LOSS WILD-TYPE                   1
D53V11, multiclass
                         clus
vv                        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  MINIMAL (T3)                           0                130
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   4                324
  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
  18Q LOSS MUTATED     4   0   0   0
  18Q LOSS WILD-TYPE 374  51   4  30
D53V12, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0                4                374
  R1                0                 51
  R2                0                  4
  RX                0                 30
[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"
D53V13, continuous
D53V14, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1   3
  18Q LOSS WILD-TYPE 223 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    3
  18Q LOSS WILD-TYPE  223  258
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  MULTIFOCAL                1                223
  UNIFOCAL                  3                258
[1] 2 2
[1] FALSE
D53V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     0
  18Q LOSS WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           0     1
  18Q LOSS WILD-TYPE                        26   320
D53V16, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                396 
        TCGA-BJ-A0YZ         TCGA-BJ-A0Z2         TCGA-BJ-A0Z3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0Z5         TCGA-BJ-A0Z9         TCGA-BJ-A0ZA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZB         TCGA-BJ-A0ZC         TCGA-BJ-A0ZE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A0ZG         TCGA-BJ-A0ZH         TCGA-BJ-A0ZJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A18Y         TCGA-BJ-A18Z         TCGA-BJ-A190 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A191         TCGA-BJ-A192         TCGA-BJ-A28R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A28S         TCGA-BJ-A28T         TCGA-BJ-A28V 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A28W         TCGA-BJ-A28X         TCGA-BJ-A28Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A290         TCGA-BJ-A291         TCGA-BJ-A2N7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A2P4         TCGA-BJ-A3EZ         TCGA-BJ-A3F0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A3PR         TCGA-BJ-A3PT         TCGA-BJ-A3PU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45E 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A45F         TCGA-BJ-A45G         TCGA-BJ-A45H 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A45I         TCGA-BJ-A45J         TCGA-BJ-A45K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BJ-A4O8         TCGA-BJ-A4O9         TCGA-CE-A13K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CE-A27D         TCGA-CE-A3MD         TCGA-CE-A3ME 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CE-A481         TCGA-CE-A482         TCGA-CE-A483 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CE-A484         TCGA-CE-A485         TCGA-DE-A0XZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A0Y2         TCGA-DE-A0Y3         TCGA-DE-A2OL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A3KN         TCGA-DE-A4M8         TCGA-DE-A4M9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A4MA         TCGA-DE-A4MB         TCGA-DE-A4MC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A4MD         TCGA-DE-A69J         TCGA-DE-A69K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DE-A7U5         TCGA-DJ-A13M         TCGA-DJ-A13O 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A13P         TCGA-DJ-A13R         TCGA-DJ-A13S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A13T         TCGA-DJ-A13U         TCGA-DJ-A13W 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QD         TCGA-DJ-A1QE         TCGA-DJ-A1QF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QG         TCGA-DJ-A1QH         TCGA-DJ-A1QI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A1QO         TCGA-DJ-A1QQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PN         TCGA-DJ-A2PO         TCGA-DJ-A2PQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PR         TCGA-DJ-A2PT         TCGA-DJ-A2PU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PV         TCGA-DJ-A2PW         TCGA-DJ-A2PX 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2PY         TCGA-DJ-A2PZ         TCGA-DJ-A2Q1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q2         TCGA-DJ-A2Q3         TCGA-DJ-A2Q4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A2Q9         TCGA-DJ-A2QA         TCGA-DJ-A2QB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UK         TCGA-DJ-A3UM         TCGA-DJ-A3UN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UO         TCGA-DJ-A3UQ         TCGA-DJ-A3UR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3US         TCGA-DJ-A3UT         TCGA-DJ-A3UU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UW         TCGA-DJ-A3UX         TCGA-DJ-A3UY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3UZ         TCGA-DJ-A3V2         TCGA-DJ-A3V3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V4         TCGA-DJ-A3V5         TCGA-DJ-A3V7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3V8         TCGA-DJ-A3V9         TCGA-DJ-A3VD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3VE         TCGA-DJ-A3VF         TCGA-DJ-A3VG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A3VJ         TCGA-DJ-A3VL         TCGA-DJ-A3VM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A4UL         TCGA-DJ-A4UQ         TCGA-DJ-A4UR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A4UT         TCGA-DJ-A4UW         TCGA-DJ-A4V0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DJ-A4V4         TCGA-DJ-A4V5         TCGA-DO-A1JZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-DO-A2HM         TCGA-E3-A3DY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E3-A3DZ         TCGA-E3-A3E0         TCGA-E3-A3E1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E3-A3E2         TCGA-E3-A3E3         TCGA-E3-A3E5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A242         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A3X7         TCGA-E8-A413         TCGA-E8-A414 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A415         TCGA-E8-A416         TCGA-E8-A417 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A418         TCGA-E8-A419         TCGA-E8-A432 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A433         TCGA-E8-A434         TCGA-E8-A436 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A437         TCGA-E8-A438         TCGA-E8-A44K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-E8-A44M         TCGA-EL-A3CL         TCGA-EL-A3CM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CN         TCGA-EL-A3CO         TCGA-EL-A3CP 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CR         TCGA-EL-A3CS         TCGA-EL-A3CT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CU         TCGA-EL-A3CV         TCGA-EL-A3CW 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3CX         TCGA-EL-A3CY         TCGA-EL-A3CZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3D0         TCGA-EL-A3D1         TCGA-EL-A3D4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3D5         TCGA-EL-A3D6         TCGA-EL-A3GO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3GP         TCGA-EL-A3GQ         TCGA-EL-A3GR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3GS         TCGA-EL-A3GU         TCGA-EL-A3GV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3GW         TCGA-EL-A3GX         TCGA-EL-A3GY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3GZ         TCGA-EL-A3H1         TCGA-EL-A3H2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3H3         TCGA-EL-A3H4         TCGA-EL-A3H5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3H7         TCGA-EL-A3H8         TCGA-EL-A3MW 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3MX         TCGA-EL-A3MY         TCGA-EL-A3MZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3N2         TCGA-EL-A3N3         TCGA-EL-A3T0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3T1         TCGA-EL-A3T2         TCGA-EL-A3T3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3T6         TCGA-EL-A3T7         TCGA-EL-A3T8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3T9         TCGA-EL-A3TA         TCGA-EL-A3TB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZG         TCGA-EL-A3ZH         TCGA-EL-A3ZK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZL         TCGA-EL-A3ZN         TCGA-EL-A3ZO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZP         TCGA-EL-A3ZQ         TCGA-EL-A3ZR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A3ZS         TCGA-EL-A3ZT         TCGA-EL-A4JV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4JW         TCGA-EL-A4JX         TCGA-EL-A4JZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4K0         TCGA-EL-A4K1         TCGA-EL-A4K2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4K4         TCGA-EL-A4K6         TCGA-EL-A4K7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4K9         TCGA-EL-A4KD         TCGA-EL-A4KG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EL-A4KH         TCGA-EL-A4KI         TCGA-ET-A25G 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A25I         TCGA-ET-A25J         TCGA-ET-A25K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A25L         TCGA-ET-A25M         TCGA-ET-A25N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A25P         TCGA-ET-A25R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A2MX         TCGA-ET-A2MY         TCGA-ET-A2MZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A2N0         TCGA-ET-A2N1         TCGA-ET-A2N3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A2N4         TCGA-ET-A2N5         TCGA-ET-A39I 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A39J         TCGA-ET-A39K         TCGA-ET-A39M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A39N         TCGA-ET-A39O         TCGA-ET-A39P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A39R         TCGA-ET-A39S         TCGA-ET-A39T 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3BN         TCGA-ET-A3BO         TCGA-ET-A3BQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3BS         TCGA-ET-A3BT         TCGA-ET-A3BU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3BV         TCGA-ET-A3BW         TCGA-ET-A3DO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3DP         TCGA-ET-A3DQ         TCGA-ET-A3DR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A3DV         TCGA-ET-A3DW         TCGA-ET-A40P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A40Q         TCGA-ET-A40R         TCGA-ET-A40S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ET-A40T         TCGA-ET-A4KN         TCGA-ET-A4KQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A22Z         TCGA-FE-A230         TCGA-FE-A231 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A232         TCGA-FE-A233         TCGA-FE-A234 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A235         TCGA-FE-A236         TCGA-FE-A237 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A238         TCGA-FE-A239         TCGA-FE-A23A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A3PA         TCGA-FE-A3PB         TCGA-FE-A3PC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FE-A3PD         TCGA-FK-A3S3         TCGA-FK-A3SB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FK-A3SD         TCGA-FK-A3SE         TCGA-FK-A3SG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FK-A3SH         TCGA-FK-A4UB         TCGA-FY-A2QD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A3BL         TCGA-FY-A3I4         TCGA-FY-A3I5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A3NM         TCGA-FY-A3ON         TCGA-FY-A3R6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A3R7         TCGA-FY-A3R8         TCGA-FY-A3R9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A3RA         TCGA-FY-A3W9         TCGA-FY-A3WA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A3YR         TCGA-FY-A40K         TCGA-FY-A40L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A40M         TCGA-FY-A40N         TCGA-FY-A4B0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FY-A4B3         TCGA-FY-A4B4         TCGA-FY-A76V 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GE-A2C6         TCGA-H2-A26U         TCGA-H2-A2K9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-H2-A3RH         TCGA-H2-A3RI         TCGA-H2-A421 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-H2-A422         TCGA-IM-A3EB         TCGA-IM-A3ED 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IM-A3U2         TCGA-IM-A3U3         TCGA-IM-A41Y 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IM-A41Z         TCGA-IM-A420         TCGA-IM-A4EB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A3NZ         TCGA-J8-A3O0         TCGA-J8-A3O1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A3O2         TCGA-J8-A3YD         TCGA-J8-A3YE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A3YF         TCGA-J8-A3YG         TCGA-J8-A3YH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-J8-A42S         TCGA-J8-A4HW         TCGA-J8-A4HY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A41F         TCGA-KS-A41I         TCGA-KS-A41J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A41L         TCGA-KS-A4I1         TCGA-KS-A4I3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A4I5         TCGA-KS-A4I7         TCGA-KS-A4I9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KS-A4IB         TCGA-KS-A4IC         TCGA-KS-A4ID 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-L6-A4EP         TCGA-L6-A4EQ         TCGA-L6-A4ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-L6-A4EU         TCGA-MK-A4N6         TCGA-MK-A4N7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-MK-A4N9         TCGA-MK-A84Z         TCGA-QD-A8IV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D53V17, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1   1
  18Q LOSS WILD-TYPE  37 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    1
  18Q LOSS WILD-TYPE   37  349
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 37
  NOT HISPANIC OR LATINO                1                349
[1] 2 2
[1] FALSE

Clustering(54) Variable = 19P LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED     4   1
  19P LOSS WILD-TYPE 473  13
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                486 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 13 
$`19P LOSS MUTATED`
TCGA-BJ-A0YZ TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-ET-A39N TCGA-FY-A3WA 
       24.79        33.47        33.50        98.56        17.06 

$`19P LOSS WILD-TYPE`
TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       13.78        18.21        16.34        14.73         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-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       23.34        20.71        20.58         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        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-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
        1.45        74.30        45.40       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 
      147.75       101.13       139.99        49.32        43.36        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-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        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-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        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-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        39.95        33.63        81.83       106.36        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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR TCGA-FY-A40K 
       16.57        18.08         0.30         0.76         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
       86.70         6.02        12.43         6.74        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        0.72        16.64        32.45         8.71        10.98         5.19 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             17.06               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             98.56             158.83 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             33.47              16.44 
[1] "17.1 - 98.6 (33.5)" "0.0 - 158.8 (16.4)"
[1] "hr=" "4.5"
D54V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  19P LOSS MUTATED         3        2         0        0         0         0
  19P LOSS WILD-TYPE     277       49       109        2        45         6
D54V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  3                277
  STAGE II                 2                 49
  STAGE III                0                109
  STAGE IV                 0                  2
  STAGE IVA                0                 45
  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
  19P LOSS MUTATED     1   2   2   0
  19P LOSS WILD-TYPE 139 164 163  21
D54V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                139
  T2                2                164
  T3                2                163
  T4                0                 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"
D54V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2   1
  19P LOSS WILD-TYPE 221 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE  221  221
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                2                221
  1                1                221
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19P LOSS MUTATED     2   0   3
  19P LOSS WILD-TYPE 271   9 209
D54V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                2                271
  M1                0                  9
  MX                3                209
[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"
D54V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3   2
  19P LOSS WILD-TYPE 361 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    2
  19P LOSS WILD-TYPE  361  129
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                3                361
  MALE                  2                129
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  19P LOSS MUTATED                0
  19P LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  19P LOSS MUTATED                                               4
  19P LOSS WILD-TYPE                                           349
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  19P LOSS MUTATED                                                                        1
  19P LOSS WILD-TYPE                                                                     97
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  19P LOSS MUTATED                                                                     0
  19P LOSS WILD-TYPE                                                                  35
D54V8, multiclass
                                                                        clus
vv                                                                       19P LOSS 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                                                                       19P LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D54V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0   5
  19P LOSS WILD-TYPE  14 476
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    5
  19P LOSS WILD-TYPE   14  476
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 0                 14
  YES                5                476
[1] 2 2
[1] FALSE
D54V10, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3   2
  19P LOSS WILD-TYPE 414  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    2
  19P LOSS WILD-TYPE  414   15
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 3                414
  YES                2                 15
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  19P LOSS MUTATED              1                       0    4
  19P LOSS WILD-TYPE          129                      16  324
                    vv
clus                 VERY ADVANCED (T4B)
  19P LOSS MUTATED                     0
  19P LOSS WILD-TYPE                   1
D54V11, multiclass
                         clus
vv                        19P LOSS MUTATED 19P LOSS WILD-TYPE
  MINIMAL (T3)                           1                129
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   4                324
  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
  19P LOSS MUTATED     4   1   0   0
  19P LOSS WILD-TYPE 374  50   4  30
D54V12, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                4                374
  R1                1                 50
  R2                0                  4
  RX                0                 30
[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"
D54V13, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                390 
        TCGA-BJ-A0Z0         TCGA-BJ-A0Z3         TCGA-BJ-A0Z9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A0ZA         TCGA-BJ-A0ZB         TCGA-BJ-A0ZH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A0ZJ         TCGA-BJ-A18Y         TCGA-BJ-A18Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A190         TCGA-BJ-A191         TCGA-BJ-A28R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A28T         TCGA-BJ-A28W         TCGA-BJ-A28X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A28Z         TCGA-BJ-A290         TCGA-BJ-A291 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A2N8         TCGA-BJ-A2N9         TCGA-BJ-A2NA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A3EZ         TCGA-BJ-A3PR         TCGA-BJ-A3PU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A45C         TCGA-BJ-A45D         TCGA-BJ-A45E 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A45G         TCGA-BJ-A45I         TCGA-BJ-A45J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BJ-A45K         TCGA-BJ-A4O8         TCGA-BJ-A4O9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CE-A13K         TCGA-CE-A3MD         TCGA-DE-A0XZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A0Y2         TCGA-DE-A0Y3         TCGA-DE-A3KN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A4M8         TCGA-DE-A4MA         TCGA-DE-A4MB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A4MC         TCGA-DE-A4MD         TCGA-DE-A69K 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DE-A7U5         TCGA-DJ-A13M         TCGA-DJ-A13O 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A13P         TCGA-DJ-A13R         TCGA-DJ-A13T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A13U         TCGA-DJ-A13V         TCGA-DJ-A13W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A13X         TCGA-DJ-A1QG         TCGA-DJ-A1QH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A1QM         TCGA-DJ-A2PO         TCGA-DJ-A2PP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2PQ         TCGA-DJ-A2PR         TCGA-DJ-A2PS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2PT         TCGA-DJ-A2PU         TCGA-DJ-A2PV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2PW         TCGA-DJ-A2PX         TCGA-DJ-A2PY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2PZ         TCGA-DJ-A2Q0         TCGA-DJ-A2Q1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q2         TCGA-DJ-A2Q3         TCGA-DJ-A2Q4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q5         TCGA-DJ-A2Q6         TCGA-DJ-A2Q7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2Q8         TCGA-DJ-A2Q9         TCGA-DJ-A2QA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A2QB         TCGA-DJ-A3UK         TCGA-DJ-A3UM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3UN         TCGA-DJ-A3UO         TCGA-DJ-A3UP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3UQ         TCGA-DJ-A3UR         TCGA-DJ-A3UU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3UW         TCGA-DJ-A3UX         TCGA-DJ-A3UZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3V0         TCGA-DJ-A3V2         TCGA-DJ-A3V3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3V4         TCGA-DJ-A3V5         TCGA-DJ-A3V7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3V8         TCGA-DJ-A3V9         TCGA-DJ-A3VA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3VB         TCGA-DJ-A3VD         TCGA-DJ-A3VF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A3VG         TCGA-DJ-A3VJ         TCGA-DJ-A3VL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A4UL         TCGA-DJ-A4UQ         TCGA-DJ-A4UR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DJ-A4UW         TCGA-DJ-A4V2         TCGA-DJ-A4V5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DO-A1K0         TCGA-DO-A2HM         TCGA-E3-A3DY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E3-A3DZ         TCGA-E3-A3E0         TCGA-E3-A3E1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E3-A3E2         TCGA-E3-A3E3         TCGA-E3-A3E5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A242         TCGA-E8-A2EA         TCGA-E8-A2JQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A414         TCGA-E8-A415         TCGA-E8-A417 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A419         TCGA-E8-A433         TCGA-E8-A436 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-E8-A438         TCGA-E8-A44K         TCGA-EL-A3CM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CN         TCGA-EL-A3CO         TCGA-EL-A3CR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CS         TCGA-EL-A3CT         TCGA-EL-A3CU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CV         TCGA-EL-A3CW         TCGA-EL-A3CX 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3CY         TCGA-EL-A3CZ         TCGA-EL-A3D0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3D1         TCGA-EL-A3D4         TCGA-EL-A3D6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3GO         TCGA-EL-A3GP         TCGA-EL-A3GQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3GS         TCGA-EL-A3GU         TCGA-EL-A3GV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3GX         TCGA-EL-A3H3         TCGA-EL-A3H4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3H5         TCGA-EL-A3H7         TCGA-EL-A3H8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3MW         TCGA-EL-A3MX         TCGA-EL-A3MZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3N2         TCGA-EL-A3T0         TCGA-EL-A3T1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3T2         TCGA-EL-A3TB         TCGA-EL-A3ZH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3ZK         TCGA-EL-A3ZL         TCGA-EL-A3ZN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A3ZO         TCGA-EL-A3ZP         TCGA-EL-A3ZS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4JV         TCGA-EL-A4JW         TCGA-EL-A4JX 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4JZ         TCGA-EL-A4K0         TCGA-EL-A4K1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4K2         TCGA-EL-A4K4         TCGA-EL-A4K6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4K7         TCGA-EL-A4KD         TCGA-EL-A4KG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EL-A4KI         TCGA-EM-A1CS         TCGA-EM-A1CT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A1CU         TCGA-EM-A1CV         TCGA-EM-A1CW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A1YA         TCGA-EM-A1YB         TCGA-EM-A1YC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A1YD         TCGA-EM-A1YE         TCGA-EM-A22I 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A22J         TCGA-EM-A22K         TCGA-EM-A22L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A22M         TCGA-EM-A22N         TCGA-EM-A22O 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A22P         TCGA-EM-A22Q         TCGA-EM-A2CK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A2CN         TCGA-EM-A2CP         TCGA-EM-A2CQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A2CS         TCGA-EM-A2CT         TCGA-EM-A2CU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A2OV         TCGA-EM-A2OW         TCGA-EM-A2OX 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A2OY         TCGA-EM-A2OZ         TCGA-EM-A2P0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A2P1         TCGA-EM-A2P2         TCGA-EM-A2P3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3AJ         TCGA-EM-A3AK         TCGA-EM-A3AL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3AN         TCGA-EM-A3AO         TCGA-EM-A3AQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3AR         TCGA-EM-A3FJ         TCGA-EM-A3FK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3FL         TCGA-EM-A3FM         TCGA-EM-A3FN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3FO         TCGA-EM-A3FP         TCGA-EM-A3FQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3FR         TCGA-EM-A3O3         TCGA-EM-A3O7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3O8         TCGA-EM-A3O9         TCGA-EM-A3OA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3OB         TCGA-EM-A3ST         TCGA-EM-A3SU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A3SX         TCGA-EM-A3SY         TCGA-EM-A3SZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A4FF         TCGA-EM-A4FH         TCGA-EM-A4FK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A4FM         TCGA-EM-A4FN         TCGA-EM-A4FO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A4FQ         TCGA-EM-A4FR         TCGA-EM-A4FU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EM-A4FV         TCGA-EM-A4G1         TCGA-ET-A25G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A25I         TCGA-ET-A25J         TCGA-ET-A25K 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A25L         TCGA-ET-A25M         TCGA-ET-A25N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A25O         TCGA-ET-A25P         TCGA-ET-A2MX 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A2MZ         TCGA-ET-A2N0         TCGA-ET-A2N1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A2N4         TCGA-ET-A39K         TCGA-ET-A39L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A39O         TCGA-ET-A39P         TCGA-ET-A39R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A39S         TCGA-ET-A39T         TCGA-ET-A3BO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3BP         TCGA-ET-A3BQ         TCGA-ET-A3BS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3BT         TCGA-ET-A3BU         TCGA-ET-A3BV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3BX         TCGA-ET-A3DQ         TCGA-ET-A3DR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3DS         TCGA-ET-A3DT         TCGA-ET-A3DU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A3DV         TCGA-ET-A3DW         TCGA-ET-A40P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A40Q         TCGA-ET-A40R         TCGA-ET-A40S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ET-A40T         TCGA-ET-A4KN         TCGA-FE-A22Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A230         TCGA-FE-A231         TCGA-FE-A232 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A233         TCGA-FE-A234         TCGA-FE-A235 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A236         TCGA-FE-A237         TCGA-FE-A238 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A239         TCGA-FE-A23A         TCGA-FE-A3PB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FE-A3PC         TCGA-FE-A3PD         TCGA-FK-A3S3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FK-A3SB         TCGA-FK-A3SE         TCGA-FK-A3SG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FK-A3SH         TCGA-FK-A4UB         TCGA-FY-A2QD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3I4         TCGA-FY-A3I5         TCGA-FY-A3NM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3NN         TCGA-FY-A3ON         TCGA-FY-A3R6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3R7         TCGA-FY-A3R9         TCGA-FY-A3TY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A3W9         TCGA-FY-A3YR         TCGA-FY-A40K 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A40L         TCGA-FY-A40M         TCGA-FY-A40N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FY-A4B3         TCGA-FY-A4B4         TCGA-GE-A2C6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-H2-A26U         TCGA-H2-A2K9         TCGA-H2-A3RH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-H2-A3RI         TCGA-H2-A421         TCGA-H2-A422 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IM-A3EB         TCGA-IM-A3ED         TCGA-IM-A3U2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IM-A3U3         TCGA-IM-A41Y         TCGA-IM-A41Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IM-A420         TCGA-IM-A4EB         TCGA-J8-A3NZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A3O0         TCGA-J8-A3O1         TCGA-J8-A3O2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A3YD         TCGA-J8-A3YE         TCGA-J8-A3YF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A3YG         TCGA-J8-A3YH         TCGA-J8-A42S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-J8-A4HW         TCGA-J8-A4HY         TCGA-KS-A41F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-KS-A41I         TCGA-KS-A41J         TCGA-KS-A41L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-KS-A4I1         TCGA-KS-A4I3         TCGA-KS-A4I5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-KS-A4I7         TCGA-KS-A4I9         TCGA-KS-A4IB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-KS-A4IC         TCGA-KS-A4ID         TCGA-L6-A4EP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-L6-A4EQ         TCGA-L6-A4EU         TCGA-MK-A4N6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MK-A4N7         TCGA-MK-A4N9         TCGA-QD-A8IV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D54V14, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1   4
  19P LOSS WILD-TYPE 223 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1    4
  19P LOSS WILD-TYPE  223  257
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  MULTIFOCAL                1                223
  UNIFOCAL                  4                257
[1] 2 2
[1] FALSE
D54V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     0
  19P LOSS WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           0     5
  19P LOSS WILD-TYPE                        26   316
D54V16, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 49
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           5                316
[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"
D54V17, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0   5
  19P LOSS WILD-TYPE  38 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    5
  19P LOSS WILD-TYPE   38  345
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                345
[1] 2 2
[1] FALSE

Clustering(55) Variable = 21Q LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED     8   0
  21Q LOSS WILD-TYPE 469  14
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                483 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                 14 
$`21Q LOSS MUTATED`
TCGA-BJ-A190 TCGA-CE-A485 TCGA-DJ-A2Q0 TCGA-E8-A432 TCGA-EM-A22P TCGA-EM-A2OY 
       20.58         0.10         8.12        14.43        11.15        17.59 
TCGA-FY-A3I5 TCGA-J8-A4HW 
        1.64         2.60 

$`21Q LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
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-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.39        20.22        15.42        36.46         5.98        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        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-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42         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-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        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-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        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-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
       77.36        78.97        31.50        50.33        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        45.53        48.16         7.07        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       19.30        45.96        37.94        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       33.60        28.73        41.13        37.78        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-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.74        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         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-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        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-A238 
       24.69        68.22       102.90        66.77        81.34        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY 
       27.85        24.69        22.29         5.75         2.47         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             20.58             158.83 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             9.635             16.730 
[1] "0.1 - 20.6 (9.6)"   "0.0 - 158.8 (16.7)"
[1] "hr="     "1200000"
D55V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  21Q LOSS MUTATED         1        4         2        0         1         0
  21Q LOSS WILD-TYPE     279       47       107        2        44         6
D55V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  1                279
  STAGE II                 4                 47
  STAGE III                2                107
  STAGE IV                 0                  2
  STAGE IVA                1                 44
  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
  21Q LOSS MUTATED     1   6   1   0
  21Q LOSS WILD-TYPE 139 160 164  21
D55V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                1                139
  T2                6                160
  T3                1                164
  T4                0                 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"
D55V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     5   3
  21Q LOSS WILD-TYPE 218 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    3
  21Q LOSS WILD-TYPE  218  219
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0                5                218
  1                3                219
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  21Q LOSS MUTATED     4   0   4
  21Q LOSS WILD-TYPE 269   9 208
D55V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                4                269
  M1                0                  9
  MX                4                208
[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"
D55V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     5   3
  21Q LOSS WILD-TYPE 359 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    3
  21Q LOSS WILD-TYPE  359  128
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                5                359
  MALE                  3                128
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  21Q LOSS MUTATED                0
  21Q LOSS WILD-TYPE              9
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  21Q LOSS MUTATED                                               6
  21Q LOSS WILD-TYPE                                           347
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  21Q LOSS MUTATED                                                                        2
  21Q LOSS WILD-TYPE                                                                     96
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  21Q LOSS MUTATED                                                                     0
  21Q LOSS WILD-TYPE                                                                  35
D55V8, multiclass
                                                                        clus
vv                                                                       21Q LOSS MUTATED
  OTHER  SPECIFY                                                                        0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   0
                                                                        clus
vv                                                                       21Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    35
[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"
D55V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     0   8
  21Q LOSS WILD-TYPE  14 473
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0    8
  21Q LOSS WILD-TYPE   14  473
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 0                 14
  YES                8                473
[1] 2 2
[1] FALSE
D55V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     7   0
  21Q LOSS WILD-TYPE 410  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7    0
  21Q LOSS WILD-TYPE  410   17
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 7                410
  YES                0                 17
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  21Q LOSS MUTATED              0                       0    8
  21Q LOSS WILD-TYPE          130                      16  320
                    vv
clus                 VERY ADVANCED (T4B)
  21Q LOSS MUTATED                     0
  21Q LOSS WILD-TYPE                   1
D55V11, multiclass
                         clus
vv                        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  MINIMAL (T3)                           0                130
  MODERATE/ADVANCED (T4A)                0                 16
  NONE                                   8                320
  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
  21Q LOSS MUTATED     7   1   0   0
  21Q LOSS WILD-TYPE 371  50   4  30
D55V12, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0                7                371
  R1                1                 50
  R2                0                  4
  RX                0                 30
[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"
D55V13, continuous
D55V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     6   2
  21Q LOSS WILD-TYPE 218 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6    2
  21Q LOSS WILD-TYPE  218  259
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  MULTIFOCAL                6                218
  UNIFOCAL                  2                259
[1] 2 2
[1] FALSE
D55V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     2
  21Q LOSS WILD-TYPE                                1    47
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           0     4
  21Q LOSS WILD-TYPE                        26   317
D55V16, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 47
  BLACK OR AFRICAN AMERICAN                       0                 26
  WHITE                                           4                317
[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"
D55V17, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     0   5
  21Q LOSS WILD-TYPE  38 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0    5
  21Q LOSS WILD-TYPE   38  345
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 38
  NOT HISPANIC OR LATINO                5                345
[1] 2 2
[1] FALSE

Clustering(56) Variable = 22Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    86   1
  22Q LOSS WILD-TYPE 391  13
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                87                404 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 13 
$`22Q LOSS MUTATED`
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A2P4 
       18.21        14.73        15.12        23.34        20.58         7.04 
TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A4M8 
       23.31         6.48         3.45         0.39        20.22        18.54 
TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q0 
       17.26        25.35        13.12         8.88         1.51         8.12 
TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.09        12.43        10.85        15.09        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E3-A3E5 TCGA-E8-A432 
       16.41        27.62        10.98        12.07        14.04        14.43 
TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP 
       14.10        31.66         1.45        74.30        45.40         1.41 
TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4JZ 
       37.25        32.48        50.33        48.16        45.80        37.94 
TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L 
       28.73        37.78         8.71        26.86        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OY TCGA-EM-A3AP TCGA-EM-A3FO 
       14.53        11.15        16.44        17.59         8.35        17.49 
TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU 
        9.24        15.62        12.79         8.38         5.03        37.87 
TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       14.79        27.09         2.66        65.36        84.89        98.56 
TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB 
        4.18         0.30         3.22         2.14        81.34        85.15 
TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-IM-A3U3 
        0.03         0.76        17.06         1.15        12.53        16.90 
TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH TCGA-KS-A41I TCGA-KS-A4I7 
        9.63        43.17        31.82         5.75        15.98        32.45 
TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       84.72        10.98         5.19 

$`22Q LOSS 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-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 
       11.57        16.73         7.56        17.69        20.71         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
        8.09         4.87        21.04         2.79         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU 
       20.48        18.97        16.01        13.94        15.48        18.64 
TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        5.75         0.03         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 
        0.23        11.38        10.68         0.10         0.10        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       36.46         5.98        15.85        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13O 
       30.02        25.12         4.27         3.22         2.76        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
      137.88         3.39         8.71        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI 
        7.99        11.01       100.01        18.51         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        7.20         1.45         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
        5.33         8.48        10.45         9.60        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        7.69         5.52         8.78         8.42         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.21         9.44         9.90         8.61         7.07        10.36 
TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       15.88        31.04        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UT 
        8.32        17.36        17.23        18.21        10.78        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-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-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       30.31         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 
       13.81        14.07        14.27         3.02        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        20.68        13.78        13.58        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D5 
       37.94        57.01        80.91         4.18        58.82        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        39.32        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.37       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-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
      129.57       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
       66.90        82.82        77.36        78.97        31.50        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW 
       47.38        52.50        45.53         7.07        44.65        19.30 
TCGA-EL-A4JX TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       45.96        31.04        19.59        30.51        33.60        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       29.95        13.32        11.87        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-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK 
       14.73        14.50        10.65        11.74        14.24        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        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-A3AQ TCGA-EM-A3AR 
       15.68        14.14        19.63        13.38        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP 
       27.95        23.77        16.80        21.01        12.07        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-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF 
       13.91         7.82        11.51        16.41        13.51        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV 
       16.90         9.01         4.83         8.61         9.80        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M 
        0.95        47.47        48.20        29.69        32.35        12.33 
TCGA-ET-A25N TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       14.79        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       16.08        29.19        19.76        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       80.02        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24         5.85         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-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q 
       43.50        17.98        25.32       132.36        24.72         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        4.80         5.03         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        33.63        81.83       106.36        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       91.17         1.25         1.15        17.82         1.64         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        1.51         0.76         4.67        16.57        18.08         0.30 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A76V TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
        1.68        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 
       18.61        48.92        47.41        10.26         9.80         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF 
        8.65        17.23        27.19        11.24        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J 
       22.29         2.47         2.60         0.20       143.57        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC 
       86.70         6.02        12.43         6.74        87.39        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.03               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             98.56             158.83 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            15.090             17.115 
[1] "0.0 - 98.6 (15.1)"  "0.0 - 158.8 (17.1)"
[1] "hr=" "1.9"
D56V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  22Q LOSS MUTATED        49       11        16        1         9         1
  22Q LOSS WILD-TYPE     231       40        93        1        36         5
D56V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 49                231
  STAGE II                11                 40
  STAGE III               16                 93
  STAGE IV                 1                  1
  STAGE IVA                9                 36
  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
  22Q LOSS MUTATED    25  34  25   3
  22Q LOSS WILD-TYPE 115 132 140  18
D56V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               25                115
  T2               34                132
  T3               25                140
  T4                3                 18
[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"
D56V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    44  35
  22Q LOSS WILD-TYPE 179 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     44   35
  22Q LOSS WILD-TYPE  179  187
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               44                179
  1               35                187
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  22Q LOSS MUTATED    43   2  42
  22Q LOSS WILD-TYPE 230   7 170
D56V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               43                230
  M1                2                  7
  MX               42                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"
D56V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    61  26
  22Q LOSS WILD-TYPE 303 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     61   26
  22Q LOSS WILD-TYPE  303  105
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               61                303
  MALE                 26                105
[1] 2 2
[1] FALSE
                    vv
clus                 OTHER  SPECIFY
  22Q LOSS MUTATED                1
  22Q LOSS WILD-TYPE              8
                    vv
clus                 THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  22Q LOSS MUTATED                                              60
  22Q LOSS WILD-TYPE                                           293
                    vv
clus                 THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  22Q LOSS MUTATED                                                                       23
  22Q LOSS WILD-TYPE                                                                     75
                    vv
clus                 THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  22Q LOSS MUTATED                                                                     3
  22Q LOSS WILD-TYPE                                                                  32
D56V8, multiclass
                                                                        clus
vv                                                                       22Q LOSS MUTATED
  OTHER  SPECIFY                                                                        1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        60
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               23
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   3
                                                                        clus
vv                                                                       22Q LOSS WILD-TYPE
  OTHER  SPECIFY                                                                          8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                         293
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                 75
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                    32
[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"
D56V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     1  86
  22Q LOSS WILD-TYPE  13 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   86
  22Q LOSS WILD-TYPE   13  395
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 1                 13
  YES               86                395
[1] 2 2
[1] FALSE
D56V10, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    78   1
  22Q LOSS WILD-TYPE 339  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     78    1
  22Q LOSS WILD-TYPE  339   16
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                78                339
  YES                1                 16
[1] 2 2
[1] FALSE
                    vv
clus                 MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  22Q LOSS MUTATED             18                       1   63
  22Q LOSS WILD-TYPE          112                      15  265
                    vv
clus                 VERY ADVANCED (T4B)
  22Q LOSS MUTATED                     0
  22Q LOSS WILD-TYPE                   1
D56V11, multiclass
                         clus
vv                        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  MINIMAL (T3)                          18                112
  MODERATE/ADVANCED (T4A)                1                 15
  NONE                                  63                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
  22Q LOSS MUTATED    66   6   1   8
  22Q LOSS WILD-TYPE 312  45   3  22
D56V12, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               66                312
  R1                6                 45
  R2                1                  3
  RX                8                 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"
D56V13, continuous
D56V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    45  40
  22Q LOSS WILD-TYPE 179 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     45   40
  22Q LOSS WILD-TYPE  179  221
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  MULTIFOCAL               45                179
  UNIFOCAL                 40                221
[1] 2 2
[1] FALSE
D56V15, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0    10
  22Q LOSS WILD-TYPE                                1    39
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           6    51
  22Q LOSS WILD-TYPE                        20   270
D56V16, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          10                 39
  BLACK OR AFRICAN AMERICAN                       6                 20
  WHITE                                          51                270
[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"
D56V17, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     6  60
  22Q LOSS WILD-TYPE  32 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   60
  22Q LOSS WILD-TYPE   32  290
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 32
  NOT HISPANIC OR LATINO               60                290
[1] 2 2
[1] FALSE

Clustering(57) Variable = XQ LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED     3   0
  XQ LOSS WILD-TYPE 474  14
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               488 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                0                14 
$`XQ LOSS MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-EM-A1YE 
       13.78        20.58        54.08 

$`XQ LOSS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        18.21        16.34        14.73         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-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       22.88        18.38        16.57        20.48        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         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-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        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-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
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-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       38.66        52.73       139.00       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
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-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        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-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
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-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         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-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        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-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        39.95        33.63        81.83       106.36 
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-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68        86.70         6.02        12.43         6.74 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            13.78              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            54.08            158.83 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            20.58             16.57 
[1] "13.8 - 54.1 (20.6)" "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  XQ LOSS MUTATED         0        3         0        0         0         0
  XQ LOSS WILD-TYPE     280       48       109        2        45         6
D57V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 0               280
  STAGE II                3                48
  STAGE III               0               109
  STAGE IV                0                 2
  STAGE IVA               0                45
  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
  XQ LOSS MUTATED     0   3   0   0
  XQ LOSS WILD-TYPE 140 163 165  21
D57V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               0               140
  T2               3               163
  T3               0               165
  T4               0                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"
D57V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3   0
  XQ LOSS WILD-TYPE 220 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    0
  XQ LOSS WILD-TYPE  220  222
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               3               220
  1               0               222
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  XQ LOSS MUTATED     0   0   3
  XQ LOSS WILD-TYPE 273   9 209
D57V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               0               273
  M1               0                 9
  MX               3               209
[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"
D57V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1   2
  XQ LOSS WILD-TYPE 363 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    2
  XQ LOSS WILD-TYPE  363  129
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               1               363
  MALE                 2               129
[1] 2 2
[1] FALSE
                   vv
clus                OTHER  SPECIFY
  XQ LOSS MUTATED                0
  XQ LOSS WILD-TYPE              9
                   vv
clus                THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  XQ LOSS MUTATED                                               2
  XQ LOSS WILD-TYPE                                           351
                   vv
clus                THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  XQ LOSS MUTATED                                                                        1
  XQ LOSS WILD-TYPE                                                                     97
                   vv
clus                THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  XQ LOSS MUTATED                                                                     0
  XQ LOSS WILD-TYPE                                                                  35
D57V8, multiclass
                                                                        clus
vv                                                                       XQ LOSS 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                                                                       XQ LOSS WILD-TYPE
  OTHER  SPECIFY                                                                         9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                        351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                   35
[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"
D57V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0   3
  XQ LOSS WILD-TYPE  14 478
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    3
  XQ LOSS WILD-TYPE   14  478
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                0                14
  YES               3               478
[1] 2 2
[1] FALSE
D57V10, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2   0
  XQ LOSS WILD-TYPE 415  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    0
  XQ LOSS WILD-TYPE  415   17
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                2               415
  YES               0                17
[1] 2 2
[1] FALSE
                   vv
clus                MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  XQ LOSS MUTATED              0                       0    3
  XQ LOSS WILD-TYPE          130                      16  325
                   vv
clus                VERY ADVANCED (T4B)
  XQ LOSS MUTATED                     0
  XQ LOSS WILD-TYPE                   1
D57V11, multiclass
                         clus
vv                        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  MINIMAL (T3)                          0               130
  MODERATE/ADVANCED (T4A)               0                16
  NONE                                  3               325
  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
  XQ LOSS MUTATED     3   0   0   0
  XQ LOSS WILD-TYPE 375  51   4  30
D57V12, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0               3               375
  R1               0                51
  R2               0                 4
  RX               0                30
[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"
D57V13, continuous
D57V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1   2
  XQ LOSS WILD-TYPE 223 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    2
  XQ LOSS WILD-TYPE  223  259
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  MULTIFOCAL               1               223
  UNIFOCAL                 2               259
[1] 2 2
[1] FALSE
D57V15, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2               395 
       TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z9        TCGA-BJ-A0ZA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0ZB        TCGA-BJ-A0ZC        TCGA-BJ-A0ZE        TCGA-BJ-A0ZG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ        TCGA-BJ-A18Y        TCGA-BJ-A18Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A191        TCGA-BJ-A192        TCGA-BJ-A28R        TCGA-BJ-A28S 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A28T        TCGA-BJ-A28V        TCGA-BJ-A28W        TCGA-BJ-A28Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A290        TCGA-BJ-A291        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A2P4        TCGA-BJ-A3PU        TCGA-BJ-A45C        TCGA-BJ-A45D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45E        TCGA-BJ-A45F        TCGA-BJ-A45G        TCGA-BJ-A45H 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K        TCGA-BJ-A4O8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A27D        TCGA-CE-A3MD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CE-A3ME        TCGA-CE-A481        TCGA-CE-A482        TCGA-CE-A483 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0XZ        TCGA-DE-A0Y2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN        TCGA-DE-A4M8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB        TCGA-DE-A4MC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K        TCGA-DE-A7U5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13R        TCGA-DJ-A13S 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A13U        TCGA-DJ-A13V        TCGA-DJ-A13W        TCGA-DJ-A13X 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF        TCGA-DJ-A1QG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QL        TCGA-DJ-A1QM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QN        TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PO        TCGA-DJ-A2PP        TCGA-DJ-A2PQ        TCGA-DJ-A2PR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PS        TCGA-DJ-A2PT        TCGA-DJ-A2PU        TCGA-DJ-A2PV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PW        TCGA-DJ-A2PY        TCGA-DJ-A2PZ        TCGA-DJ-A2Q0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2Q1        TCGA-DJ-A2Q2        TCGA-DJ-A2Q3        TCGA-DJ-A2Q4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2Q5        TCGA-DJ-A2Q6        TCGA-DJ-A2Q7        TCGA-DJ-A2Q8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QC        TCGA-DJ-A3UK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO        TCGA-DJ-A3UP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3US        TCGA-DJ-A3UT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3V0        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3VA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3VB        TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3VG        TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A4UL        TCGA-DJ-A4UQ        TCGA-DJ-A4UT        TCGA-DJ-A4V0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A4V2        TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A419        TCGA-EL-A3CN        TCGA-EL-A3CO        TCGA-EL-A3CR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CS        TCGA-EL-A3CT        TCGA-EL-A3CU        TCGA-EL-A3CV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CW        TCGA-EL-A3CX        TCGA-EL-A3CY        TCGA-EL-A3CZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3D0        TCGA-EL-A3D1        TCGA-EL-A3D4        TCGA-EL-A3D5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3D6        TCGA-EL-A3GO        TCGA-EL-A3GP        TCGA-EL-A3GQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GR        TCGA-EL-A3GS        TCGA-EL-A3GU        TCGA-EL-A3GV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GW        TCGA-EL-A3GX        TCGA-EL-A3GY        TCGA-EL-A3GZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3H2        TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3H7        TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3MY        TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3T7        TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3TB        TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3ZQ        TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-EM-A1CS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A1CT        TCGA-EM-A1CU        TCGA-EM-A1CV        TCGA-EM-A1CW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A1YA        TCGA-EM-A1YB        TCGA-EM-A1YC        TCGA-EM-A1YD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A22I        TCGA-EM-A22J        TCGA-EM-A22K        TCGA-EM-A22L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A22N        TCGA-EM-A22O        TCGA-EM-A22P        TCGA-EM-A22Q 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A2CJ        TCGA-EM-A2CK        TCGA-EM-A2CL        TCGA-EM-A2CN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A2CO        TCGA-EM-A2CP        TCGA-EM-A2CQ        TCGA-EM-A2CS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A2CT        TCGA-EM-A2CU        TCGA-EM-A2OW        TCGA-EM-A2OX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A2OY        TCGA-EM-A2P0        TCGA-EM-A2P1        TCGA-EM-A2P2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A2P3        TCGA-EM-A3AI        TCGA-EM-A3AJ        TCGA-EM-A3AK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3AL        TCGA-EM-A3AN        TCGA-EM-A3AO        TCGA-EM-A3AP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3AQ        TCGA-EM-A3AR        TCGA-EM-A3FJ        TCGA-EM-A3FM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3FN        TCGA-EM-A3FO        TCGA-EM-A3FP        TCGA-EM-A3FR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3O3        TCGA-EM-A3O6        TCGA-EM-A3O7        TCGA-EM-A3O8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3O9        TCGA-EM-A3OA        TCGA-EM-A3OB        TCGA-EM-A3ST 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A3SU        TCGA-EM-A3SX        TCGA-EM-A3SY        TCGA-EM-A3SZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A4FF        TCGA-EM-A4FH        TCGA-EM-A4FK        TCGA-EM-A4FM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A4FN        TCGA-EM-A4FQ        TCGA-EM-A4FR        TCGA-EM-A4FU 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EM-A4FV        TCGA-EM-A4G1        TCGA-ET-A25G        TCGA-ET-A25I 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L        TCGA-ET-A25M 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P        TCGA-ET-A25R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A2MY        TCGA-ET-A2MZ        TCGA-ET-A2N0        TCGA-ET-A2N5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A39J        TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39O 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A39P        TCGA-ET-A39T        TCGA-ET-A3BN        TCGA-ET-A3BO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3BP        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3BX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3DO        TCGA-ET-A3DS        TCGA-ET-A3DT        TCGA-ET-A40P 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S        TCGA-ET-A4KN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A4KQ        TCGA-FE-A22Z        TCGA-FE-A230        TCGA-FE-A232 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A233        TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A237        TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A3PA        TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A2QD        TCGA-FY-A3I4        TCGA-FY-A3I5        TCGA-FY-A3ON 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3R8        TCGA-FY-A3TY        TCGA-FY-A3W9        TCGA-FY-A3YR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A4B3        TCGA-FY-A76V        TCGA-GE-A2C6        TCGA-H2-A421 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IM-A3EB        TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IM-A41Y        TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3YD        TCGA-J8-A3YG        TCGA-KS-A41F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9        TCGA-KS-A4IB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP        TCGA-L6-A4EQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-L6-A4ET        TCGA-L6-A4EU        TCGA-MK-A4N6        TCGA-MK-A4N7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-MK-A4N9        TCGA-MK-A84Z        TCGA-QD-A8IV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     0
  XQ LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           0     1
  XQ LOSS WILD-TYPE                        26   320
D57V16, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1               396 
       TCGA-BJ-A0YZ        TCGA-BJ-A0Z2        TCGA-BJ-A0Z3        TCGA-BJ-A0Z5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0Z9        TCGA-BJ-A0ZA        TCGA-BJ-A0ZB        TCGA-BJ-A0ZC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A0ZE        TCGA-BJ-A0ZG        TCGA-BJ-A0ZH        TCGA-BJ-A0ZJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A18Y        TCGA-BJ-A18Z        TCGA-BJ-A191        TCGA-BJ-A192 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A28R        TCGA-BJ-A28S        TCGA-BJ-A28T        TCGA-BJ-A28V 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A28W        TCGA-BJ-A28X        TCGA-BJ-A28Z        TCGA-BJ-A290 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A291        TCGA-BJ-A2N7        TCGA-BJ-A2N8        TCGA-BJ-A2N9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A2NA        TCGA-BJ-A2P4        TCGA-BJ-A3EZ        TCGA-BJ-A3F0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A3PR        TCGA-BJ-A3PT        TCGA-BJ-A3PU        TCGA-BJ-A45C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45D        TCGA-BJ-A45E        TCGA-BJ-A45F        TCGA-BJ-A45G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A45H        TCGA-BJ-A45I        TCGA-BJ-A45J        TCGA-BJ-A45K 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BJ-A4O8        TCGA-BJ-A4O9        TCGA-CE-A13K        TCGA-CE-A27D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CE-A3MD        TCGA-CE-A3ME        TCGA-CE-A481        TCGA-CE-A482 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CE-A483        TCGA-CE-A484        TCGA-CE-A485        TCGA-DE-A0XZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A0Y2        TCGA-DE-A0Y3        TCGA-DE-A2OL        TCGA-DE-A3KN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A4M8        TCGA-DE-A4M9        TCGA-DE-A4MA        TCGA-DE-A4MB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A4MC        TCGA-DE-A4MD        TCGA-DE-A69J        TCGA-DE-A69K 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DE-A7U5        TCGA-DJ-A13M        TCGA-DJ-A13O        TCGA-DJ-A13P 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A13R        TCGA-DJ-A13S        TCGA-DJ-A13T        TCGA-DJ-A13U 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A13W        TCGA-DJ-A1QD        TCGA-DJ-A1QE        TCGA-DJ-A1QF 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QG        TCGA-DJ-A1QH        TCGA-DJ-A1QI        TCGA-DJ-A1QM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A1QO        TCGA-DJ-A1QQ        TCGA-DJ-A2PN        TCGA-DJ-A2PO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PQ        TCGA-DJ-A2PR        TCGA-DJ-A2PT        TCGA-DJ-A2PU 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PV        TCGA-DJ-A2PW        TCGA-DJ-A2PX        TCGA-DJ-A2PY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2PZ        TCGA-DJ-A2Q0        TCGA-DJ-A2Q1        TCGA-DJ-A2Q2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2Q3        TCGA-DJ-A2Q4        TCGA-DJ-A2Q5        TCGA-DJ-A2Q6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A2Q7        TCGA-DJ-A2Q9        TCGA-DJ-A2QA        TCGA-DJ-A2QB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UK        TCGA-DJ-A3UM        TCGA-DJ-A3UN        TCGA-DJ-A3UO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UQ        TCGA-DJ-A3UR        TCGA-DJ-A3US        TCGA-DJ-A3UT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UU        TCGA-DJ-A3UW        TCGA-DJ-A3UX        TCGA-DJ-A3UY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3UZ        TCGA-DJ-A3V2        TCGA-DJ-A3V3        TCGA-DJ-A3V4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3V5        TCGA-DJ-A3V7        TCGA-DJ-A3V8        TCGA-DJ-A3V9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3VD        TCGA-DJ-A3VE        TCGA-DJ-A3VF        TCGA-DJ-A3VG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A3VJ        TCGA-DJ-A3VL        TCGA-DJ-A3VM        TCGA-DJ-A4UL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A4UQ        TCGA-DJ-A4UR        TCGA-DJ-A4UT        TCGA-DJ-A4UW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DJ-A4V0        TCGA-DJ-A4V4        TCGA-DJ-A4V5        TCGA-DO-A1JZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DO-A1K0        TCGA-DO-A2HM        TCGA-E3-A3DY        TCGA-E3-A3DZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E3-A3E0        TCGA-E3-A3E1        TCGA-E3-A3E2        TCGA-E3-A3E3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E3-A3E5        TCGA-E8-A242        TCGA-E8-A2EA        TCGA-E8-A2JQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A3X7        TCGA-E8-A413        TCGA-E8-A414        TCGA-E8-A415 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A416        TCGA-E8-A417        TCGA-E8-A418        TCGA-E8-A419 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A432        TCGA-E8-A433        TCGA-E8-A434        TCGA-E8-A436 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-E8-A437        TCGA-E8-A438        TCGA-E8-A44K        TCGA-E8-A44M 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CL        TCGA-EL-A3CM        TCGA-EL-A3CN        TCGA-EL-A3CO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CP        TCGA-EL-A3CR        TCGA-EL-A3CS        TCGA-EL-A3CT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CU        TCGA-EL-A3CV        TCGA-EL-A3CW        TCGA-EL-A3CX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3CY        TCGA-EL-A3CZ        TCGA-EL-A3D0        TCGA-EL-A3D1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3D4        TCGA-EL-A3D5        TCGA-EL-A3D6        TCGA-EL-A3GO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GP        TCGA-EL-A3GQ        TCGA-EL-A3GR        TCGA-EL-A3GS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GU        TCGA-EL-A3GV        TCGA-EL-A3GW        TCGA-EL-A3GX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3GY        TCGA-EL-A3GZ        TCGA-EL-A3H1        TCGA-EL-A3H2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3H3        TCGA-EL-A3H4        TCGA-EL-A3H5        TCGA-EL-A3H7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3H8        TCGA-EL-A3MW        TCGA-EL-A3MX        TCGA-EL-A3MY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3MZ        TCGA-EL-A3N2        TCGA-EL-A3N3        TCGA-EL-A3T0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3T1        TCGA-EL-A3T2        TCGA-EL-A3T3        TCGA-EL-A3T6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3T7        TCGA-EL-A3T8        TCGA-EL-A3T9        TCGA-EL-A3TA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3TB        TCGA-EL-A3ZG        TCGA-EL-A3ZH        TCGA-EL-A3ZK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3ZL        TCGA-EL-A3ZN        TCGA-EL-A3ZO        TCGA-EL-A3ZP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A3ZQ        TCGA-EL-A3ZR        TCGA-EL-A3ZS        TCGA-EL-A3ZT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4JV        TCGA-EL-A4JW        TCGA-EL-A4JX        TCGA-EL-A4JZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4K0        TCGA-EL-A4K1        TCGA-EL-A4K2        TCGA-EL-A4K4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4K6        TCGA-EL-A4K7        TCGA-EL-A4K9        TCGA-EL-A4KD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EL-A4KG        TCGA-EL-A4KH        TCGA-EL-A4KI        TCGA-ET-A25G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A25I        TCGA-ET-A25J        TCGA-ET-A25K        TCGA-ET-A25L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A25M        TCGA-ET-A25N        TCGA-ET-A25O        TCGA-ET-A25P 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A25R        TCGA-ET-A2MX        TCGA-ET-A2MY        TCGA-ET-A2MZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A2N0        TCGA-ET-A2N1        TCGA-ET-A2N3        TCGA-ET-A2N4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A2N5        TCGA-ET-A39I        TCGA-ET-A39J        TCGA-ET-A39K 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A39M        TCGA-ET-A39N        TCGA-ET-A39O        TCGA-ET-A39P 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A39R        TCGA-ET-A39S        TCGA-ET-A39T        TCGA-ET-A3BN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3BO        TCGA-ET-A3BQ        TCGA-ET-A3BS        TCGA-ET-A3BT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3BU        TCGA-ET-A3BV        TCGA-ET-A3BW        TCGA-ET-A3DO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3DP        TCGA-ET-A3DQ        TCGA-ET-A3DR        TCGA-ET-A3DS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A3DT        TCGA-ET-A3DU        TCGA-ET-A3DV        TCGA-ET-A3DW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A40P        TCGA-ET-A40Q        TCGA-ET-A40R        TCGA-ET-A40S 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ET-A40T        TCGA-ET-A4KN        TCGA-ET-A4KQ        TCGA-FE-A22Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A230        TCGA-FE-A231        TCGA-FE-A232        TCGA-FE-A233 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A234        TCGA-FE-A235        TCGA-FE-A236        TCGA-FE-A237 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A238        TCGA-FE-A239        TCGA-FE-A23A        TCGA-FE-A3PA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FE-A3PB        TCGA-FE-A3PC        TCGA-FE-A3PD        TCGA-FK-A3S3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FK-A3SB        TCGA-FK-A3SD        TCGA-FK-A3SE        TCGA-FK-A3SG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FK-A3SH        TCGA-FK-A4UB        TCGA-FY-A2QD        TCGA-FY-A3BL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3I4        TCGA-FY-A3I5        TCGA-FY-A3NM        TCGA-FY-A3ON 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3R6        TCGA-FY-A3R7        TCGA-FY-A3R8        TCGA-FY-A3R9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A3RA        TCGA-FY-A3W9        TCGA-FY-A3WA        TCGA-FY-A3YR 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A40K        TCGA-FY-A40L        TCGA-FY-A40M        TCGA-FY-A40N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FY-A4B0        TCGA-FY-A4B3        TCGA-FY-A4B4        TCGA-FY-A76V 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GE-A2C6        TCGA-H2-A26U        TCGA-H2-A2K9        TCGA-H2-A3RH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-H2-A3RI        TCGA-H2-A421        TCGA-H2-A422        TCGA-IM-A3EB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IM-A3ED        TCGA-IM-A3U2        TCGA-IM-A3U3        TCGA-IM-A41Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IM-A41Z        TCGA-IM-A420        TCGA-IM-A4EB        TCGA-J8-A3NZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A3O0        TCGA-J8-A3O1        TCGA-J8-A3O2        TCGA-J8-A3YD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A3YE        TCGA-J8-A3YF        TCGA-J8-A3YG        TCGA-J8-A3YH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J8-A42S        TCGA-J8-A4HW        TCGA-J8-A4HY        TCGA-KS-A41F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A41I        TCGA-KS-A41J        TCGA-KS-A41L        TCGA-KS-A4I1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A4I3        TCGA-KS-A4I5        TCGA-KS-A4I7        TCGA-KS-A4I9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KS-A4IB        TCGA-KS-A4IC        TCGA-KS-A4ID        TCGA-L6-A4EP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-L6-A4EQ        TCGA-L6-A4ET        TCGA-L6-A4EU        TCGA-MK-A4N6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-MK-A4N7        TCGA-MK-A4N9        TCGA-MK-A84Z        TCGA-QD-A8IV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D57V17, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0   2
  XQ LOSS WILD-TYPE  38 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    2
  XQ LOSS WILD-TYPE   38  348
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                38
  NOT HISPANIC OR LATINO               2               348
[1] 2 2
[1] FALSE
