[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"        "-oTSKCM-TM"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/11541723/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/11573323/transformed.cor.cli.txt"

nPatients in clinical file=349, in cluster file=366, common to both=348
[1]  80 348
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               83               265 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               83               265 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              162               186 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              162               186 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               63               285 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               63               285 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               61               287 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               61               287 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               62               286 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               62               286 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               71               277 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               71               277 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               54               294 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               54               294 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               46               302 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               46               302 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               75               273 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               75               273 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               50               298 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               50               298 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              136               212 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              136               212 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               47               301 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               47               301 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              191               157 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              191               157 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              189               159 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              189               159 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              116               232 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              116               232 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              162               186 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              162               186 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               332 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               332 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               328 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               328 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                336 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                336 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                345 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                345 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                34                314 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                34                314 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                319 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                319 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                60                288 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                60                288 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                312 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                312 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                91                257 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                91                257 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                41                307 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                41                307 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                83                265 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                83                265 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                54                294 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                54                294 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                42                306 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                42                306 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                36                312 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                36                312 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                64                284 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                64                284 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                51                297 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                51                297 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                43                305 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                43                305 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                54                294 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                54                294 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                54                294 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                54                294 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               142                206 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               142                206 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               173                175 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               173                175 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                67                281 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                67                281 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               120                228 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               120                228 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               38               310 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               38               310 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               51               297 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               51               297 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               26               322 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               26               322 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               49               299 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               49               299 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               50               298 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               50               298 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               58               290 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               58               290 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               50               298 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               50               298 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               75               273 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               75               273 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               79               269 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               79               269 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               76               272 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               76               272 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               95               253 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               95               253 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               65               283 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               65               283 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              162               186 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              162               186 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               330 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               330 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               331 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               331 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               64               284 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               64               284 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               26               322 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               26               322 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              227               121 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              227               121 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              178               170 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              178               170 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               195                153 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               195                153 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               214                134 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               214                134 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               121                227 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               121                227 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               142                206 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               142                206 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                55                293 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                55                293 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                62                286 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                62                286 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                75                273 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                75                273 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               110                238 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               110                238 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                49                299 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                49                299 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                66                282 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                66                282 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               100                248 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               100                248 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               123                225 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               123                225 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                63                285 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                63                285 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               103                245 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               103                245 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                96                252 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                96                252 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                71                277 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                71                277 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                67                281 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                67                281 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                23                325 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                23                325 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                341 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                341 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                65                283 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                65                283 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                37                311 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                37                311 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               89               259 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               89               259 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DAYSTOSUBMITTEDSPECIMENDX"             
 [6] "PRIMARYSITEOFDISEASE"                  
 [7] "NEOPLASM.DISEASESTAGE"                 
 [8] "PATHOLOGY.T.STAGE"                     
 [9] "PATHOLOGY.N.STAGE"                     
[10] "PATHOLOGY.M.STAGE"                     
[11] "MELANOMA.ULCERATION"                   
[12] "MELANOMA.PRIMARY.KNOWN"                
[13] "BRESLOW.THICKNESS"                     
[14] "DCCUPLOADDATE"                         
[15] "GENDER"                                
[16] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[17] "RADIATIONTHERAPY"                      
[18] "RADIATIONS.RADIATION.REGIMENINDICATION"
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 348 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
          NA         1856           NA           NA           NA         3408 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
          NA           NA         4053           NA           NA         2765 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
        2912           NA           NA           NA           NA         3514 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
          NA         2639           NA         1888           NA         1280 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
          NA         5219         1709         2010         1812         3976 
TCGA-D3-A3C1 TCGA-D3-A3C3 TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
          NA           NA           NA         1429         1409         5065 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
        2644           NA           NA           NA           NA         3151 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51G TCGA-D3-A51H 
        1209         1378         5318         1695           NA         1714 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
        4414         1002          688         1941          818         3826 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
        4129         4195         5424          553         3808           NA 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
          NA          353          462           NA         6965         5177 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GO TCGA-D3-A8GP TCGA-D3-A8GQ 
          NA         2897         4897           NA         4191           NA 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
          NA           NA         4609         1663          111          195 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
         551          345          678          338          301          766 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2015           NA         1487           NA         3565           NA 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        5926           NA           NA         3265         1861           NA 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
          NA          713           NA          870           NA         6553 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
         477          422          309          543         2076         1643 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
         526         1582          193          371           NA           NA 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
          NA         4070           NA         2785           NA           NA 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
          NA         2452         1455           NA         1940           NA 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        1966           NA         1729           NA         1716         1136 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
         440         1701        11252           NA         5932           NA 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
          NA         3130         1120           NA         2620         1803 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
        2051         9568         4898         6328         1482         2717 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
        1665         2423         2296         2767         3857           NA 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
         435         1691         1365         2884           NA         3932 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
          NA           NA           NA           NA         4825         6176 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
          NA           NA         7563           NA         4088         4942 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
        2166         1620         3781         3733         1570          112 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        1658           NA          714           NA           NA           NA 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
          NA         1949           NA           NA         6138           NA 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        1562         3333         4504           NA           NA           NA 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
          NA           NA         2365           NA           NA           NA 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
          NA           NA         8180           NA           NA           NA 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
          NA         1340           NA           NA           NA         1133 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
          NA           NA         2433           NA           NA           NA 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
         498          951          975           NA         2443         1429 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FR-A69P 
        1010          206         2828           NA         5299          478 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
        6390          461          213         1164           NA          896 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        2871           NA           NA           NA           NA           NA 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        1225           NA           NA           NA           NA           NA 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
        3080           NA           NA           NA         4526         1617 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
          NA         1505           NA           NA         2367           NA 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
          NA           NA           NA          378           NA         1504 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2369            6          697         1446            5          587 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
         301          220           62          357         4255           NA 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
        2577           NA           NA           NA           NA         1204 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OG 
        1410          384           NA           NA           NA           NA 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
          NA        10860         8966          203           NA           10 
TCGA-RP-A694 TCGA-RP-A695 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
          21           NA         6455           NA           NA           NA 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
          NA         6666           NA          731         1173         1654 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
         262         2746         1733         1807         1592          114 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
         690         1330           67          918          315          461 
TCGA-YD-A9TB TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
          NA         1096          439          719         2831          357 
Variable 1:'AGE':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=165,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=189,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=274,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'NEOPLASM.DISEASESTAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.T.STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.N.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA.ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MELANOMA.PRIMARY.KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BRESLOW.THICKNESS':	nDistinctValues=124,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=21,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
 [3] "NEOPLASM.DISEASESTAGE"   "PATHOLOGY.T.STAGE"      
 [5] "PATHOLOGY.N.STAGE"       "PATHOLOGY.M.STAGE"      
 [7] "MELANOMA.ULCERATION"     "MELANOMA.PRIMARY.KNOWN" 
 [9] "BRESLOW.THICKNESS"       "GENDER"                 
[11] "RACE"                    "ETHNICITY"              
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 348 columns, 2 survival variables, and 12 non-survival variables.
AGE, nv=68, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
NEOPLASM.DISEASESTAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
23 40 71 74 67 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   63    71    74    67 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 40 71 74 67 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   63    71    74    67 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
168  61  38  47 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
168  61  38  47 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
168  61  38  47 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
168  61  38  47 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
MELANOMA.ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA.PRIMARY.KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW.THICKNESS, nv=124, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, 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    39  40
  1P GAIN WILD-TYPE 129 125
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               79               254 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               125 
$`1P GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
        6.97        88.50        86.76        11.41        92.42        56.19 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D3-A8GD TCGA-D3-A8GI 
      114.67        15.25       103.59        47.87        10.22         4.18 
TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
      142.45        75.65         4.01         9.90        11.31        13.22 
TCGA-DA-A1I0 TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       10.03        13.35        10.55         8.12         1.12        12.20 
TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29T 
       60.23        11.15        62.79         8.55         1.08        30.44 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GP 
       32.15         8.09        36.30        30.08        28.31         5.42 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN 
       13.02        98.27         9.53        63.42        56.02        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J7 
       21.60        60.49         5.56       122.73        15.95        21.60 
TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A3ET TCGA-ER-A3PL 
       22.22         5.72        11.11       114.15         6.58         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA TCGA-FS-A1YX 
        5.62        18.41        85.74         6.71        13.28         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 TCGA-GF-A6C9 
       23.80        30.87         8.65         8.68        28.73        11.61 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-HR-A2OH TCGA-W3-A828 
       10.13        16.24        12.16        14.50        15.81        60.03 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AAA0 
        2.99       185.16        11.84         5.49         5.36        19.96 
TCGA-YG-AA3O 
        6.18 

$`1P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97        16.47         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       70.16       110.79        28.08        22.55        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF 
       10.29        85.32         8.38        21.14        68.22        44.19 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
        7.50        36.16         6.31        64.44        59.57        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32        82.29        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34        26.37        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.31        32.28        21.44        32.61        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       52.01        13.68        17.72        23.11        29.72        22.06 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
       15.19       108.79        38.93       124.47        87.62        11.44 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV 
        5.56        24.07        21.93         5.72        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       23.15        19.00        13.22         0.20        11.57         6.31 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        1.35         5.13         4.31         4.34        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
        1.18         7.99         9.90        37.97        36.85        39.62 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        49.22         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        47.21        19.43        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       33.83        55.69         1.15        34.98        36.33         8.84 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        2.70         6.18        47.51        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS 
        7.96        14.56       125.65       111.91        26.99        53.16 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       52.67       124.31        51.62         3.68        30.15        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB 
       12.72         3.22        22.92        21.60        16.14         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       12.95        38.40        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.90        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC 
        9.04        22.49        15.72         3.58         5.36         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.70         3.29        64.47        11.01        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       11.08         7.17        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15        40.64        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         3.22         7.36        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       17.33         9.90         7.23         0.85        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
       84.72        15.42        14.70        11.84        10.65        14.50 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       14.50         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 
        0.69       164.19         8.98        10.98        71.01         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        7.10        18.67        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT 
       21.83         1.08         1.94        12.07         4.70         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.08              0.13 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           185.16            164.19 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            13.35             15.01 
[1] "1.1 - 185.2 (13.3)" "0.1 - 164.2 (15.0)"
[1] "hr=" "1.1"
D1V2, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    40  40
  1P GAIN WILD-TYPE 133 126
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               80               259 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               126 
$`1P GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN 
       12.99       115.53        86.76        11.87       171.58        56.19 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D3-A8GD TCGA-D3-A8GI 
      130.72        58.06       103.59       137.92        11.61        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
      228.99        95.24         3.65        11.34         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       66.25        20.38        17.29        27.22        94.98        33.73 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
       26.89       133.81        13.97        63.78        72.07         2.60 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2GM 
      369.93       195.02        17.92        36.82        48.72        75.48 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MM 
       13.91        55.59       129.27        47.28        96.23       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AG 
       47.54        43.23       134.40        53.26       122.73        23.47 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A3ET 
       64.08        53.19         9.17        26.37       268.93        80.32 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA 
       33.21         6.77        92.98       174.21       210.08        38.27 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 
       48.59       202.65        32.75       133.55        26.56        28.73 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-HR-A2OH 
       11.74        10.13        64.44        32.48        50.10        65.88 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZY 
      121.08         4.01       219.16        24.03        38.56        43.73 
TCGA-WE-AAA0 TCGA-YG-AA3O 
       30.18        36.03 

$`1P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF 
       43.43       103.10        65.49        23.77       168.00        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
      113.52        42.08        12.10        66.08        59.57        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      135.75       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
       15.19       170.20        89.13       161.00       137.79        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       117.17       151.53        54.67         6.41        18.12 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       22.29        11.11        22.95        48.89        36.03       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.16        17.85        68.25        54.02 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       52.01         6.35        12.20        29.82         8.65        14.70 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       68.15         4.96       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       63.35        80.61        47.84        64.64        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 
       56.42        37.35        14.47        55.92        25.87        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      161.03       208.04        89.33        54.74        79.66        90.97 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
      126.81        14.30        44.88        94.82        21.67        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
      204.66       158.63       203.05       248.65       162.48        71.21 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      124.31        51.62         3.68        54.51        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      172.18       127.20        36.95        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       50.76        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD 
       46.98        15.72        15.16         7.00        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       94.39       216.92       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
        9.70        47.38        23.93       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       62.79        39.58        46.36        12.62        21.37        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      357.04       294.77         6.67        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 
      212.22        63.02        42.08       105.04        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       90.28        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        2.20        10.36        15.16        14.43        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2.60              0.16 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           369.93            357.37 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            49.41             50.76 
[1] "2.6 - 369.9 (49.4)" "0.2 - 357.4 (50.8)"
[1] "hr=" "1"  
D1V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P GAIN MUTATED                   12             3
  1P GAIN WILD-TYPE                 49             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1P GAIN MUTATED                                          21
  1P GAIN WILD-TYPE                                        51
                   vv
clus                REGIONAL LYMPH NODE
  1P GAIN MUTATED                    47
  1P GAIN WILD-TYPE                 162
D1V4, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  DISTANT METASTASIS                                     12                49
  PRIMARY TUMOR                                           3                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              21                51
  REGIONAL LYMPH NODE                                    47               162
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1P GAIN MUTATED             3       3       7        5        8        8
  1P GAIN WILD-TYPE           9       4      21       12       19       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1P GAIN MUTATED           1         2         2         9          9
  1P GAIN WILD-TYPE        13        17        10        26          6
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED            6         10        3
  1P GAIN WILD-TYPE         26         48       16
D1V5, multiclass
             clus
vv            1P GAIN MUTATED 1P GAIN WILD-TYPE
  I OR II NOS               3                 9
  STAGE 0                   3                 4
  STAGE I                   7                21
  STAGE IA                  5                12
  STAGE IB                  8                19
  STAGE II                  8                14
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 2                10
  STAGE III                 9                26
  STAGE IIIA                9                 6
  STAGE IIIB                6                26
  STAGE IIIC               10                48
  STAGE IV                  3                16
[1] 14  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                T0+T1 T2 T3 T4
  1P GAIN MUTATED      14 15 21 18
  1P GAIN WILD-TYPE    49 56 53 49
D1V6, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1              14                49
  T2                 15                56
  T3                 21                53
  T4                 18                49
[1] 4 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                 N0  N1  N2  N3
  1P GAIN MUTATED    42  17   9   8
  1P GAIN WILD-TYPE 126  44  29  39
D1V7, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              42               126
  N1              17                44
  N2               9                29
  N3               8                39
[1] 4 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                 M0  M1 M1A M1B M1C
  1P GAIN MUTATED    75   0   2   0   1
  1P GAIN WILD-TYPE 231   4   1   4   8
D1V8, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               75               231
  M1                0                 4
  M1A               2                 1
  M1B               0                 4
  M1C               1                 8
[1] 5 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   36 20
  1P GAIN WILD-TYPE 93 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     36   20
  1P GAIN WILD-TYPE   93   67
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               36                93
  YES              20                67
[1] 2 2
[1] FALSE
D1V10, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     8  74
  1P GAIN WILD-TYPE  35 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8   74
  1P GAIN WILD-TYPE   35  230
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                8                35
  YES              74               230
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    30  53
  1P GAIN WILD-TYPE 101 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     30   53
  1P GAIN WILD-TYPE  101  164
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              30               101
  MALE                53               164
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         0    76
  1P GAIN WILD-TYPE     4                         1   250
D1V13, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  76               250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2  77
  1P GAIN WILD-TYPE   5 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   77
  1P GAIN WILD-TYPE    5  257
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              77               257
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   77 79
  1Q GAIN WILD-TYPE 91 86
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              156               177 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               79                86 
$`1Q GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QB TCGA-D3-A2J8 
        3.02         6.97        16.47         8.52        81.24         8.38 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ 
       88.50        86.76        11.41        92.42        56.19       114.67 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       15.25        13.32         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       29.23        32.28        32.61       110.24        52.01        47.87 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.11        10.22         4.18       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       75.65        87.62        11.44         5.56         4.01        21.93 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        11.31        13.22        14.60        10.03        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 
        9.99        44.52         4.93         6.64         7.00        17.56 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z 
        0.20        19.00        13.35        13.22        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29B 
        8.12         1.12         5.13        60.23         1.18         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R 
       11.15        62.79         8.55         1.08        39.62         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        9.99        30.44        32.15        49.22        36.30        36.33 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN 
       17.98        60.00        47.21        30.08        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MJ 
       55.69        13.02        36.33         2.70         9.53        63.42 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        21.60        60.49        53.16        52.67         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JA 
      122.73        51.62         3.68        15.95        21.60        22.22 
TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       21.73        12.95         5.72         3.52        11.11       114.15 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ET 
       34.68         9.57         1.87        13.08        11.74         6.58 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7UA 
        1.71         5.62        18.41        85.74         6.71        13.28 
TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC 
        2.20         3.45        23.80        14.24         7.30        20.38 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       11.08        30.87        12.89        52.08         8.65        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-GF-A6C9 
        8.68         0.82         5.23        28.73         2.27        11.61 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        16.24        12.16        14.70        11.84        10.65 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-W3-A825 
       14.50        14.50        15.81         0.43         5.79         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
       60.03         2.99       185.16        71.01        11.84         5.49 
TCGA-WE-A8ZO TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O 
       13.12        21.83         5.36        19.96        12.07         6.18 

$`1Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        6.97       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB 
       22.55        45.83        10.29        85.32        21.14        68.22 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP 
       44.19         7.50        36.16         6.31        64.44        59.57 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51E 
       46.98        46.32        82.29        61.38        24.00        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GR 
       54.74        31.30        54.31        21.44        25.78        13.68 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS 
       17.72        29.72        22.06        15.19       124.47        24.07 
TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 
        5.72        48.79        35.80        51.12        13.68        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       25.15        22.36        19.36        14.83        13.15         0.13 
TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       23.15         0.20        11.57         1.35        12.20         4.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H 
        4.34        15.85         9.21         7.99        37.97        36.85 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
        9.50        12.03         8.09         2.43         8.09        11.31 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
        9.67        51.12        34.29        19.43        16.01        35.54 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
        5.42         1.15        34.98         8.84        98.27         6.18 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AE 
      125.65       111.91        56.02        26.99       124.31        30.15 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        0.95        27.35        18.41        33.60        31.40        18.61 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H 
       38.40        76.41        25.18         3.78        11.90        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19T 
        4.21        13.45        28.60        42.84        36.07         6.58 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES 
       17.72        78.44        11.80         1.51        12.62         9.04 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YD TCGA-FR-A8YE 
       22.49        15.72         3.58         5.36         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
       64.47        11.01        15.52         7.33         3.39         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       19.53         7.17        12.92        47.38         8.81        49.15 
TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.39        53.85         3.22         7.36        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       17.33         9.90         7.23         0.85        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A8LL TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 
       84.72        15.42        14.50        11.05        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1V TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
        0.69       164.19        10.98         6.48         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3P 
       21.07         3.72         3.42         1.08         1.94         4.70 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        8.22         6.67         5.98 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.20              0.13 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           185.16            164.19 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           13.335            15.850 
[1] "0.2 - 185.2 (13.3)" "0.1 - 164.2 (15.8)"
[1] "hr=" "1"  
D2V2, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   78 79
  1Q GAIN WILD-TYPE 95 87
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              157               182 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               79                87 
$`1Q GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QB TCGA-D3-A2J8 
       17.03        12.99        16.57        16.67        95.74        65.49 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ 
      115.53        86.76        11.87       171.58        56.19       130.72 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       58.06        60.23        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       45.30        32.94        63.81       125.79       135.75       137.92 
TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      125.19        11.61        58.52       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A3Z1 
       95.24       137.79        29.06       129.63         3.65        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 
       22.29         9.90        25.18        66.25        22.95        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 
      194.83        35.93       107.34        65.92        68.09        10.49 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y 
      215.44        10.16        54.02        17.29        52.01        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20I 
        8.65        94.98        33.73        68.15       133.81        13.55 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M 
       80.61        13.97        63.78        72.07         2.60        56.84 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        55.92       369.93       195.02       102.90        36.82 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
       86.14       314.56       161.03       208.04        48.72        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MD 
       90.97       126.81        55.59        94.82        28.83        47.28 
TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       96.23        47.54        43.23       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J7 
       53.26       122.73        51.62         3.68        23.47        64.08 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19F 
       53.19       109.58        13.94         9.17        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH 
      268.93       162.08        50.89        23.34        16.37        32.05 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
       80.32        33.21         6.77        92.98       174.21       210.08 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       38.27        34.82        48.59       202.65        20.91        27.72 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
      357.37        15.45        32.75        23.93        74.73       133.55 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FD 
       53.16        26.56        27.09        27.02        28.73        77.88 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       11.74        10.13        64.44        32.48        39.58        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS 
       12.62        50.10        59.41        65.88       357.04         6.67 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       63.02       121.08         4.01       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8ZO TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       38.56        59.41        22.68        43.73        30.18        15.16 
TCGA-YG-AA3O 
       36.03 

$`1Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       61.02       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB 
       31.59        90.90        43.43       103.10        23.77       168.00 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP 
       62.07       113.52        42.08        12.10        66.08        59.57 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51E 
       46.98        46.32       166.52        86.93        24.53       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GR 
       55.73        56.35       145.12        22.62        26.89       178.32 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GN TCGA-D3-A8GS 
       18.18        30.84        79.59        15.19       161.00       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV 
      151.53        54.67         6.41        18.12        11.11        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       36.03       117.21       176.55        61.18        53.92        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV 
       28.60        15.68        13.87        17.85        68.25         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
       12.20        29.82        14.70        26.89         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N 
       91.56       168.26        63.35        47.84        64.64        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 
       56.42        37.35        25.87        17.92        46.82        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP 
       59.28        67.43        89.33        54.74        79.66        13.91 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
       14.30        44.88        21.67       129.27        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF 
      203.05       167.90       248.65       124.31        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB 
      138.81       172.18       127.20        36.95        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        51.35       148.08        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J 
       77.75        98.40        48.89        13.02       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
      131.51        61.05        44.05        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3EV 
       79.99        43.82        20.15        31.27       247.04        46.98 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       15.72        15.16         7.00        29.46        94.39       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
      228.59        28.08         7.79        48.85        53.52        40.27 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW 
        9.70        47.38       101.26        11.41       148.80        49.48 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A8LL TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
       62.79        21.37       294.77        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-AA1V TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      212.22        42.08        54.38         8.61        90.28        56.98 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3P TCGA-Z2-A8RT 
       52.34         3.75         2.20        10.36        14.43        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             2.60              0.16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           369.93            294.77 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            53.16             48.89 
[1] "2.6 - 369.9 (53.2)" "0.2 - 294.8 (48.9)"
[1] "hr=" "1"  
D2V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q GAIN MUTATED                   36             4
  1Q GAIN WILD-TYPE                 25             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1Q GAIN MUTATED                                          33
  1Q GAIN WILD-TYPE                                        39
                   vv
clus                REGIONAL LYMPH NODE
  1Q GAIN MUTATED                    88
  1Q GAIN WILD-TYPE                 121
D2V4, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     36                25
  PRIMARY TUMOR                                           4                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              33                39
  REGIONAL LYMPH NODE                                    88               121
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1Q GAIN MUTATED             4       3       9        9       16       15
  1Q GAIN WILD-TYPE           8       4      19        8       11        7
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1Q GAIN MUTATED           5         8         6        17         12
  1Q GAIN WILD-TYPE         9        11         6        18          3
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           17         22        7
  1Q GAIN WILD-TYPE         15         36       12
D2V5, multiclass
             clus
vv            1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  I OR II NOS               4                 8
  STAGE 0                   3                 4
  STAGE I                   9                19
  STAGE IA                  9                 8
  STAGE IB                 16                11
  STAGE II                 15                 7
  STAGE IIA                 5                 9
  STAGE IIB                 8                11
  STAGE IIC                 6                 6
  STAGE III                17                18
  STAGE IIIA               12                 3
  STAGE IIIB               17                15
  STAGE IIIC               22                36
  STAGE IV                  7                12
[1] 14  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                T0+T1 T2 T3 T4
  1Q GAIN MUTATED      30 33 41 30
  1Q GAIN WILD-TYPE    33 38 33 37
D2V6, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              30                33
  T2                 33                38
  T3                 41                33
  T4                 30                37
[1] 4 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                N0 N1 N2 N3
  1Q GAIN MUTATED   81 27 22 18
  1Q GAIN WILD-TYPE 87 34 16 29
D2V7, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              81                87
  N1              27                34
  N2              22                16
  N3              18                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"
                   vv
clus                 M0  M1 M1A M1B M1C
  1Q GAIN MUTATED   146   1   2   0   4
  1Q GAIN WILD-TYPE 160   3   1   4   5
D2V8, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              146               160
  M1                1                 3
  M1A               2                 1
  M1B               0                 4
  M1C               4                 5
[1] 5 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   67 39
  1Q GAIN WILD-TYPE 62 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     67   39
  1Q GAIN WILD-TYPE   62   48
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               67                62
  YES              39                48
[1] 2 2
[1] FALSE
D2V10, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    17 144
  1Q GAIN WILD-TYPE  26 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17  144
  1Q GAIN WILD-TYPE   26  160
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               17                26
  YES             144               160
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    60 102
  1Q GAIN WILD-TYPE  71 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     60  102
  1Q GAIN WILD-TYPE   71  115
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              60                71
  MALE               102               115
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       2                         0   151
  1Q GAIN WILD-TYPE     3                         1   175
D2V13, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 151               175
[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"
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     5 153
  1Q GAIN WILD-TYPE   2 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5  153
  1Q GAIN WILD-TYPE    2  181
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             153               181
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    30  30
  2P GAIN WILD-TYPE 138 135
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               60               273 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               30               135 
$`2P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JN 
       16.47        70.16        22.55        88.50        11.41        56.19 
TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MV TCGA-D3-A5GN 
       64.44        82.29        61.38         6.31        29.23        52.01 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GQ TCGA-D9-A6E9 TCGA-DA-A1HY TCGA-DA-A1I8 
       22.06         4.18        11.44         9.90        51.12        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D 
       17.56        14.83        19.00         9.21         7.99        11.15 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W 
        1.08        39.62         8.09         8.84        30.44        32.15 
TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MR 
       49.22        28.31        33.83        98.27         2.70        60.49 
TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A197 
        5.56        30.15        15.95         0.95        33.60        12.95 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A2NC 
       25.18        11.90       114.15        34.88        42.84        11.80 
TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3I3 
       18.41         8.22        12.89        47.38         8.65         0.20 
TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8ZX TCGA-WE-A8ZY 
       18.05         8.98         2.99        11.84        21.83         5.36 

$`2P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      110.79        28.08        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
        8.38        21.14        68.22        86.76        44.19         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       36.16         6.31        92.42        59.57       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98        46.32        13.32        24.00         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61        25.78       110.24        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       17.72        23.11        29.72        10.22        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
      108.79        38.93        75.65       124.47        87.62         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
       24.07         4.01        21.93         5.72        11.31        13.22 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       14.60        48.79        35.80        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        36.69         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       19.36         7.00        13.15         0.20         0.13        23.15 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
       60.23         4.34        15.85         1.18         9.90        37.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       62.79         8.55        36.85         9.50        12.03         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        2.43         8.09        11.31        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       19.43        16.01        35.54        55.69         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       13.02        34.98        36.33         8.84         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       125.65       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       21.60        53.16        52.67       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        13.81        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35        18.41        21.73 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       31.40        18.61        38.40         5.72        76.41         3.78 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
        3.52        11.11         4.21        13.45        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
        9.57        36.07         6.58        17.72        78.44         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       22.49         1.71         5.62        85.74        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        3.58         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         7.30         3.39        20.38        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.17        30.87        12.92        52.08         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        3.22         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.99         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       11.84        10.65        14.50        14.50        14.50        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.43        11.05         5.79         0.33         0.69       164.19 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       60.03        10.98       185.16        71.01         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        7.10        18.67        21.07        13.12         3.72         3.42 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        1.08        19.96         1.94        12.07         6.18         4.70 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        8.22         6.67         5.98 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.20              0.13 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           114.15            185.16 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            18.23             14.50 
[1] "0.2 - 114.2 (18.2)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.1"
D3V2, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    31  30
  2P GAIN WILD-TYPE 142 136
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               61               278 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               30               136 
$`2P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JN 
       16.57        71.80        31.59       115.53        11.87        56.19 
TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MV TCGA-D3-A5GN 
       66.08       166.52        86.93        13.87        45.30       135.75 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A6E9 TCGA-DA-A1HY 
       79.59        58.52        29.06       151.53         9.90       117.21 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29A 
       53.92       215.44        15.68        54.02       168.26        63.35 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T 
       13.97         2.60        56.84        37.35        14.47       369.93 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 
      195.02       102.90        75.48        90.97       129.27        28.83 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JB TCGA-EE-A3JI 
      134.40        53.26        54.51        23.47       201.80       148.08 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N 
       13.94        98.40        13.02       268.93       152.35        44.05 
TCGA-ER-A2NC TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       43.82        92.98        53.52        23.93       101.26       133.55 
TCGA-FW-A3I3 TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8ZX 
        0.20        18.05        63.02         4.01        24.03        22.68 
TCGA-WE-A8ZY 
       43.73 

$`2P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
       65.49        23.77       168.00        86.76        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10       171.58        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       46.98        46.32        60.23        24.53         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81        26.89       125.79       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        11.61        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR 
      170.20        89.13        95.24       161.00       137.79       129.63 
TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      117.17        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        11.11        25.18        66.25        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        65.92        23.44        68.09        28.60        10.49 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        17.85        68.25        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        6.35        12.20        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      151.27        91.56        13.55        80.61        47.84        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V 
       72.07        64.64        18.61        56.42        55.92        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66       126.81        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        21.67        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        71.21       124.31       122.73        51.62         3.68 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       34.32        53.19        27.35        51.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       35.44        50.76         9.17        77.75        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
       26.37         6.44       131.51        61.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25         8.88       148.18        79.99        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       33.21         6.77       174.21        15.72       210.08        15.16 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        7.00        38.27        34.82        29.46        94.39       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       32.75        47.38        74.73        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88        22.92        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       10.13        64.44        62.79        32.48        39.58        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       12.62        50.10        21.37        59.41        65.88       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
      294.77         6.67         0.33         0.69       212.22       121.08 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       42.08       219.16       105.04        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       90.28        56.98        59.41        52.34         3.75         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       30.18        10.36        15.16        36.03        14.43        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.20              0.16 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           369.93            357.37 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            56.19             48.87 
[1] "0.2 - 369.9 (56.2)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.1"
D3V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P GAIN MUTATED                    9             1
  2P GAIN WILD-TYPE                 52             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2P GAIN MUTATED                                          17
  2P GAIN WILD-TYPE                                        55
                   vv
clus                REGIONAL LYMPH NODE
  2P GAIN MUTATED                    35
  2P GAIN WILD-TYPE                 174
D3V4, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  DISTANT METASTASIS                                      9                52
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              17                55
  REGIONAL LYMPH NODE                                    35               174
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2P GAIN MUTATED             3       2       5        3        5        4
  2P GAIN WILD-TYPE           9       5      23       14       22       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2P GAIN MUTATED           3         1         2         7          4
  2P GAIN WILD-TYPE        11        18        10        28         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED            6         11        1
  2P GAIN WILD-TYPE         26         47       18
D3V5, multiclass
             clus
vv            2P GAIN MUTATED 2P GAIN WILD-TYPE
  I OR II NOS               3                 9
  STAGE 0                   2                 5
  STAGE I                   5                23
  STAGE IA                  3                14
  STAGE IB                  5                22
  STAGE II                  4                18
  STAGE IIA                 3                11
  STAGE IIB                 1                18
  STAGE IIC                 2                10
  STAGE III                 7                28
  STAGE IIIA                4                11
  STAGE IIIB                6                26
  STAGE IIIC               11                47
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  2P GAIN MUTATED       9 17 11 12
  2P GAIN WILD-TYPE    54 54 63 55
D3V6, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1               9                54
  T2                 17                54
  T3                 11                63
  T4                 12                55
[1] 4 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                 N0  N1  N2  N3
  2P GAIN MUTATED    32  12   7   9
  2P GAIN WILD-TYPE 136  49  31  38
D3V7, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              32               136
  N1              12                49
  N2               7                31
  N3               9                38
[1] 4 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                 M0  M1 M1A M1B M1C
  2P GAIN MUTATED    60   1   0   1   0
  2P GAIN WILD-TYPE 246   3   3   3   9
D3V8, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               60               246
  M1                1                 3
  M1A               0                 3
  M1B               1                 3
  M1C               0                 9
[1] 5 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
  2P GAIN MUTATED    20  17
  2P GAIN WILD-TYPE 109  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     20   17
  2P GAIN WILD-TYPE  109   70
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               20               109
  YES              17                70
[1] 2 2
[1] FALSE
D3V10, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     8  55
  2P GAIN WILD-TYPE  35 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8   55
  2P GAIN WILD-TYPE   35  249
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                8                35
  YES              55               249
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    22  41
  2P GAIN WILD-TYPE 109 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     22   41
  2P GAIN WILD-TYPE  109  176
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              22               109
  MALE                41               176
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0    60
  2P GAIN WILD-TYPE     5                         1   266
D3V13, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  60               266
[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"
D3V14, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  61
  2P GAIN WILD-TYPE   7 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   61
  2P GAIN WILD-TYPE    7  273
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              61               273
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    31  27
  2Q GAIN WILD-TYPE 137 138
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               58               275 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               27               138 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       16.47        70.16        22.55        88.50        86.76        11.41 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MV 
       56.19        64.44        82.29        61.38         6.31        29.23 
TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GQ TCGA-D9-A6E9 TCGA-DA-A1HY 
       52.01        22.06         4.18        11.44         9.90        51.12 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A20H 
       25.15        17.56        14.83        19.00        13.35         9.21 
TCGA-EE-A29A TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T 
        7.99         1.08        39.62         8.09         8.84        30.44 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 
       32.15        49.22        28.31        33.83        98.27         2.70 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JB TCGA-EE-A3JI 
       60.49         5.56        30.15        15.95         0.95        33.60 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A2NC TCGA-FR-A3YN 
       25.18        11.90       114.15        42.84        11.80        18.41 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GN-A9SD TCGA-QB-AA9O 
        8.22        47.38        28.73         0.20        14.50        18.05 
TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8ZX 
        8.98         2.99        11.84        21.83 

$`2Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      110.79        28.08        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
        8.38        21.14        68.22        44.19         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
        6.31        92.42        59.57       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       46.32        13.32        24.00         9.34       103.59        26.37 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.61        25.78       110.24        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       23.11        29.72        10.22        15.19       142.45       108.79 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS 
       38.93        75.65       124.47        87.62         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01        21.93         5.72        11.31        13.22        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        35.80        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       44.52        36.69         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN 
        7.00        13.15         0.20         0.13        23.15        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        0.20        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       15.85         1.18         9.90        37.97        11.15        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V 
        8.55        36.85         9.50        12.03         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        35.54        55.69         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       34.98        36.33         8.84         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16        52.67       124.31       122.73        51.62         3.68 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       16.14        22.22        27.35        18.41        21.73        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       18.61        12.95        38.40         5.72        76.41         3.78 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        3.52        11.11        34.88         4.21        13.45        28.60 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        17.72        78.44 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71         5.62        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
        6.71         3.58         5.36        13.28         2.20         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.29        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       15.52         7.33         7.30         3.39        20.38        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        12.89        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
        0.82         5.23        53.85         3.22         7.36        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       10.78         5.98         6.41         2.27         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.81         0.43        11.05         5.79         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      164.19        60.03        10.98       185.16        71.01         5.49 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        6.48         7.10        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.42         5.36         1.08        19.96         1.94        12.07 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         4.70         8.22         6.67         5.98 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.20              0.13 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           114.15            185.16 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           20.415            13.810 
[1] "0.2 - 114.2 (20.4)" "0.1 - 185.2 (13.8)"
[1] "hr=" "1.3"
D4V2, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    31  27
  2Q GAIN WILD-TYPE 142 139
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               58               281 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               27               139 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       16.57        71.80        31.59       115.53        86.76        11.87 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MV 
       56.19        66.08       166.52        86.93        13.87        45.30 
TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GQ TCGA-D9-A6E9 TCGA-DA-A1HY 
      135.75        79.59        58.52        29.06         9.90       117.21 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A20H 
       53.92       215.44        15.68        54.02        17.29       168.26 
TCGA-EE-A29A TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T 
       63.35         2.60        56.84        37.35        14.47       369.93 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 
      195.02       102.90        75.48        90.97       129.27        28.83 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JB TCGA-EE-A3JI 
      134.40        53.26        54.51        23.47       201.80       148.08 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A2NC TCGA-FR-A3YN 
       98.40        13.02       268.93        44.05        43.82        92.98 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GN-A9SD TCGA-QB-AA9O 
       53.52       101.26        28.73         0.20        59.41        18.05 
TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8JZ TCGA-WE-A8ZX 
       63.02         4.01        24.03        22.68 

$`2Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       65.49        23.77       168.00        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       12.10       171.58        59.57       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       46.32        60.23        24.53         9.34       103.59        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       63.81        26.89       125.79       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      125.19        30.84        11.61        15.19       228.99       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13        95.24       161.00       137.79       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        11.11        25.18        66.25        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        65.92        23.44        68.09        28.60        10.49 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.16        17.85        68.25        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       12.20        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       91.56        13.55        80.61        47.84        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V 
       72.07        64.64        18.61        56.42        55.92        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       17.92        46.82        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66       126.81        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        21.67        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        71.21       124.31       122.73        51.62         3.68 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       34.32        53.19        27.35        51.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       35.44        13.94        50.76         9.17        77.75        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       12.59        26.37       152.35         6.44       131.51        61.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21         6.77       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      210.08        15.16         7.00        38.27        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       94.39       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       28.08         7.79        27.72        48.85       357.37        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       15.45         9.70        32.75        47.38        23.93        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
       27.09        27.02        77.82        50.14        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       32.48        39.58        46.36        12.62        50.10        21.37 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       65.88       357.04       294.77         6.67         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      212.22       121.08        42.08       219.16       105.04        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       54.38         8.61        90.28        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.75        43.73         2.20        30.18        10.36        15.16 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        23.64        93.07        11.74 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.20              0.16 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           369.93            357.37 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           56.515            48.850 
[1] "0.2 - 369.9 (56.5)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.2"
D4V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q GAIN MUTATED                    7             1
  2Q GAIN WILD-TYPE                 54             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2Q GAIN MUTATED                                          16
  2Q GAIN WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  2Q GAIN MUTATED                    37
  2Q GAIN WILD-TYPE                 172
D4V4, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      7                54
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              16                56
  REGIONAL LYMPH NODE                                    37               172
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2Q GAIN MUTATED             3       2       5        4        6        3
  2Q GAIN WILD-TYPE           9       5      23       13       21       19
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2Q GAIN MUTATED           2         1         2         9          4
  2Q GAIN WILD-TYPE        12        18        10        26         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED            5         10        1
  2Q GAIN WILD-TYPE         27         48       18
D4V5, multiclass
             clus
vv            2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  I OR II NOS               3                 9
  STAGE 0                   2                 5
  STAGE I                   5                23
  STAGE IA                  4                13
  STAGE IB                  6                21
  STAGE II                  3                19
  STAGE IIA                 2                12
  STAGE IIB                 1                18
  STAGE IIC                 2                10
  STAGE III                 9                26
  STAGE IIIA                4                11
  STAGE IIIB                5                27
  STAGE IIIC               10                48
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  2Q GAIN MUTATED      11 18  9 10
  2Q GAIN WILD-TYPE    52 53 65 57
D4V6, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              11                52
  T2                 18                53
  T3                  9                65
  T4                 10                57
[1] 4 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                 N0  N1  N2  N3
  2Q GAIN MUTATED    31  11   8   8
  2Q GAIN WILD-TYPE 137  50  30  39
D4V7, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              31               137
  N1              11                50
  N2               8                30
  N3               8                39
[1] 4 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                 M0  M1 M1A M1B M1C
  2Q GAIN MUTATED    59   1   0   0   0
  2Q GAIN WILD-TYPE 247   3   3   4   9
D4V8, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               59               247
  M1                1                 3
  M1A               0                 3
  M1B               0                 4
  M1C               0                 9
[1] 5 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
  2Q GAIN MUTATED    20  15
  2Q GAIN WILD-TYPE 109  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     20   15
  2Q GAIN WILD-TYPE  109   72
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               20               109
  YES              15                72
[1] 2 2
[1] FALSE
D4V10, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     9  52
  2Q GAIN WILD-TYPE  34 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9   52
  2Q GAIN WILD-TYPE   34  252
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                9                34
  YES              52               252
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    24  37
  2Q GAIN WILD-TYPE 107 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     24   37
  2Q GAIN WILD-TYPE  107  180
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              24               107
  MALE                37               180
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0    59
  2Q GAIN WILD-TYPE     5                         1   267
D4V13, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  59               267
[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"
D4V14, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  59
  2Q GAIN WILD-TYPE   7 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   59
  2Q GAIN WILD-TYPE    7  275
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              59               275
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    37  22
  3P GAIN WILD-TYPE 131 143
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               59               274 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               22               143 
$`3P GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV 
        8.38        44.19        82.29        61.38       103.59        29.23 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN 
       52.01        13.68        10.22         4.18        75.65       124.47 
TCGA-D3-A8GQ TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG 
       11.44         4.93         7.00        17.56        14.83        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H 
       19.00        13.35         8.12         5.13        60.23         9.21 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GI 
        1.08        39.62         8.84        30.44        32.15        30.08 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AE 
       33.83         5.42         8.84        26.99         5.56        30.15 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19G TCGA-ER-A3ET 
       21.60        22.22        21.73        33.60       114.15         6.58 
TCGA-ER-A3PL TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F2 
        1.71        13.28         4.70        23.80        12.89         3.22 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A8LL TCGA-HR-A2OH TCGA-W3-AA1W TCGA-WE-A8JZ 
       11.61        10.13        14.50        15.81       185.16        11.84 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-Z2-AA3V 
        5.49         7.10         5.36         1.94         5.98 

$`3P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       81.24        10.29        85.32        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.41         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        64.44        59.57       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       46.32        13.32        24.00         6.31         9.34        26.37 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       32.61        25.78       110.24        47.87        17.72        23.11 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       29.72        22.06        15.19       142.45       108.79        38.93 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       87.62         5.56        24.07         4.01        21.93         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        11.31        13.22        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-EB-A44Q 
       36.69        25.15        22.36         6.64        19.36        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.13        13.22         0.20        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
        6.31         1.12         1.35        12.20         4.31         4.34 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       15.85         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       62.79         8.55        36.85         9.50        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         2.43         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       47.21        19.43        16.01        35.54        28.31        55.69 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       25.08        21.60        60.49        53.16        52.67       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62         3.68        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
        3.22        22.92        21.60        16.14         0.95        27.35 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       18.41        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       22.49         5.62        18.41        85.74        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
        3.58         5.36         2.20         3.29        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       11.01        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         0.85        44.28        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       16.24        15.42        12.16        14.70        11.84        10.65 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        14.50         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       10.98        71.01         6.48        18.67        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
        3.72         3.42        21.83         1.08        19.96        12.07 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        6.18         4.70         8.22         6.67 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.08              0.13 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           185.16            164.19 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            13.68             15.22 
[1] "1.1 - 185.2 (13.7)" "0.1 - 164.2 (15.2)"
[1] "hr=" "1.4"
D5V2, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    37  22
  3P GAIN WILD-TYPE 136 144
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               59               280 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               22               144 
$`3P GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV 
       65.49        62.07       166.52        86.93       103.59        45.30 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN 
      135.75       178.32        11.61        58.52        95.24       161.00 
TCGA-D3-A8GQ TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG 
       29.06        65.92        10.49       215.44        15.68        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H 
       54.02        17.29        94.98        68.15       133.81       168.26 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GI 
        2.60        56.84        14.47       369.93       195.02        48.72 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AE 
       90.97        13.91        21.67       248.65        53.26        54.51 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19G TCGA-ER-A3ET 
       36.95        53.19       109.58       148.08       268.93        80.32 
TCGA-ER-A3PL TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F2 
       33.21        38.27        29.46       202.65        23.93        50.14 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A8LL TCGA-HR-A2OH TCGA-W3-AA1W TCGA-WE-A8JZ 
       11.74        10.13        21.37        65.88       219.16        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-Z2-AA3V 
       38.56         8.61        43.73        10.36        11.74 

$`3P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74        43.43       103.10        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       86.76        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       46.32        60.23        24.53        13.87         9.34        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       63.81        26.89       125.79       137.92        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       30.84        79.59        15.19       228.99       170.20        89.13 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      137.79       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        6.41        18.12        11.34        22.29        11.11         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A44R 
       53.92        23.44        68.09        28.60        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       17.85        52.01         6.35        12.20        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
        8.65        33.73        14.70        26.89         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        72.07        64.64        18.61        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       55.92        25.87        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
      208.04        89.33        54.74        79.66        75.48       126.81 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       47.54        43.23       134.40       162.48        71.21       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62         3.68        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      172.18       127.20        64.08        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       51.35        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98         6.77        92.98       174.21        15.72       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       15.16         7.00        34.82        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       64.44        62.79        32.48        39.58        46.36        12.62 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       50.10        59.41       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       42.08       105.04        54.38        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       52.34         3.75        22.68         2.20        30.18        15.16 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       36.03        14.43        23.64        93.07 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2.60              0.16 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           369.93            357.37 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            54.51             48.89 
[1] "2.6 - 369.9 (54.5)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.6"
D5V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P GAIN MUTATED                   15             0
  3P GAIN WILD-TYPE                 46             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3P GAIN MUTATED                                          14
  3P GAIN WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  3P GAIN MUTATED                    33
  3P GAIN WILD-TYPE                 176
D5V4, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  DISTANT METASTASIS                                     15                46
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              14                58
  REGIONAL LYMPH NODE                                    33               176
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3P GAIN MUTATED             4       1       5        7        6        4
  3P GAIN WILD-TYPE           8       6      23       10       21       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3P GAIN MUTATED           2         1         4         6          1
  3P GAIN WILD-TYPE        12        18         8        29         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED            9          6        1
  3P GAIN WILD-TYPE         23         52       18
D5V5, multiclass
             clus
vv            3P GAIN MUTATED 3P GAIN WILD-TYPE
  I OR II NOS               4                 8
  STAGE 0                   1                 6
  STAGE I                   5                23
  STAGE IA                  7                10
  STAGE IB                  6                21
  STAGE II                  4                18
  STAGE IIA                 2                12
  STAGE IIB                 1                18
  STAGE IIC                 4                 8
  STAGE III                 6                29
  STAGE IIIA                1                14
  STAGE IIIB                9                23
  STAGE IIIC                6                52
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  3P GAIN MUTATED      12 16 10 13
  3P GAIN WILD-TYPE    51 55 64 54
D5V6, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1              12                51
  T2                 16                55
  T3                 10                64
  T4                 13                54
[1] 4 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                 N0  N1  N2  N3
  3P GAIN MUTATED    36  10   5   4
  3P GAIN WILD-TYPE 132  51  33  43
D5V7, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              36               132
  N1              10                51
  N2               5                33
  N3               4                43
[1] 4 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                 M0  M1 M1A M1B M1C
  3P GAIN MUTATED    57   0   1   0   0
  3P GAIN WILD-TYPE 249   4   2   4   9
D5V8, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               57               249
  M1                0                 4
  M1A               1                 2
  M1B               0                 4
  M1C               0                 9
[1] 5 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
  3P GAIN MUTATED    22  17
  3P GAIN WILD-TYPE 107  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     22   17
  3P GAIN WILD-TYPE  107   70
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               22               107
  YES              17                70
[1] 2 2
[1] FALSE
D5V10, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     5  57
  3P GAIN WILD-TYPE  38 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5   57
  3P GAIN WILD-TYPE   38  247
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                5                38
  YES              57               247
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    27  35
  3P GAIN WILD-TYPE 104 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     27   35
  3P GAIN WILD-TYPE  104  182
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              27               104
  MALE                35               182
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0    57
  3P GAIN WILD-TYPE     5                         1   269
D5V13, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  57               269
[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"
D5V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  59
  3P GAIN WILD-TYPE   7 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   59
  3P GAIN WILD-TYPE    7  275
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              59               275
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    42  26
  3Q GAIN WILD-TYPE 126 139
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               68               265 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               26               139 
$`3Q GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB 
        8.38        88.50        44.19        92.42        56.19        82.29 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GI 
      103.59        29.23        52.01        13.68        10.22         4.18 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A6EC TCGA-DA-A1IA TCGA-DA-A3F3 
       75.65       124.47        11.44        13.22         4.93         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A182 
       17.56        14.83        23.15        13.35         8.12         1.35 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29R 
        5.13        60.23        15.85         9.21        39.62         8.84 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 
       30.44        32.15        30.08        33.83         5.42         8.84 
TCGA-EE-A2M6 TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE 
       98.27       111.91        26.99         5.56       124.31        30.15 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A19G TCGA-ER-A19M 
       21.60        21.60        22.22        21.73       114.15        28.60 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 
        1.87         6.58         1.71        13.28         4.70        23.80 
TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A26A TCGA-HR-A2OH 
       12.89         3.22        11.61        10.13        12.16        15.81 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZY 
        2.99       185.16        11.84         5.49         7.10         5.36 
TCGA-WE-AAA3 TCGA-Z2-AA3V 
        1.94         5.98 

$`3Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       81.24        10.29        85.32        21.14        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP 
       11.41         7.50        36.16         6.31        64.44        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        15.25        46.98        46.32        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.00         6.31         9.34        26.37        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      110.24        47.87        17.72        23.11        29.72        22.06 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
       15.19       142.45       108.79        38.93        87.62         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       24.07         4.01        21.93         5.72         9.90        11.31 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       14.60        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       13.68         9.99        44.52        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
        6.64        19.36        13.15         0.20         0.13        19.00 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
       13.22         0.20        11.57        10.55         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       12.20         4.31         4.34         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        62.79         8.55        36.85         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        9.50        12.03         8.09         9.99         2.43         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       35.54        28.31        55.69         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       36.33         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        21.60        60.49        53.16        52.67 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62         3.68        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
        3.22        22.92        16.14         0.95        27.35        18.41 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       34.88         4.21        13.45        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       36.07         6.58        17.72        78.44        11.80         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K 
       13.08        12.62        11.74         9.04        22.49         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74        15.72         6.71         3.58         5.36 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
        2.20         3.29        64.47         3.45        11.01        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       19.53        11.08         7.17        30.87        12.92        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        0.85        44.28        31.33        84.72        16.24        15.42 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       14.70        11.84        10.65        14.50        14.50        14.50 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
        0.43        11.05         5.79        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 
      164.19         8.98        60.03        10.98        71.01         6.48 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       18.67        21.07        13.12         3.72         3.42        21.83 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
        1.08        19.96        12.07         6.18         4.70         8.22 
TCGA-Z2-AA3S 
        6.67 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1.35              0.13 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           185.16            164.19 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           14.255            14.700 
[1] "1.4 - 185.2 (14.3)" "0.1 - 164.2 (14.7)"
[1] "hr=" "1.5"
D6V2, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    42  26
  3Q GAIN WILD-TYPE 131 140
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               68               271 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               26               140 
$`3Q GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB 
       65.49       115.53        62.07       171.58        56.19       166.52 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GD TCGA-D3-A8GI 
      103.59        45.30       135.75       178.32        11.61        58.52 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A6EC TCGA-DA-A1IA TCGA-DA-A3F3 
       95.24       161.00        29.06        66.25        65.92        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A182 
      215.44        15.68        68.25        17.29        94.98        14.70 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29R 
       68.15       133.81        91.56       168.26        56.84        14.47 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 
      369.93       195.02        48.72        90.97        13.91        21.67 
TCGA-EE-A2M6 TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE 
      129.27       203.05       248.65        53.26       124.31        54.51 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A19G TCGA-ER-A19M 
       36.95        64.08        53.19       109.58       268.93        61.05 
TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1Z0 
       23.34        80.32        33.21        38.27        29.46       202.65 
TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A26A TCGA-HR-A2OH 
       23.93        50.14        11.74        10.13        32.48        65.88 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZY 
        4.01       219.16        24.03        38.56         8.61        43.73 
TCGA-WE-AAA3 TCGA-Z2-AA3V 
       10.36        11.74 

$`3Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       95.74        43.43       103.10        23.77       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP 
       11.87       113.52        42.08        12.10        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        58.06        46.98        46.32        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53        13.87         9.34        39.75       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      125.79       137.92        18.18       125.19        30.84        79.59 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR 
       15.19       228.99       170.20        89.13       137.79       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       11.34        22.29        11.11         9.90        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       107.34        61.18        53.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN 
       28.60        13.87        10.16        17.85        54.02        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        6.35        12.20        29.82        27.22         8.65        33.73 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       26.89         4.96       151.27        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        63.78        72.07        64.64         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       18.61        56.42        37.35        55.92        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       161.03       208.04        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48       126.81        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       94.82        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54        43.23       134.40       162.48        71.21 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62         3.68        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
      172.18       127.20        34.32       201.80        27.35        51.35 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44       131.51        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       37.25         8.88       148.18        79.99        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K 
       16.37        31.27        32.05       247.04        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
       34.82        94.39       216.92        48.59       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       40.27        15.45         9.70        32.75        47.38       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        2.04       139.89       117.93        84.72        64.44        62.79 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       39.58        46.36        12.62        50.10        21.37        59.41 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      357.04       294.77         6.67        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K5 
      212.22        63.02       121.08        42.08       105.04        54.38 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       90.28        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
        2.20        30.18        15.16        36.03        14.43        23.64 
TCGA-Z2-AA3S 
       93.07 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             4.01              0.16 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           369.93            357.37 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           59.785            48.590 
[1] "4.0 - 369.9 (59.8)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.7"
D6V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q GAIN MUTATED                   17             1
  3Q GAIN WILD-TYPE                 44             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3Q GAIN MUTATED                                          16
  3Q GAIN WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  3Q GAIN MUTATED                    37
  3Q GAIN WILD-TYPE                 172
D6V4, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     17                44
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              16                56
  REGIONAL LYMPH NODE                                    37               172
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3Q GAIN MUTATED             5       1       7        7        7        5
  3Q GAIN WILD-TYPE           7       6      21       10       20       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3Q GAIN MUTATED           2         1         2         8          4
  3Q GAIN WILD-TYPE        12        18        10        27         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED            9          7        1
  3Q GAIN WILD-TYPE         23         51       18
D6V5, multiclass
             clus
vv            3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  I OR II NOS               5                 7
  STAGE 0                   1                 6
  STAGE I                   7                21
  STAGE IA                  7                10
  STAGE IB                  7                20
  STAGE II                  5                17
  STAGE IIA                 2                12
  STAGE IIB                 1                18
  STAGE IIC                 2                10
  STAGE III                 8                27
  STAGE IIIA                4                11
  STAGE IIIB                9                23
  STAGE IIIC                7                51
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  3Q GAIN MUTATED      17 18 13 10
  3Q GAIN WILD-TYPE    46 53 61 57
D6V6, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              17                46
  T2                 18                53
  T3                 13                61
  T4                 10                57
[1] 4 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                 N0  N1  N2  N3
  3Q GAIN MUTATED    39  15   7   4
  3Q GAIN WILD-TYPE 129  46  31  43
D6V7, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              39               129
  N1              15                46
  N2               7                31
  N3               4                43
[1] 4 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                 M0  M1 M1A M1B M1C
  3Q GAIN MUTATED    66   0   1   0   0
  3Q GAIN WILD-TYPE 240   4   2   4   9
D6V8, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               66               240
  M1                0                 4
  M1A               1                 2
  M1B               0                 4
  M1C               0                 9
[1] 5 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
  3Q GAIN MUTATED    28  15
  3Q GAIN WILD-TYPE 101  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     28   15
  3Q GAIN WILD-TYPE  101   72
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               28               101
  YES              15                72
[1] 2 2
[1] FALSE
D6V10, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     8  63
  3Q GAIN WILD-TYPE  35 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8   63
  3Q GAIN WILD-TYPE   35  241
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                8                35
  YES              63               241
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    30  41
  3Q GAIN WILD-TYPE 101 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     30   41
  3Q GAIN WILD-TYPE  101  176
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              30               101
  MALE                41               176
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         0    66
  3Q GAIN WILD-TYPE     5                         1   260
D6V13, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  66               260
[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"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     0  68
  3Q GAIN WILD-TYPE   7 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   68
  3Q GAIN WILD-TYPE    7  266
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              68               266
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    28  24
  4P GAIN WILD-TYPE 140 141
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               52               281 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               24               141 
$`4P GAIN MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MU 
        6.97         8.52        15.25        46.98        13.32        26.37 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A6EA TCGA-DA-A1HV 
       23.11        29.72        87.62        24.07        11.31        48.79 
TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 
       39.19        22.36        17.56        19.00         0.20         5.13 
TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GP 
       15.85         8.55        12.03        51.12        30.08         5.42 
TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
       63.42        26.99       124.31         3.22        21.60        22.22 
TCGA-EE-A3JB TCGA-ER-A19H TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC 
        0.95        34.88         6.58         1.71        18.41         2.20 
TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU 
        3.45        12.92        12.89        47.38         8.65         8.68 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
        3.22        28.73         7.23        31.33        15.42        14.70 
TCGA-GN-A8LK TCGA-QB-AA9O TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       14.50        18.05        21.07         3.72 

$`4P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97        16.47       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.79        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        44.19         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        64.44        59.57       114.67        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
       61.38        24.00         6.31         9.34       103.59        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.61        25.78       110.24        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       17.72        22.06        10.22        15.19         4.18       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      108.79        38.93        75.65       124.47        11.44         5.56 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01        21.93         5.72         9.90        13.22        14.60 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        10.03        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15         4.93         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL 
       14.83        13.15         0.20         0.13        23.15        13.35 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22        11.57        10.55         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H 
        1.35        12.20         4.31        60.23         4.34         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        62.79 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       36.85         1.08        39.62         9.50         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       60.00        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83        55.69         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       29.46         2.73        44.25         7.96        14.56       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      111.91        56.02        25.08        21.60        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67         5.56       122.73        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        15.95        12.72        22.92        21.60        16.14 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.90        11.11       114.15         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       28.60        42.84        34.68         9.57        36.07         6.58 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A 
       12.62        11.74         9.04        22.49         5.62        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
       15.72         6.71         3.58         5.36        13.28         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        3.29        64.47        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       11.08         7.17        30.87        52.08         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       40.64        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
        0.99         0.13         0.16        17.33         9.90         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       11.61        44.28        84.72        10.13        16.24        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       11.84        10.65        14.50        14.50        15.81         0.43 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       11.05         5.79         0.33         0.69       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       60.03         2.99        10.98       185.16        71.01        11.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZT 
        5.49         6.48         7.10        18.67        13.12         3.42 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       21.83         5.36         1.08        19.96         1.94        12.07 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         4.70         8.22         6.67         5.98 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.20              0.13 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           124.31            185.16 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           15.635            14.500 
[1] "0.2 - 124.3 (15.6)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1"  
D7V2, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    28  24
  4P GAIN WILD-TYPE 145 142
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               52               287 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               24               142 
$`4P GAIN MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MU 
       61.02        16.67        58.06        46.98        60.23        39.75 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A6EA TCGA-DA-A1HV 
      125.19        30.84       137.79       117.17        25.18        48.89 
TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 
      194.83        23.44       215.44        54.02        12.20        68.15 
TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GP 
       91.56        72.07        56.42        59.28        48.72        13.91 
TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
       96.23       248.65       124.31       172.18        64.08        53.19 
TCGA-EE-A3JB TCGA-ER-A19H TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC 
      201.80       152.35        80.32        33.21        92.98        34.82 
TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZU 
       48.59        47.38        23.93       101.26       133.55        26.56 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
       50.14        28.73         7.23       117.93        62.79        39.58 
TCGA-GN-A8LK TCGA-QB-AA9O TCGA-WE-A8ZN TCGA-WE-A8ZQ 
       50.10        18.05        56.98        52.34 

$`4P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        12.99        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        66.08        59.57       130.72        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
       86.93        24.53        13.87         9.34       103.59        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       18.18        79.59        11.61        15.19        58.52       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13        95.24       161.00        29.06       129.63 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       22.29        11.11         9.90        66.25        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       53.92        65.92        68.09        28.60        10.49        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        17.85        68.25        17.29        52.01 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        6.35        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H 
       14.70        26.89         4.96       133.81       151.27       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        63.78 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       64.64         2.60        56.84        18.61        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       55.92       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        36.82        39.29        86.14        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      161.03       208.04        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97       126.81        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
      103.27       268.73       103.20        16.96       204.66       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      203.05       167.90        47.54        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21        53.26       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        23.47       138.81       127.20        36.95        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02        26.37       268.93         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A 
       31.27        32.05       247.04        46.98         6.77       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
       15.72       210.08        15.16         7.00        38.27        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       94.39       216.92       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       15.45         9.70        32.75        74.73        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       53.16        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       22.92        47.54         0.16        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       11.74       139.89        84.72        10.13        64.44        32.48 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       46.36        12.62        21.37        59.41        65.88       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
      294.77         6.67         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      121.08         4.01        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZO TCGA-WE-A8ZT 
       38.56        54.38         8.61        90.28        59.41         3.75 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       22.68        43.73         2.20        30.18        10.36        15.16 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        23.64        93.07        11.74 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             7.23              0.16 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           248.65            369.93 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            56.70             47.84 
[1] "7.2 - 248.7 (56.7)" "0.2 - 369.9 (47.8)"
[1] "hr=" "1.2"
D7V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P GAIN MUTATED                   10             1
  4P GAIN WILD-TYPE                 51             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4P GAIN MUTATED                                          14
  4P GAIN WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  4P GAIN MUTATED                    29
  4P GAIN WILD-TYPE                 180
D7V4, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  DISTANT METASTASIS                                     10                51
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              14                58
  REGIONAL LYMPH NODE                                    29               180
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4P GAIN MUTATED             2       0       6        1        8        1
  4P GAIN WILD-TYPE          10       7      22       16       19       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4P GAIN MUTATED           2         3         5         8          3
  4P GAIN WILD-TYPE        12        16         7        27         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED            4          7        1
  4P GAIN WILD-TYPE         28         51       18
D7V5, multiclass
             clus
vv            4P GAIN MUTATED 4P GAIN WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   0                 7
  STAGE I                   6                22
  STAGE IA                  1                16
  STAGE IB                  8                19
  STAGE II                  1                21
  STAGE IIA                 2                12
  STAGE IIB                 3                16
  STAGE IIC                 5                 7
  STAGE III                 8                27
  STAGE IIIA                3                12
  STAGE IIIB                4                28
  STAGE IIIC                7                51
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  4P GAIN MUTATED      12 16  7 13
  4P GAIN WILD-TYPE    51 55 67 54
D7V6, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1              12                51
  T2                 16                55
  T3                  7                67
  T4                 13                54
[1] 4 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                 N0  N1  N2  N3
  4P GAIN MUTATED    29   7   7   6
  4P GAIN WILD-TYPE 139  54  31  41
D7V7, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              29               139
  N1               7                54
  N2               7                31
  N3               6                41
[1] 4 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                 M0  M1 M1A M1B M1C
  4P GAIN MUTATED    49   0   1   0   0
  4P GAIN WILD-TYPE 257   4   2   4   9
D7V8, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               49               257
  M1                0                 4
  M1A               1                 2
  M1B               0                 4
  M1C               0                 9
[1] 5 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
  4P GAIN MUTATED    20  14
  4P GAIN WILD-TYPE 109  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     20   14
  4P GAIN WILD-TYPE  109   73
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               20               109
  YES              14                73
[1] 2 2
[1] FALSE
D7V10, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     7  47
  4P GAIN WILD-TYPE  36 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      7   47
  4P GAIN WILD-TYPE   36  257
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                7                36
  YES              47               257
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    20  34
  4P GAIN WILD-TYPE 111 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     20   34
  4P GAIN WILD-TYPE  111  183
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              20               111
  MALE                34               183
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         0    51
  4P GAIN WILD-TYPE     4                         1   275
D7V13, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  51               275
[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"
D7V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  53
  4P GAIN WILD-TYPE   6 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   53
  4P GAIN WILD-TYPE    6  281
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              53               281
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    23  21
  4Q GAIN WILD-TYPE 145 144
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               44               289 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               144 
$`4Q GAIN MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP 
       15.25        13.32        26.37        23.11        29.72        87.62 
TCGA-D3-A8GS TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 
       24.07        11.31        48.79        39.19        22.36        17.56 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G 
       19.00         0.20         5.13        15.85        11.15         8.55 
TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MR 
       12.03        51.12         5.42        63.42        26.99        60.49 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-ER-A19H 
        3.68         3.22        21.60        22.22         0.95        34.88 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        1.71        18.41         2.20         3.45        47.38         8.65 
TCGA-FS-A1ZU TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
        8.68        28.73         7.23        31.33        15.42        14.70 
TCGA-GN-A9SD TCGA-WE-A8ZQ 
       14.50         3.72 

$`4Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        86.76        11.41        44.19         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        59.57       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32        82.29        61.38        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.31        32.28        21.44        32.61        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD 
       52.01        47.87        13.68        17.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19         4.18       142.45       108.79        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      124.47        11.44         5.56         4.01        21.93         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        13.22        14.60        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
        6.64        19.36         7.00        14.83        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y 
        0.13        23.15        13.35        13.22        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
        6.31         8.12         1.12         1.35        12.20         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       60.23         4.34         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97        62.79        36.85         1.08        39.62         9.50 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        8.09         8.84         9.99        30.44         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83        55.69         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       125.65       111.91        56.02        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       51.62        30.15        13.81        15.95        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        16.14        27.35        18.41        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       22.49         5.62        85.74        15.72         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
        5.36        13.28         4.70         3.29        64.47        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.92        12.89        52.08         8.81        49.15        40.64 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       27.39         0.82         5.23        53.85         3.22         7.36 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
        0.99         0.13         0.16        17.33         9.90         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       11.61        44.28        84.72        10.13        16.24        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB 
       11.84        10.65        14.50        14.50        15.81         0.43 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       11.05         5.79        18.05         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        8.98        60.03         2.99        10.98       185.16        71.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       11.84         5.49         6.48         7.10        18.67        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       13.12         3.42        21.83         5.36         1.08        19.96 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        1.94        12.07         6.18         4.70         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.20              0.13 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            87.62            185.16 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           15.635            14.500 
[1] "0.2 - 87.6 (15.6)"  "0.1 - 185.2 (14.5)"
[1] "hr=" "1"  
D8V2, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    23  21
  4Q GAIN WILD-TYPE 150 145
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               44               295 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               145 
$`4Q GAIN MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP 
       58.06        60.23        39.75       125.19        30.84       137.79 
TCGA-D3-A8GS TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 
      117.17        25.18        48.89       194.83        23.44       215.44 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29G 
       54.02        12.20        68.15        91.56        13.97        72.07 
TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A2MR 
       56.42        59.28        13.91        96.23       248.65       134.40 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-ER-A19H 
        3.68       172.18        64.08        53.19       201.80       152.35 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       33.21        92.98        34.82        48.59       101.26       133.55 
TCGA-FS-A1ZU TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
       26.56        28.73         7.23       117.93        62.79        39.58 
TCGA-GN-A9SD TCGA-WE-A8ZQ 
       59.41        52.34 

$`4Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        86.76        11.87        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        59.57       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32       166.52        86.93        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GD 
      135.75       137.92       178.32        18.18        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19        58.52       228.99       170.20        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      161.00        29.06       129.63       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        6.41        18.12        11.34        22.29        11.11         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       66.25        22.95        36.03       117.21        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
       35.93       107.34        61.18        53.92        65.92        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       28.60        10.49        15.68        13.87        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y 
       68.25        17.29        52.01         6.35        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
        8.65        94.98        33.73        14.70        26.89         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      133.81       151.27       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       47.84        63.78        64.64         2.60        56.84        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       37.35        14.47        55.92       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       54.74        79.66        75.48        90.97       126.81        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66       158.63       203.05       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       51.62        54.51        13.81        23.47       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       36.95        34.32        27.35        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       46.98         6.77       174.21        15.72       210.08        15.16 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
        7.00        38.27        29.46        94.39       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        23.93        74.73        11.41       148.80        53.16 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       22.92        47.54         0.16        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       11.74       139.89        84.72        10.13        64.44        32.48 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB 
       46.36        12.62        50.10        21.37        65.88       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      294.77         6.67        18.05         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
       63.02       121.08         4.01        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        38.56        54.38         8.61        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       59.41         3.75        22.68        43.73         2.20        30.18 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       10.36        15.16        36.03        14.43        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3.68              0.16 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           248.65            369.93 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           59.345            48.720 
[1] "3.7 - 248.7 (59.3)" "0.2 - 369.9 (48.7)"
[1] "hr=" "1.2"
D8V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q GAIN MUTATED                    7             1
  4Q GAIN WILD-TYPE                 54             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4Q GAIN MUTATED                                          11
  4Q GAIN WILD-TYPE                                        61
                   vv
clus                REGIONAL LYMPH NODE
  4Q GAIN MUTATED                    27
  4Q GAIN WILD-TYPE                 182
D8V4, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      7                54
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              11                61
  REGIONAL LYMPH NODE                                    27               182
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4Q GAIN MUTATED             2       0       6        1        7        0
  4Q GAIN WILD-TYPE          10       7      22       16       20       22
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4Q GAIN MUTATED           1         2         3         7          2
  4Q GAIN WILD-TYPE        13        17         9        28         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED            4          7        1
  4Q GAIN WILD-TYPE         28         51       18
D8V5, multiclass
             clus
vv            4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   0                 7
  STAGE I                   6                22
  STAGE IA                  1                16
  STAGE IB                  7                20
  STAGE II                  0                22
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 3                 9
  STAGE III                 7                28
  STAGE IIIA                2                13
  STAGE IIIB                4                28
  STAGE IIIC                7                51
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  4Q GAIN MUTATED      10 15  7  9
  4Q GAIN WILD-TYPE    53 56 67 58
D8V6, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1              10                53
  T2                 15                56
  T3                  7                67
  T4                  9                58
[1] 4 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                 N0  N1  N2  N3
  4Q GAIN MUTATED    25   7   6   5
  4Q GAIN WILD-TYPE 143  54  32  42
D8V7, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              25               143
  N1               7                54
  N2               6                32
  N3               5                42
[1] 4 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                 M0  M1 M1A M1B M1C
  4Q GAIN MUTATED    42   0   1   0   0
  4Q GAIN WILD-TYPE 264   4   2   4   9
D8V8, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               42               264
  M1                0                 4
  M1A               1                 2
  M1B               0                 4
  M1C               0                 9
[1] 5 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
  4Q GAIN MUTATED    18  12
  4Q GAIN WILD-TYPE 111  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     18   12
  4Q GAIN WILD-TYPE  111   75
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               18               111
  YES              12                75
[1] 2 2
[1] FALSE
D8V10, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5  41
  4Q GAIN WILD-TYPE  38 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5   41
  4Q GAIN WILD-TYPE   38  263
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                5                38
  YES              41               263
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    17  29
  4Q GAIN WILD-TYPE 114 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     17   29
  4Q GAIN WILD-TYPE  114  188
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              17               114
  MALE                29               188
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         0    44
  4Q GAIN WILD-TYPE     4                         1   282
D8V13, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  44               282
[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"
D8V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  45
  4Q GAIN WILD-TYPE   6 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   45
  4Q GAIN WILD-TYPE    6  289
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              45               289
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    38  32
  5P GAIN WILD-TYPE 130 133
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               70               263 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               32               133 
$`5P GAIN MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JN 
        3.02         8.52        32.42        44.19         6.31        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51N TCGA-D3-A5GN 
       59.57        15.25        26.37        93.21        21.44        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A6E9 
       13.68        17.72        23.11         4.18        75.65         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-EB-A44R TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B 
       11.31        13.22         0.20         8.12         1.12        60.23 
TCGA-EE-A20H TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2M6 
        9.21        30.44        32.15        11.31        28.31        98.27 
TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE 
        2.70        26.99        53.16       124.31       122.73        30.15 
TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G 
        3.22        22.22        33.60        25.18         3.78       114.15 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3PL 
       28.60        42.84        34.68         6.58         1.87         1.71 
TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX 
       85.74         5.36         2.20         4.70         3.29         3.45 
TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-FW-A3TU 
       19.53        12.89         8.65        28.73         0.20         0.13 
TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U9 TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1V 
        7.23        84.72        10.65        18.05         2.99        10.98 
TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-YG-AA3P TCGA-Z2-A8RT 
       11.84         3.72         4.70         8.22 

$`5P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        6.97         6.97        16.47       111.09        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        86.76        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 
        7.50        36.16        92.42        64.44       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32        82.29        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34       103.59        29.23        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GB 
       32.28        32.61        25.78       110.24        47.87        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       22.06        10.22        15.19       142.45       108.79        38.93 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      124.47        87.62        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       21.93         5.72        14.60        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.13        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        1.35        12.20         5.13         4.31         4.34        15.85 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        8.09         8.84         9.99         2.43         8.09        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       60.00        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        55.69         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       36.33         8.84         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      111.91        56.02        25.08        21.60        60.49        52.67 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
        5.56        51.62         3.68        13.81        15.95        12.72 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       18.41        21.73        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
        5.72        76.41         3.52        11.90        11.11        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
        4.21        13.45         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       11.80         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 
        6.58        22.49         5.62        18.41        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.58        13.28        64.47        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         3.22         7.36        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
        5.98         6.41         2.27         0.99         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        9.90         0.85        11.61        44.28        31.33        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK 
       16.24        15.42        12.16        14.70        11.84        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1W 
        0.33         0.69       164.19         8.98        60.03       185.16 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       71.01         5.49         6.48         7.10        18.67        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       13.12         3.42        21.83         5.36         1.08        19.96 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94        12.07         6.18         6.67         5.98 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.13              0.13 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           124.31            185.16 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            13.45             14.83 
[1] "0.1 - 124.3 (13.4)" "0.1 - 185.2 (14.8)"
[1] "hr=" "1.1"
D9V2, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    40  32
  5P GAIN WILD-TYPE 133 134
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               72               267 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               32               134 
$`5P GAIN MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JN 
       17.03        16.67       112.57        62.07        12.10        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51N TCGA-D3-A5GN 
       59.57        58.06        39.75       174.84        22.62       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A148 
      178.32        18.18       125.19        58.52        95.24       151.53 
TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-EB-A44R TCGA-EE-A180 
        3.65         9.90        25.18        66.25        10.16        94.98 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
       33.73       133.81       168.26       369.93       195.02        46.82 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA 
       75.48       129.27        28.83       248.65       162.48       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19B 
      122.73        54.51       172.18        53.19       148.08        98.40 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T 
       48.89       268.93        61.05        44.05       162.08         8.88 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD 
       23.34        33.21       174.21         7.00        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A4F5 
       94.39        48.59        40.27        23.93       133.55        28.73 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U9 TCGA-QB-AA9O 
        0.20        47.54         7.23        84.72        12.62        18.05 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-YG-AA3P TCGA-Z2-A8RT 
        4.01        42.08        24.03        52.34        14.43        23.64 

$`5P GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       61.02        12.99        16.57       112.04        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 
      113.52        42.08       171.58        66.08       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34       103.59        45.30        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GB 
       32.94        63.81        26.89       125.79       137.92        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        11.61        15.19       228.99       170.20        89.13 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 
      161.00       137.79        29.06       129.63       117.17        54.67 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG 
        6.41        18.12        11.34        22.29        11.11        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       17.85        68.25        54.02        17.29        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       12.20        29.82        27.22         8.65        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       68.15         4.96       151.27        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       55.92        25.87        17.92       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        89.33        54.74        79.66        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC 
       47.54        43.23       134.40        71.21        53.26        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        13.81        23.47       138.81       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32       201.80        27.35        51.35       109.58 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02        26.37       152.35         6.44       131.51 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       50.89        37.25       148.18        79.99        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
        6.77        92.98        15.72       210.08        15.16        38.27 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        53.52        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       32.75        47.38       101.26        74.73        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       77.88        22.92         0.16        19.30         9.90         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       11.74       139.89       117.93        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       32.48        39.58        46.36        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       65.88       357.04       294.77         6.67         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      212.22        63.02       121.08       219.16       105.04        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       54.38         8.61        90.28        56.98        59.41         3.75 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       22.68        43.73         2.20        30.18        10.36        15.16 
TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        93.07        11.74 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.20              0.16 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           369.93            357.37 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           52.765            50.100 
[1] "0.2 - 369.9 (52.8)" "0.2 - 357.4 (50.1)"
[1] "hr=" "1.3"
D9V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P GAIN MUTATED                   13             4
  5P GAIN WILD-TYPE                 48             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5P GAIN MUTATED                                          10
  5P GAIN WILD-TYPE                                        62
                   vv
clus                REGIONAL LYMPH NODE
  5P GAIN MUTATED                    48
  5P GAIN WILD-TYPE                 161
D9V4, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  DISTANT METASTASIS                                     13                48
  PRIMARY TUMOR                                           4                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              10                62
  REGIONAL LYMPH NODE                                    48               161
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5P GAIN MUTATED             4       2       7        5        6        7
  5P GAIN WILD-TYPE           8       5      21       12       21       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5P GAIN MUTATED           2         4         4         6          3
  5P GAIN WILD-TYPE        12        15         8        29         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED            3          8        5
  5P GAIN WILD-TYPE         29         50       14
D9V5, multiclass
             clus
vv            5P GAIN MUTATED 5P GAIN WILD-TYPE
  I OR II NOS               4                 8
  STAGE 0                   2                 5
  STAGE I                   7                21
  STAGE IA                  5                12
  STAGE IB                  6                21
  STAGE II                  7                15
  STAGE IIA                 2                12
  STAGE IIB                 4                15
  STAGE IIC                 4                 8
  STAGE III                 6                29
  STAGE IIIA                3                12
  STAGE IIIB                3                29
  STAGE IIIC                8                50
  STAGE IV                  5                14
[1] 14  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                T0+T1 T2 T3 T4
  5P GAIN MUTATED      18 13 17 12
  5P GAIN WILD-TYPE    45 58 57 55
D9V6, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              18                45
  T2                 13                58
  T3                 17                57
  T4                 12                55
[1] 4 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                 N0  N1  N2  N3
  5P GAIN MUTATED    45   7   7  10
  5P GAIN WILD-TYPE 123  54  31  37
D9V7, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              45               123
  N1               7                54
  N2               7                31
  N3              10                37
[1] 4 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                 M0  M1 M1A M1B M1C
  5P GAIN MUTATED    66   1   2   1   2
  5P GAIN WILD-TYPE 240   3   1   3   7
D9V8, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               66               240
  M1                1                 3
  M1A               2                 1
  M1B               1                 3
  M1C               2                 7
[1] 5 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
  5P GAIN MUTATED   31 12
  5P GAIN WILD-TYPE 98 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     31   12
  5P GAIN WILD-TYPE   98   75
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               31                98
  YES              12                75
[1] 2 2
[1] FALSE
D9V10, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    11  64
  5P GAIN WILD-TYPE  32 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11   64
  5P GAIN WILD-TYPE   32  240
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               11                32
  YES              64               240
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    29  46
  5P GAIN WILD-TYPE 102 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     29   46
  5P GAIN WILD-TYPE  102  171
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              29               102
  MALE                46               171
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       1                         0    71
  5P GAIN WILD-TYPE     4                         1   255
D9V13, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  71               255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     2  72
  5P GAIN WILD-TYPE   5 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   72
  5P GAIN WILD-TYPE    5  262
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              72               262
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    27  20
  5Q GAIN WILD-TYPE 141 145
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               47               286 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               145 
$`5Q GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP 
        3.02         6.97         8.52        44.19        56.19        59.57 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GM 
       26.37        32.28        13.68        17.72        23.11        75.65 
TCGA-D9-A6E9 TCGA-EB-A44R TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29W 
        9.90         0.20         8.12         1.12        60.23        32.15 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JA 
       26.99        53.16       124.31        30.15         3.22        22.22 
TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2ND 
       33.60         3.78        42.84        34.68         6.58         1.87 
TCGA-ER-A3PL TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1ZD 
        1.71         5.36         2.20         4.70         3.29         8.22 
TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U9 
       12.89        28.73         0.13         7.23        84.72        10.65 
TCGA-QB-AA9O TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-YG-AA3P TCGA-Z2-A8RT 
       18.05        11.84         3.72         4.70         8.22 

$`5Q GAIN WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        6.97        16.47       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        86.76        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ 
        7.50        36.16         6.31        92.42        64.44       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E 
       24.00         6.31         9.34       103.59        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       54.74        31.30        54.31        21.44        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      110.24        52.01        47.87        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       15.19         4.18       142.45       108.79        38.93       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        5.72        11.31        13.22        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
        7.00        17.56        14.83        13.15         0.13        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       19.00        13.35        13.22         0.20        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
        6.31         1.35        12.20         5.13         4.31         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       11.15        62.79         8.55        36.85         1.08        39.62 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        9.50        12.03         8.09         8.84         9.99        30.44 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       55.69         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      125.65       111.91        56.02        25.08        21.60        60.49 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       52.67         5.56       122.73        51.62         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72        22.92        21.60        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
        0.95        27.35        18.41        21.73        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       12.95        38.40         5.72        76.41        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       28.60         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       22.49         5.62        18.41        85.74        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        3.58        13.28        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       19.53        11.08         7.17        30.87        12.92        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       27.39         0.82         5.23        53.85         3.22         7.36 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.99         0.16        17.33         9.90         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       14.70        11.84        14.50        14.50        14.50        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.43        11.05         5.79         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        8.98        60.03         2.99        10.98       185.16        71.01 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        5.49         6.48         7.10        18.67        21.07        13.12 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        3.42        21.83         5.36         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         6.67         5.98 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.13              0.13 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           124.31            185.16 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            11.84             15.22 
[1] "0.1 - 124.3 (11.8)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1"  
D10V2, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    29  20
  5Q GAIN WILD-TYPE 144 146
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               49               290 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               146 
$`5Q GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP 
       17.03        61.02        16.67        62.07        56.19        59.57 
TCGA-D3-A3MU TCGA-D3-A51K TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GM 
       39.75        32.94       178.32        18.18       125.19        95.24 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-EB-A44R TCGA-EE-A180 TCGA-EE-A181 
      151.53         3.65         9.90        10.16        94.98        33.73 
TCGA-EE-A20B TCGA-EE-A29W TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE 
      133.81       195.02       248.65       162.48       124.31        54.51 
TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19N TCGA-ER-A19P 
      172.18        53.19       148.08        48.89        44.05       162.08 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD 
        8.88        23.34        33.21         7.00        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3TU TCGA-GF-A4EO 
       94.39        53.52        23.93        28.73        47.54         7.23 
TCGA-GN-A265 TCGA-GN-A4U9 TCGA-QB-AA9O TCGA-WE-A8JZ TCGA-WE-A8ZQ TCGA-YG-AA3P 
       84.72        12.62        18.05        24.03        52.34        14.43 
TCGA-Z2-A8RT 
       23.64 

$`5Q GAIN WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       12.99        16.57       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ 
      113.52        42.08        12.10       171.58        66.08       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E 
       24.53        13.87         9.34       103.59        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       55.73        56.35       145.12        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      125.79       135.75       137.92        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       15.19        58.52       228.99       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX 
      137.79        29.06       129.63       117.17        54.67         6.41 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
       18.12        11.34        22.29        11.11        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        17.85        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 
        6.35        12.20        29.82        27.22         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
       37.35        14.47        55.92       369.93        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54        43.23       134.40        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62         3.68        13.81        23.47       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       109.58        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        98.40        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q 
      268.93       152.35         6.44       131.51        61.05        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       31.27        32.05       247.04        80.32        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       92.98       174.21        15.72       210.08        15.16        38.27 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        27.72        48.85       357.37        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        50.14        66.67       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         2.04        11.74       139.89       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       10.13        64.44        62.79        32.48        39.58        46.36 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       50.10        21.37        59.41        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        6.67         0.33         0.69       212.22        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
        4.01        42.08       219.16       105.04        38.56        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
        8.61        90.28        56.98        59.41         3.75        22.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       43.73         2.20        30.18        10.36        15.16        36.03 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             3.65              0.16 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           248.65            369.93 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           47.540            50.825 
[1] "3.6 - 248.7 (47.5)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.1"
D10V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q GAIN MUTATED                   10             2
  5Q GAIN WILD-TYPE                 51             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5Q GAIN MUTATED                                           5
  5Q GAIN WILD-TYPE                                        67
                   vv
clus                REGIONAL LYMPH NODE
  5Q GAIN MUTATED                    33
  5Q GAIN WILD-TYPE                 176
D10V4, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     10                51
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               5                67
  REGIONAL LYMPH NODE                                    33               176
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5Q GAIN MUTATED             1       1       3        4        4        4
  5Q GAIN WILD-TYPE          11       6      25       13       23       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5Q GAIN MUTATED           3         4         2         4          2
  5Q GAIN WILD-TYPE        11        15        10        31         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED            3          6        3
  5Q GAIN WILD-TYPE         29         52       16
D10V5, multiclass
             clus
vv            5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  I OR II NOS               1                11
  STAGE 0                   1                 6
  STAGE I                   3                25
  STAGE IA                  4                13
  STAGE IB                  4                23
  STAGE II                  4                18
  STAGE IIA                 3                11
  STAGE IIB                 4                15
  STAGE IIC                 2                10
  STAGE III                 4                31
  STAGE IIIA                2                13
  STAGE IIIB                3                29
  STAGE IIIC                6                52
  STAGE IV                  3                16
[1] 14  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                T0+T1 T2 T3 T4
  5Q GAIN MUTATED      13 10 11  7
  5Q GAIN WILD-TYPE    50 61 63 60
D10V6, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1              13                50
  T2                 10                61
  T3                 11                63
  T4                  7                60
[1] 4 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                 N0  N1  N2  N3
  5Q GAIN MUTATED    26   5   5   8
  5Q GAIN WILD-TYPE 142  56  33  39
D10V7, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              26               142
  N1               5                56
  N2               5                33
  N3               8                39
[1] 4 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                 M0  M1 M1A M1B M1C
  5Q GAIN MUTATED    43   0   2   1   1
  5Q GAIN WILD-TYPE 263   4   1   3   8
D10V8, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               43               263
  M1                0                 4
  M1A               2                 1
  M1B               1                 3
  M1C               1                 8
[1] 5 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
  5Q GAIN MUTATED    20  11
  5Q GAIN WILD-TYPE 109  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     20   11
  5Q GAIN WILD-TYPE  109   76
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               20               109
  YES              11                76
[1] 2 2
[1] FALSE
D10V10, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7  43
  5Q GAIN WILD-TYPE  36 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   43
  5Q GAIN WILD-TYPE   36  261
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                7                36
  YES              43               261
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    17  33
  5Q GAIN WILD-TYPE 114 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     17   33
  5Q GAIN WILD-TYPE  114  184
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              17               114
  MALE                33               184
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       1                         0    46
  5Q GAIN WILD-TYPE     4                         1   280
D10V13, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  46               280
[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"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3  46
  5Q GAIN WILD-TYPE   4 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   46
  5Q GAIN WILD-TYPE    4  288
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO              46               288
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    55  74
  6P GAIN WILD-TYPE 113  91
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              129               204 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               74                91 
$`6P GAIN MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
        6.97        16.47         8.52       110.79        45.83        81.24 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        44.19        64.44        15.25        61.38 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
      103.59        26.37        93.21        25.78        52.01        47.87 
TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A4Z6 
       23.11       142.45        38.93        87.62        11.44         5.72 
TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F3 
        9.90        48.79        10.03        13.68         4.93         7.00 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
        0.13        23.15        19.00         6.31         1.12        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29P 
        5.13         4.31        60.23         9.21         9.90        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH 
        8.84         9.99         9.67        51.12        17.98        47.21 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
       29.46         2.73        14.56       125.65        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD 
       26.99        21.60        53.16         5.56       124.31         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        15.95         3.22        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E 
       22.22        33.60        12.95         5.72         3.78        11.90 
TCGA-ER-A19F TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       11.11        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A8YD 
       11.80        13.08         9.04        22.49         1.71         4.70 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       23.80        14.24        20.38        19.53        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 
       47.38        52.08         8.68         0.82         5.23         3.22 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 
       28.73        14.20         2.27         0.20         7.23        11.61 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
       31.33        10.13        16.24        12.16        14.70        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-AA9O TCGA-RP-A694 
       14.50        14.50        14.50         0.43        18.05         0.69 
TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       10.98        71.01        13.12         3.72         3.42        21.83 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        1.94        12.07         6.18 

$`6P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
        3.02         6.97       111.09        32.42        70.16        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       22.55        10.29        85.32        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.41         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       59.57       114.67        46.98        46.32        82.29        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H 
       24.00         6.31         9.34        29.23        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR 
       54.31        32.28        21.44        32.61       110.24        13.68 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       17.72        29.72        22.06        10.22        15.19         4.18 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      108.79        75.65       124.47         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
       21.93        11.31        13.22        14.60        35.80        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       39.19         9.99        44.52        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
        6.64        19.36        17.56        14.83        13.15         0.20 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 
       13.35        13.22         0.20        11.57        10.55         8.12 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C 
        1.35         4.34        15.85         1.18         7.99        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       11.15        62.79         8.55        36.85         1.08        39.62 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        9.50         8.09        30.44         2.43        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE 
       11.31        49.22        36.30        36.33        34.29        60.00 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       30.08        19.43        16.01        35.54        28.31        55.69 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT 
       44.25         7.96        63.42       111.91        60.49        52.67 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JB 
      122.73        51.62        30.15        12.72        22.92         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        18.41        21.73        31.40        18.61        38.40 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       76.41        25.18         3.52       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       13.45         6.58        17.72        78.44         1.87         1.51 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       12.62        11.74         6.58         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72         6.71         3.58         5.36        13.28         2.20 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.29        64.47         3.45        11.01        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.30         3.39         8.22        11.08         7.17        30.87 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 
        8.65         8.81        49.15        40.64        27.39        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
        7.36        10.78         5.98         6.41         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
        0.16        17.33         9.90         0.85        44.28        84.72 
TCGA-GN-A268 TCGA-GN-A4U8 TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       15.42        11.84        15.81        11.05         5.79         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ 
      164.19         8.98        60.03         2.99       185.16        11.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZY 
        5.49         6.48         7.10        18.67        21.07         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.08        19.96         4.70         8.22         6.67         5.98 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.13              0.13 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           142.45            185.16 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           14.240            15.765 
[1] "0.1 - 142.4 (14.2)" "0.1 - 185.2 (15.8)"
[1] "hr=" "1.4"
D11V2, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    59  74
  6P GAIN WILD-TYPE 114  92
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              133               206 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               74                92 
$`6P GAIN MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB 
       61.02        16.57        16.67       133.25        90.90        95.74 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC 
       65.49        23.77        62.07        66.08        58.06        86.93 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
      103.59        39.75       174.84        26.89       135.75       137.92 
TCGA-D3-A5GU TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A148 
      125.19       228.99        89.13       137.79        29.06       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HV 
       54.67         3.65        18.12        11.11         9.90        48.89 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A5KH TCGA-EB-A5SG 
       20.38       176.55        65.92        10.49        17.85        68.25 
TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       54.02         8.65        33.73        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
      133.81       168.26        80.61        56.42        14.47        55.92 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GN TCGA-EE-A2GP 
       39.29        59.28       314.56       208.04        90.97        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2ME TCGA-EE-A2MF 
       14.30        55.59        44.88        94.82       103.27       268.73 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      204.66       158.63       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      162.48        53.26       124.31         3.68        13.81        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI 
      172.18        36.95        64.08        34.32        53.19       148.08 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19M 
       13.94         9.17        48.89        13.02        26.37        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2NF 
       44.05       162.08        50.89        37.25        43.82        16.37 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A8YD TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      247.04        46.98        33.21        29.46       202.65        20.91 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
      357.37        40.27        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       26.56        27.09        27.02        50.14        28.73       174.84 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A266 
       77.88         0.20         7.23        11.74       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       64.44        32.48        39.58        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-AA1V TCGA-W3-AA21 
       59.41       357.04        18.05         0.69        42.08       105.04 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-WE-AAA4 
       59.41        52.34         3.75        22.68        10.36        15.16 
TCGA-YG-AA3O 
       36.03 

$`6P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       17.03        12.99       112.04       112.57        71.80        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       31.59        43.43       103.10       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       11.87       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       59.57       130.72        46.98        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H 
       24.53        13.87         9.34        45.30        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR 
      145.12        32.94        22.62        63.81       125.79       178.32 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       18.18        30.84        79.59        11.61        15.19        58.52 
TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JX 
      170.20        95.24       161.00       129.63       117.17         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       11.34        22.29        25.18        66.25        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      117.21       194.83        35.93       107.34        61.18        53.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        68.09        28.60       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       10.16        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       27.22        94.98        14.70       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        47.84        13.97        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29V 
        2.60        56.84        18.61        37.35       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      195.02        17.92        46.82       102.90        36.82        86.14 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       67.43       161.03        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       75.48       126.81        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML 
       61.51        47.28       103.20        16.96        96.23       203.05 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AH 
      134.40        71.21       122.73        51.62        54.51       138.81 
TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
      127.20       201.80        27.35        51.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19G 
       35.44        50.76        77.75        98.40        12.59       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      152.35         6.44       131.51         8.88       148.18        79.99 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A42K 
       23.34        20.15        31.27        32.05        80.32         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       38.27        34.82        94.39       216.92        48.59       228.59 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF 
       28.08         7.79        27.72        48.85        53.52        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
        9.70        32.75       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       49.48        77.82        66.67        12.43        26.73        49.45 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
       22.92        47.54         0.16        19.30         9.90         2.04 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-HR-A2OH TCGA-OD-A75X 
      139.89        84.72        62.79        46.36        65.88       294.77 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        6.67         0.33       212.22        63.02       121.08         4.01 
TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      219.16        24.03        38.56        54.38         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YG-AA3P TCGA-Z2-A8RT 
       56.98        43.73         2.20        30.18        14.43        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.20              0.16 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           357.37            369.93 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           50.100            51.055 
[1] "0.2 - 357.4 (50.1)" "0.2 - 369.9 (51.1)"
[1] "hr=" "1.2"
D11V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P GAIN MUTATED                   28             2
  6P GAIN WILD-TYPE                 33             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6P GAIN MUTATED                                          29
  6P GAIN WILD-TYPE                                        43
                   vv
clus                REGIONAL LYMPH NODE
  6P GAIN MUTATED                    76
  6P GAIN WILD-TYPE                 133
D11V4, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  DISTANT METASTASIS                                     28                33
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              29                43
  REGIONAL LYMPH NODE                                    76               133
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6P GAIN MUTATED             2       2      14        5       15       10
  6P GAIN WILD-TYPE          10       5      14       12       12       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6P GAIN MUTATED           5         6         9        12          6
  6P GAIN WILD-TYPE         9        13         3        23          9
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           11         17        6
  6P GAIN WILD-TYPE         21         41       13
D11V5, multiclass
             clus
vv            6P GAIN MUTATED 6P GAIN WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   2                 5
  STAGE I                  14                14
  STAGE IA                  5                12
  STAGE IB                 15                12
  STAGE II                 10                12
  STAGE IIA                 5                 9
  STAGE IIB                 6                13
  STAGE IIC                 9                 3
  STAGE III                12                23
  STAGE IIIA                6                 9
  STAGE IIIB               11                21
  STAGE IIIC               17                41
  STAGE IV                  6                13
[1] 14  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                T0+T1 T2 T3 T4
  6P GAIN MUTATED      22 34 23 33
  6P GAIN WILD-TYPE    41 37 51 34
D11V6, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1              22                41
  T2                 34                37
  T3                 23                51
  T4                 33                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"
                   vv
clus                N0 N1 N2 N3
  6P GAIN MUTATED   72 21 13 14
  6P GAIN WILD-TYPE 96 40 25 33
D11V7, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              72                96
  N1              21                40
  N2              13                25
  N3              14                33
[1] 4 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                 M0  M1 M1A M1B M1C
  6P GAIN MUTATED   116   2   2   2   1
  6P GAIN WILD-TYPE 190   2   1   2   8
D11V8, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              116               190
  M1                2                 2
  M1A               2                 1
  M1B               2                 2
  M1C               1                 8
[1] 5 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
  6P GAIN MUTATED   50 34
  6P GAIN WILD-TYPE 79 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     50   34
  6P GAIN WILD-TYPE   79   53
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               50                79
  YES              34                53
[1] 2 2
[1] FALSE
D11V10, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    18 118
  6P GAIN WILD-TYPE  25 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     18  118
  6P GAIN WILD-TYPE   25  186
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               18                25
  YES             118               186
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    55  81
  6P GAIN WILD-TYPE  76 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     55   81
  6P GAIN WILD-TYPE   76  136
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              55                76
  MALE                81               136
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         0   128
  6P GAIN WILD-TYPE     4                         1   198
D11V13, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 128               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"
D11V14, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2 134
  6P GAIN WILD-TYPE   5 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2  134
  6P GAIN WILD-TYPE    5  200
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             134               200
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    16  29
  6Q GAIN WILD-TYPE 152 136
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               45               288 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               29               136 
$`6Q GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A3CC TCGA-D3-A51E TCGA-D3-A5GO TCGA-D9-A6E9 
        8.52       110.79        61.38        93.21        47.87         9.90 
TCGA-DA-A1I0 TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29R TCGA-EE-A2GS 
       10.03        19.00         9.21         9.90         8.84        13.02 
TCGA-EE-A2GT TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MS 
       34.98        29.46        14.56       125.65        25.08        53.16 
TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI 
        5.56         3.22        21.60        16.14        22.22        33.60 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S 
       12.95         3.78        11.90        28.60         9.57        36.07 
TCGA-ER-A2NC TCGA-ER-A3EV TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FW-A3I3 
       11.80        22.49        12.89         3.22        14.20         0.20 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-AA1V 
       11.61        10.13        14.50        14.50        18.05        10.98 
TCGA-W3-AA21 TCGA-WE-A8ZT TCGA-WE-A8ZX 
       71.01         3.42        21.83 

$`6Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97        16.47       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        44.19         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        64.44        59.57       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        82.29        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        26.37        29.23        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.28        21.44        32.61        25.78       110.24        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       13.68        17.72        23.11        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19         4.18       142.45       108.79        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      124.47        87.62        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       21.93         5.72        11.31        13.22        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        13.35        13.22         0.20        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.31        60.23         4.34        15.85         1.18         7.99 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       39.62         9.50        12.03         8.09         9.99        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M5 
       33.83        55.69         5.42         1.15        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF 
       98.27         2.70         6.18        47.51         9.53         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       44.25         7.96        63.42       111.91        56.02        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       21.60        60.49        52.67       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
        3.68        30.15        13.81        15.95        12.72        22.92 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       21.60         0.95        27.35        18.41        21.73        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       18.61        38.40         5.72        76.41        25.18         3.52 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       11.11       114.15        34.88         4.21        13.45        42.84 
TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       34.68         6.58        17.72        78.44         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       13.08        12.62        11.74         9.04         6.58         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        5.62        18.41        85.74        15.72         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        30.87        12.92        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
        5.23        53.85         7.36        28.73        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.99         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         0.85        44.28        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       16.24        15.42        12.16        14.70        11.84        10.65 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       14.50        15.81         0.43        11.05         5.79         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.69       164.19         8.98        60.03         2.99       185.16 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       11.84         5.49         6.48         7.10        18.67        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       13.12         3.72         5.36         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         4.70         8.22         6.67         5.98 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.20              0.13 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           125.65            185.16 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            14.50             15.22 
[1] "0.2 - 125.7 (14.5)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1.4"
D12V2, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    18  29
  6Q GAIN WILD-TYPE 155 137
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               47               292 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               29               137 
$`6Q GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A3CC TCGA-D3-A51E TCGA-D3-A5GO TCGA-D9-A149 
       16.67       133.25        86.93       174.84       137.92        54.67 
TCGA-D9-A1X3 TCGA-D9-A6E9 TCGA-DA-A1I0 TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29B 
       18.12         9.90        20.38        54.02       168.26        80.61 
TCGA-EE-A29R TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MK 
       14.47        55.59        44.88       103.27       204.66       158.63 
TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 
       47.54       162.48        53.26       172.18        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19M 
       53.19       148.08        13.94        48.89        13.02        61.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A3EV TCGA-FS-A1ZK TCGA-FS-A4F2 
       50.89        37.25        43.82        46.98        23.93        50.14 
TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A8LK TCGA-GN-A9SD 
      174.84         0.20        11.74        10.13        50.10        59.41 
TCGA-QB-AA9O TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8ZT TCGA-WE-A8ZX 
       18.05        42.08       105.04         3.75        22.68 

$`6Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.57       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75        45.30        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      178.32        18.18       125.19        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19        58.52       228.99       170.20        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      161.00       137.79        29.06       129.63       117.17       151.53 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA 
        3.65         6.41        11.34        22.29        11.11        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
       66.25        22.95        48.89        36.03       117.21       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        17.85        68.25        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        6.35        12.20        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
      151.27        91.56        13.55        63.35        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       63.78        72.07        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        55.92       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        14.30        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       268.73       103.20        16.96 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       203.05       167.90       248.65        43.23       134.40 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB 
       13.81        23.47       138.81       127.20        64.08       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        51.35       109.58        31.40        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        98.40        12.59        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T 
      152.35         6.44       131.51        44.05       162.08         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       32.05       247.04        80.32        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      174.21        15.72       210.08        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        29.46        94.39       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67        28.73        12.43        26.73        49.45        77.88 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        2.04       139.89       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OH 
       32.48        39.58        46.36        12.62        21.37        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      357.04       294.77         6.67         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 
       63.02       121.08         4.01       219.16        24.03        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       54.38         8.61        90.28        56.98        59.41        52.34 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       43.73         2.20        30.18        10.36        15.16        36.03 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        23.64        93.07        11.74 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.20              0.16 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           204.66            369.93 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           50.100            51.055 
[1] "0.2 - 204.7 (50.1)" "0.2 - 369.9 (51.1)"
[1] "hr=" "1.4"
D12V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q GAIN MUTATED                    9             1
  6Q GAIN WILD-TYPE                 52             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6Q GAIN MUTATED                                          12
  6Q GAIN WILD-TYPE                                        60
                   vv
clus                REGIONAL LYMPH NODE
  6Q GAIN MUTATED                    24
  6Q GAIN WILD-TYPE                 185
D12V4, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      9                52
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              12                60
  REGIONAL LYMPH NODE                                    24               185
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6Q GAIN MUTATED             1       0       7        2        8        4
  6Q GAIN WILD-TYPE          11       7      21       15       19       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6Q GAIN MUTATED           1         2         3         4          2
  6Q GAIN WILD-TYPE        13        17         9        31         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED            3          2        3
  6Q GAIN WILD-TYPE         29         56       16
D12V5, multiclass
             clus
vv            6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  I OR II NOS               1                11
  STAGE 0                   0                 7
  STAGE I                   7                21
  STAGE IA                  2                15
  STAGE IB                  8                19
  STAGE II                  4                18
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 3                 9
  STAGE III                 4                31
  STAGE IIIA                2                13
  STAGE IIIB                3                29
  STAGE IIIC                2                56
  STAGE IV                  3                16
[1] 14  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                T0+T1 T2 T3 T4
  6Q GAIN MUTATED       5 13  7 15
  6Q GAIN WILD-TYPE    58 58 67 52
D12V6, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               5                58
  T2                 13                58
  T3                  7                67
  T4                 15                52
[1] 4 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                 N0  N1  N2  N3
  6Q GAIN MUTATED    30   8   1   2
  6Q GAIN WILD-TYPE 138  53  37  45
D12V7, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              30               138
  N1               8                53
  N2               1                37
  N3               2                45
[1] 4 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                 M0  M1 M1A M1B M1C
  6Q GAIN MUTATED    39   1   1   1   0
  6Q GAIN WILD-TYPE 267   3   2   3   9
D12V8, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               39               267
  M1                1                 3
  M1A               1                 2
  M1B               1                 3
  M1C               0                 9
[1] 5 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
  6Q GAIN MUTATED    23  10
  6Q GAIN WILD-TYPE 106  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     23   10
  6Q GAIN WILD-TYPE  106   77
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               23               106
  YES              10                77
[1] 2 2
[1] FALSE
D12V10, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     6  41
  6Q GAIN WILD-TYPE  37 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6   41
  6Q GAIN WILD-TYPE   37  263
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                6                37
  YES              41               263
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    17  30
  6Q GAIN WILD-TYPE 114 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     17   30
  6Q GAIN WILD-TYPE  114  187
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              17               114
  MALE                30               187
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         0    45
  6Q GAIN WILD-TYPE     5                         1   281
D12V13, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  45               281
[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"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  47
  6Q GAIN WILD-TYPE   7 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   47
  6Q GAIN WILD-TYPE    7  287
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              47               287
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   93 89
  7P GAIN WILD-TYPE 75 76
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              182               151 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               89                76 
$`7P GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97        16.47         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       70.16        22.55        21.14        88.50        86.76        11.41 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
        7.50        92.42        56.19        59.57       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32        82.29        61.38         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
      103.59        26.37        54.31        21.44        32.61        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       13.68        17.72        23.11        29.72        22.06        10.22 
TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A3Z3 
      108.79       124.47        87.62        11.44        24.07        21.93 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        11.31        13.22        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH 
       25.15         4.93         6.64        17.56        13.15         0.13 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       13.35        13.22         0.20        10.55         8.12         1.12 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       60.23         9.21         7.99        37.97        11.15        62.79 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 
        9.50        12.03        30.44        32.15        11.31        36.33 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL 
       51.12        60.00        47.21        30.08        19.43        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 
       28.31        33.83        55.69         5.42        98.27         2.70 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
        7.96        63.42       125.65        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD 
       21.60        60.49        53.16         5.56       124.31         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
       21.60        21.60         0.95        12.95         5.72        25.18 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P 
        3.78        11.90       114.15        34.88         4.21        34.68 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       36.07         6.58         1.87        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA 
       18.41        85.74        15.72         6.71         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        2.20         4.70         3.29         3.45        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM 
        7.33        20.38         8.22         7.17        30.87        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 
        8.65         8.81         0.82         5.23         3.22        28.73 
TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
       14.20         0.20        17.33         7.23        11.61        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS 
       11.84        10.65        14.50        14.50        15.81         5.79 
TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 
       18.05         2.99       185.16        71.01        11.84         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 
        7.10        18.67         3.72        21.83         1.08         1.94 
TCGA-YG-AA3O TCGA-YG-AA3P 
        6.18         4.70 

$`7P GAIN WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
        6.97       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       85.32         8.38        68.22        44.19        36.16         6.31 
TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       64.44        13.32        24.00        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE 
       31.30        32.28        25.78       110.24        47.87        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A3Z1 
        4.18       142.45        38.93        75.65         5.56         4.01 
TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
        5.72        39.19        22.36        19.36         7.00        14.83 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
        0.20        23.15        19.00        11.57         6.31         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       12.20         5.13         4.31         4.34        15.85         1.18 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q 
        9.90         8.55        36.85         1.08        39.62         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.84         9.99         2.43         8.09        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS 
        9.67        34.29        17.98        16.01         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       34.98        36.33         8.84         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT 
       29.46         2.73        44.25        14.56       111.91        52.67 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      122.73        51.62        16.14        22.22        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       21.73        33.60        31.40        18.61        38.40        76.41 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
        3.52        11.11        13.45        28.60        42.84         9.57 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       17.72        78.44        11.80         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
       11.74         9.04         6.58         3.58        64.47        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZJ 
       23.80         7.30         3.39        19.53        11.08        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       12.89        52.08        49.15        40.64         8.68        27.39 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       53.85         7.36        10.78         5.98         6.41         2.27 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
        0.99         0.13         0.16         9.90         0.85        44.28 
TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       14.50         0.43        11.05         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO 
        8.98        60.03        10.98         5.49        21.07        13.12 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S 
        3.42         5.36        19.96        12.07         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.13              0.13 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           185.16            164.19 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            15.62             13.32 
[1] "0.1 - 185.2 (15.6)" "0.1 - 164.2 (13.3)"
[1] "hr=" "1.1"
D13V2, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   95 90
  7P GAIN WILD-TYPE 78 76
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              185               154 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               90                76 
$`7P GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       71.80        31.59        23.77       115.53        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      113.52       171.58        56.19        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32       166.52        86.93        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN 
      103.59        39.75       145.12        22.62        63.81       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      178.32        18.18       125.19        30.84        79.59        11.61 
TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 
      170.20       161.00       137.79        29.06       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       54.67         6.41        22.29         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       22.95        48.89        36.03       117.21        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
       35.93       107.34        61.18        53.92        65.92        68.09 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
      215.44        13.87        17.85        17.29        52.01        12.20 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       27.22        94.98        33.73       133.81       168.26        63.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T 
       47.84        13.97        63.78        18.61        56.42       369.93 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      195.02        46.82        86.14        59.28       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        89.33        79.66        75.48        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
       13.91       129.27        28.83        16.96        96.23       158.63 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       134.40       162.48 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       124.31         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB 
      138.81       172.18       127.20        36.95        64.08       201.80 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G 
       13.94         9.17        98.40        48.89        13.02       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND 
      152.35         6.44       162.08        37.25         8.88        23.34 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      210.08         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       48.59        20.91        28.08         7.79       357.37        53.52 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY 
        9.70        32.75       101.26       133.55        11.41        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY 
       27.02        50.14        28.73       174.84         0.20        19.30 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        7.23        11.74       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       62.79        32.48        39.58        46.36        12.62        50.10 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1W 
       59.41        65.88         6.67        18.05         4.01       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ 
      105.04        24.03        54.38         8.61        90.28        52.34 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
       22.68         2.20        10.36        36.03        14.43 

$`7P GAIN WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       12.99       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
      103.10        65.49       168.00        62.07        42.08        12.10 
TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       66.08        60.23        24.53        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE 
       56.35        32.94        26.89       125.79       137.92        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR TCGA-D9-A1JW 
       58.52       228.99        89.13        95.24       129.63         3.65 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 
       18.12        11.34        11.11       194.83        23.44        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV 
       10.49        15.68        10.16        68.25        54.02         6.35 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       29.82         8.65        14.70        26.89        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H 
      151.27        91.56        13.55        80.61        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        2.60        56.84        37.35        14.47        55.92        25.87 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD 
       17.92       102.90        36.82        39.29        67.43       314.56 
TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       54.74        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3J8 
      204.66       203.05        71.21       122.73        51.62        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        51.35       109.58       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L 
       35.44        50.76        77.75        12.59        26.37       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       61.05        44.05        50.89       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       15.16       216.92       228.59       202.65        27.72        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS 
       40.27        15.45        47.38        23.93        74.73       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       53.16        26.56        49.48        77.82        66.67        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88        22.92        47.54         0.16 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X 
        9.90         2.04       139.89        21.37       357.04       294.77 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
        0.33         0.69       212.22        63.02       121.08        42.08 
TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 
       38.56        56.98        59.41         3.75        43.73        30.18 
TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        23.64        93.07        11.74 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.20              0.16 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           369.93            357.04 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           52.010            49.465 
[1] "0.2 - 369.9 (52.0)" "0.2 - 357.0 (49.5)"
[1] "hr=" "1.1"
D13V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P GAIN MUTATED                   31             4
  7P GAIN WILD-TYPE                 30             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7P GAIN MUTATED                                          39
  7P GAIN WILD-TYPE                                        33
                   vv
clus                REGIONAL LYMPH NODE
  7P GAIN MUTATED                   116
  7P GAIN WILD-TYPE                  93
D13V4, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  DISTANT METASTASIS                                     31                30
  PRIMARY TUMOR                                           4                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              39                33
  REGIONAL LYMPH NODE                                   116                93
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7P GAIN MUTATED            10       1      17        8        9       11
  7P GAIN WILD-TYPE           2       6      11        9       18       11
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7P GAIN MUTATED           8         6         8        24         11
  7P GAIN WILD-TYPE         6        13         4        11          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           20         31       11
  7P GAIN WILD-TYPE         12         27        8
D13V5, multiclass
             clus
vv            7P GAIN MUTATED 7P GAIN WILD-TYPE
  I OR II NOS              10                 2
  STAGE 0                   1                 6
  STAGE I                  17                11
  STAGE IA                  8                 9
  STAGE IB                  9                18
  STAGE II                 11                11
  STAGE IIA                 8                 6
  STAGE IIB                 6                13
  STAGE IIC                 8                 4
  STAGE III                24                11
  STAGE IIIA               11                 4
  STAGE IIIB               20                12
  STAGE IIIC               31                27
  STAGE IV                 11                 8
[1] 14  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                T0+T1 T2 T3 T4
  7P GAIN MUTATED      39 35 40 38
  7P GAIN WILD-TYPE    24 36 34 29
D13V6, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              39                24
  T2                 35                36
  T3                 40                34
  T4                 38                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"
                   vv
clus                N0 N1 N2 N3
  7P GAIN MUTATED   85 40 20 29
  7P GAIN WILD-TYPE 83 21 18 18
D13V7, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              85                83
  N1              40                21
  N2              20                18
  N3              29                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"
                   vv
clus                 M0  M1 M1A M1B M1C
  7P GAIN MUTATED   166   3   3   1   5
  7P GAIN WILD-TYPE 140   1   0   3   4
D13V8, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              166               140
  M1                3                 1
  M1A               3                 0
  M1B               1                 3
  M1C               5                 4
[1] 5 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
  7P GAIN MUTATED   73 45
  7P GAIN WILD-TYPE 56 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     73   45
  7P GAIN WILD-TYPE   56   42
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               73                56
  YES              45                42
[1] 2 2
[1] FALSE
D13V10, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    28 162
  7P GAIN WILD-TYPE  15 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     28  162
  7P GAIN WILD-TYPE   15  142
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               28                15
  YES             162               142
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    77 114
  7P GAIN WILD-TYPE  54 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     77  114
  7P GAIN WILD-TYPE   54  103
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              77                54
  MALE               114               103
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       4                         0   177
  7P GAIN WILD-TYPE     1                         1   149
D13V13, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 177               149
[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"
D13V14, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     5 181
  7P GAIN WILD-TYPE   2 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5  181
  7P GAIN WILD-TYPE    2  153
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             181               153
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   93 87
  7Q GAIN WILD-TYPE 75 78
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              180               153 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               87                78 
$`7Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
       16.47         8.52       111.09        32.42        70.16        22.55 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
       21.14        88.50        86.76        11.41         7.50        92.42 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        59.57       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       82.29        61.38         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       29.23        54.31        32.61        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GK 
       23.11        29.72        22.06        10.22         4.18       108.79 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6E9 
      124.47        87.62        11.44        24.07        21.93         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       11.31        13.22        14.60        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UL 
        4.93         6.64        17.56        14.83        13.15        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       13.22         0.20        10.55         8.12         1.12        12.20 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N 
       60.23         9.21         7.99        37.97        62.79         9.50 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB 
       12.03        30.44        32.15        11.31        36.33        51.12 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       60.00        47.21        30.08        35.54        28.31        55.69 
TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
        5.42        98.27         2.70         7.96        63.42       125.65 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       56.02        26.99        21.60        60.49        53.16         5.56 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-ER-A193 
       22.92        21.60        21.60         0.95        27.35        31.40 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G 
       12.95         5.72        25.18         3.78        11.90       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND 
       34.88         4.21        34.68        36.07         6.58         1.87 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        6.71         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        3.45        14.24        15.52         7.33        20.38         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       11.08         7.17        30.87        47.38         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.15         0.82         5.23         3.22        28.73        14.20 
TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
        0.20        17.33         7.23        11.61        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
       10.13        16.24        15.42        12.16        14.70        10.65 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        14.50        15.81         0.43         5.79        18.05 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 
        2.99       185.16        71.01        11.84         6.48         7.10 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
        3.72        21.83         1.08         1.94         6.18         4.70 

$`7Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        3.02         6.97         6.97       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF 
       81.24        10.29        85.32         8.38        68.22        44.19 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E 
       36.16         6.31        64.44        13.32        24.00        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       54.74        31.30        32.28        21.44        25.78       110.24 
TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR 
       47.87        15.19       142.45        38.93        75.65         5.56 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
        4.01         5.72        39.19        22.36        19.36         7.00 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Z 
        0.20         0.13        23.15        19.00        11.57         6.31 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
        1.35         5.13         4.31         4.34        15.85         1.18 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        9.90        11.15         8.55        36.85         1.08        39.62 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        8.09         8.84         9.99         2.43         8.09        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK 
       36.30         9.67        34.29        17.98        19.43        16.01 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       33.83         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       14.56       111.91        25.08        52.67       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
        3.68        16.14        22.22        18.41        21.73        33.60 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L 
       18.61        38.40        76.41         3.52        11.11        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       28.60        42.84         9.57        17.72        78.44        11.80 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        3.58        64.47        11.01        23.80         7.30         3.39 
TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU 
       19.53        12.92        12.89        52.08        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       27.39        53.85         7.36        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 
        2.27         0.99         0.13         0.16         9.90         0.85 
TCGA-GN-A262 TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 
       44.28        11.84        14.50        11.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZM 
      164.19         8.98        60.03        10.98         5.49        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       21.07        13.12         3.42         5.36        19.96        12.07 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        8.22         6.67         5.98 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.20              0.13 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           185.16            164.19 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            15.62             13.12 
[1] "0.2 - 185.2 (15.6)" "0.1 - 164.2 (13.1)"
[1] "hr=" "1.2"
D14V2, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   95 88
  7Q GAIN WILD-TYPE 78 78
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              183               156 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               88                78 
$`7Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
       16.57        16.67       112.04       112.57        71.80        31.59 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
       23.77       115.53        86.76        11.87       113.52       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        86.93        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       45.30       145.12        63.81       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GK 
      125.19        30.84        79.59        11.61        58.52       170.20 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      161.00       137.79        29.06       117.17       151.53        54.67 
TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        6.41        22.29         9.90        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03       117.21        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
      107.34        61.18        53.92        65.92        68.09       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y 
       15.68        13.87        17.29        52.01        12.20        27.22 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       94.98        33.73        26.89       133.81       168.26        63.35 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W 
       47.84        63.78        18.61        56.42       369.93       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       46.82        86.14        59.28       161.03       208.04        48.72 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 
       79.66        75.48       126.81        13.91       129.27        28.83 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
       16.96        96.23       158.63       167.90       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF 
      134.40       162.48        53.26       124.31        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      201.80        27.35        31.40        13.94         9.17        98.40 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P 
       48.89        13.02       268.93       152.35         6.44       162.08 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       37.25         8.88        23.34        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA 
       92.98       174.21        15.72       210.08         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       34.82        29.46        94.39        48.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.79       357.37        53.52        15.45         9.70        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      101.26       133.55        11.41       148.80        27.09        27.02 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO 
       50.14        28.73       174.84         0.20        19.30         7.23 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       11.74       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH 
       32.48        39.58        12.62        50.10        59.41        65.88 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 
      357.04         6.67        18.05         4.01       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AA9Y 
       24.03        54.38         8.61        52.34        22.68         2.20 
TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
       10.36        36.03        14.43 

$`7Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       17.03        61.02        12.99       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JF 
       95.74        43.43       103.10        65.49       168.00        62.07 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E 
       42.08        12.10        66.08        60.23        24.53       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       55.73        56.35        32.94        22.62        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GR 
      137.92        15.19       228.99        89.13        95.24       129.63 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-DA-A1I1 TCGA-DA-A1IB 
        3.65        18.12        11.34        11.11       194.83        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       28.60        10.49        10.16        17.85        68.25        54.02 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
        6.35        29.82         8.65        14.70        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
      151.27        91.56        13.55        80.61        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       64.64         2.60        56.84        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
       25.87        17.92       102.90        36.82        39.29        67.43 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
      314.56        89.33        54.74        90.97        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        21.67        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN 
      103.27       268.73       103.20       204.66       203.05        47.54 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 TCGA-EE-A3JA 
       71.21       122.73        51.62         3.68        34.32        53.19 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       51.35       109.58       148.08        35.44        50.76        77.75 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       12.59        26.37       131.51        61.05        44.05        50.89 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        43.82        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
       32.05       247.04        80.32        15.16       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      202.65        27.72        48.85        40.27        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 
       74.73        53.16        26.56        49.48        77.82        66.67 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88        22.92        47.54 
TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U8 TCGA-GN-A8LL 
        0.16         9.90         2.04       139.89        46.36        21.37 
TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
      294.77         0.33         0.69       212.22        63.02       121.08 
TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       42.08        38.56        90.28        56.98        59.41         3.75 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       43.73        30.18        15.16        23.64        93.07        11.74 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.20              0.16 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           369.93            314.56 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           52.010            49.465 
[1] "0.2 - 369.9 (52.0)" "0.2 - 314.6 (49.5)"
[1] "hr=" "1.1"
D14V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q GAIN MUTATED                   31             4
  7Q GAIN WILD-TYPE                 30             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7Q GAIN MUTATED                                          38
  7Q GAIN WILD-TYPE                                        34
                   vv
clus                REGIONAL LYMPH NODE
  7Q GAIN MUTATED                   115
  7Q GAIN WILD-TYPE                  94
D14V4, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     31                30
  PRIMARY TUMOR                                           4                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              38                34
  REGIONAL LYMPH NODE                                   115                94
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7Q GAIN MUTATED            10       2      17        7        9       11
  7Q GAIN WILD-TYPE           2       5      11       10       18       11
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7Q GAIN MUTATED           6         7         9        23         11
  7Q GAIN WILD-TYPE         8        12         3        12          4
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           21         30       10
  7Q GAIN WILD-TYPE         11         28        9
D14V5, multiclass
             clus
vv            7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  I OR II NOS              10                 2
  STAGE 0                   2                 5
  STAGE I                  17                11
  STAGE IA                  7                10
  STAGE IB                  9                18
  STAGE II                 11                11
  STAGE IIA                 6                 8
  STAGE IIB                 7                12
  STAGE IIC                 9                 3
  STAGE III                23                12
  STAGE IIIA               11                 4
  STAGE IIIB               21                11
  STAGE IIIC               30                28
  STAGE IV                 10                 9
[1] 14  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                T0+T1 T2 T3 T4
  7Q GAIN MUTATED      35 35 40 39
  7Q GAIN WILD-TYPE    28 36 34 28
D14V6, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              35                28
  T2                 35                36
  T3                 40                34
  T4                 39                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"
                   vv
clus                N0 N1 N2 N3
  7Q GAIN MUTATED   87 36 23 28
  7Q GAIN WILD-TYPE 81 25 15 19
D14V7, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              87                81
  N1              36                25
  N2              23                15
  N3              28                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"
                   vv
clus                 M0  M1 M1A M1B M1C
  7Q GAIN MUTATED   165   3   3   1   4
  7Q GAIN WILD-TYPE 141   1   0   3   5
D14V8, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              165               141
  M1                3                 1
  M1A               3                 0
  M1B               1                 3
  M1C               4                 5
[1] 5 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
  7Q GAIN MUTATED   73 44
  7Q GAIN WILD-TYPE 56 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     73   44
  7Q GAIN WILD-TYPE   56   43
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               73                56
  YES              44                43
[1] 2 2
[1] FALSE
D14V10, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    27 161
  7Q GAIN WILD-TYPE  16 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     27  161
  7Q GAIN WILD-TYPE   16  143
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               27                16
  YES             161               143
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    79 110
  7Q GAIN WILD-TYPE  52 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     79  110
  7Q GAIN WILD-TYPE   52  107
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              79                52
  MALE               110               107
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       3                         0   177
  7Q GAIN WILD-TYPE     2                         1   149
D14V13, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 177               149
[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"
D14V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     5 179
  7Q GAIN WILD-TYPE   2 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  179
  7Q GAIN WILD-TYPE    2  155
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             179               155
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    57  56
  8P GAIN WILD-TYPE 111 109
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              113               220 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               56               109 
$`8P GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J7 
        3.02         6.97         6.97        70.16        22.55        85.32 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC 
       86.76        44.19        56.19        64.44        59.57        61.38 
TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A5GR TCGA-D3-A5GS 
       13.32       103.59        26.37        29.23        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GP TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       23.11         4.18        87.62        13.22        14.60        35.80 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EB-A44Q 
       51.12        39.19        13.68         9.99        17.56        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20B 
        0.20         0.13        19.00        10.55         1.12        60.23 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       11.15         8.55         8.84        17.98        60.00        47.21 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
       35.54        28.31        33.83        55.69         5.42        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AD 
        2.70         6.18         7.96        60.49       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A19C 
       30.15        22.92        21.60        21.60        22.22         3.78 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       11.80        13.08        85.74         6.71         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       13.28         4.70        64.47         3.45        15.52         7.33 
TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        8.22        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 
        0.82         3.22         7.36        28.73         2.27         0.20 
TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.16         9.90        10.13        16.24        12.16        14.70 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       14.50        14.50        15.81         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
        8.98        10.98        71.01         7.10        18.67        21.07 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-YG-AA3O TCGA-Z2-AA3V 
        3.72         3.42        21.83         6.18         5.98 

$`8P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        32.42       110.79        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       45.83        81.24        10.29         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       68.22        11.41         7.50        36.16         6.31        92.42 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
      114.67        15.25        46.98        46.32        82.29        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        6.31         9.34        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.28        21.44        32.61        25.78       110.24        52.01 
TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       47.87        29.72        22.06        10.22        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      108.79        38.93        75.65       124.47        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       24.07         4.01        21.93         5.72         9.90        11.31 
TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       48.79        10.03        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5SG 
       22.36         6.64        19.36         7.00        14.83        23.15 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       13.35        13.22         0.20        11.57         6.31         8.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        1.35        12.20         5.13         4.31         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        9.21         1.18         7.99         9.90        37.97        62.79 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         9.50        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       30.08        19.43        16.01         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       36.33         8.84        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        26.99        21.60        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        51.62        13.81        15.95        12.72         3.22 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14         0.95        27.35        18.41        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19Q 
       25.18         3.52        11.90        11.11        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07         6.58        17.72        78.44         1.87         1.51 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YY 
        5.62        18.41        15.72         2.20         3.29        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       23.80        14.24         7.30         3.39        20.38        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       11.08         7.17        30.87        12.92        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
        8.68        27.39         5.23        53.85        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO 
        5.98         6.41         0.99         0.13        17.33         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        0.85        11.61        44.28        31.33        84.72        15.42 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        14.50         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 
       18.05        60.03         2.99       185.16        11.84         5.49 
TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        6.48        13.12         5.36         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       12.07         4.70         8.22         6.67 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.13              0.13 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           164.19            185.16 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           14.500            15.335 
[1] "0.1 - 164.2 (14.5)" "0.1 - 185.2 (15.3)"
[1] "hr=" "1"  
D15V2, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    57  56
  8P GAIN WILD-TYPE 116 110
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              113               226 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               56               110 
$`8P GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J7 
       17.03        61.02        12.99        71.80        31.59       103.10 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC 
       86.76        62.07        56.19        66.08        59.57        86.93 
TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A5GR TCGA-D3-A5GS 
       60.23       103.59        39.75        45.30       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GP TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
      125.19        58.52       137.79        66.25        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EB-A44Q 
      117.21       194.83       176.55        35.93       215.44        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A20B 
       10.16        17.85        54.02        27.22        33.73       133.81 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       13.97        72.07        14.47       314.56       161.03       208.04 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
       79.66        75.48        90.97       126.81        13.91       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3AD 
       28.83        19.76        16.96       134.40       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A19C 
       54.51       127.20        36.95        64.08        53.19        48.89 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       43.82        16.37       174.21       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       38.27        29.46       216.92        48.59        28.08         7.79 
TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 
       27.09        50.14        66.67        28.73        77.88         0.20 
TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.16         9.90        10.13        64.44        32.48        39.58 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       21.37        59.41        65.88         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       63.02        42.08       105.04         8.61        90.28        56.98 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-YG-AA3O TCGA-Z2-AA3V 
       52.34         3.75        22.68        36.03        11.74 

$`8P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04       112.57       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74        43.43        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
      168.00        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
      130.72        58.06        46.98        46.32       166.52        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       13.87         9.34       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
      137.92        30.84        79.59        11.61        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13        95.24       161.00        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       11.34        22.29        11.11         9.90        25.18        48.89 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL 
       68.09        28.60        10.49        15.68        68.25        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       52.01         6.35        12.20        29.82         8.65        94.98 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89        68.15         4.96       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      168.26        13.55        63.35        80.61        47.84        63.78 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        18.61        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       55.92       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       48.72        89.33        54.74        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       94.82        21.67        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20       204.66        96.23       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65        43.23       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        51.62        13.81        23.47       138.81       172.18 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32       201.80        27.35        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19Q 
       98.40        12.59        13.02        26.37       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25         8.88       148.18        79.99        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YY 
        6.77        92.98        15.72        34.82        94.39       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
      202.65        20.91        27.72        48.85       357.37        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       15.45         9.70        32.75        47.38       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
       26.56        49.48        27.02        77.82       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO 
       26.73        49.45        22.92        47.54        19.30         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        2.04        11.74       139.89       117.93        84.72        62.79 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       46.36        12.62        50.10       357.04       294.77         6.67 
TCGA-QB-AA9O TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 
       18.05       121.08         4.01       219.16        24.03        38.56 
TCGA-WE-A8K5 TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       54.38        59.41        43.73         2.20        30.18        10.36 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       15.16        14.43        23.64        93.07 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.16              2.04 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           314.56            369.93 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            53.52             49.17 
[1] "0.2 - 314.6 (53.5)" "2.0 - 369.9 (49.2)"
[1] "hr=" "1"  
D15V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P GAIN MUTATED                   15             2
  8P GAIN WILD-TYPE                 46             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8P GAIN MUTATED                                          31
  8P GAIN WILD-TYPE                                        41
                   vv
clus                REGIONAL LYMPH NODE
  8P GAIN MUTATED                    68
  8P GAIN WILD-TYPE                 141
D15V4, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  DISTANT METASTASIS                                     15                46
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              31                41
  REGIONAL LYMPH NODE                                    68               141
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8P GAIN MUTATED             3       1      11        6        7       11
  8P GAIN WILD-TYPE           9       6      17       11       20       11
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8P GAIN MUTATED           6         3         6        16          7
  8P GAIN WILD-TYPE         8        16         6        19          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           10         17        6
  8P GAIN WILD-TYPE         22         41       13
D15V5, multiclass
             clus
vv            8P GAIN MUTATED 8P GAIN WILD-TYPE
  I OR II NOS               3                 9
  STAGE 0                   1                 6
  STAGE I                  11                17
  STAGE IA                  6                11
  STAGE IB                  7                20
  STAGE II                 11                11
  STAGE IIA                 6                 8
  STAGE IIB                 3                16
  STAGE IIC                 6                 6
  STAGE III                16                19
  STAGE IIIA                7                 8
  STAGE IIIB               10                22
  STAGE IIIC               17                41
  STAGE IV                  6                13
[1] 14  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                T0+T1 T2 T3 T4
  8P GAIN MUTATED      25 25 25 22
  8P GAIN WILD-TYPE    38 46 49 45
D15V6, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              25                38
  T2                 25                46
  T3                 25                49
  T4                 22                45
[1] 4 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                 N0  N1  N2  N3
  8P GAIN MUTATED    53  26  13  12
  8P GAIN WILD-TYPE 115  35  25  35
D15V7, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              53               115
  N1              26                35
  N2              13                25
  N3              12                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"
                   vv
clus                 M0  M1 M1A M1B M1C
  8P GAIN MUTATED   105   2   0   1   3
  8P GAIN WILD-TYPE 201   2   3   3   6
D15V8, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              105               201
  M1                2                 2
  M1A               0                 3
  M1B               1                 3
  M1C               3                 6
[1] 5 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
  8P GAIN MUTATED   39 33
  8P GAIN WILD-TYPE 90 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     39   33
  8P GAIN WILD-TYPE   90   54
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               39                90
  YES              33                54
[1] 2 2
[1] FALSE
D15V10, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    16 100
  8P GAIN WILD-TYPE  27 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     16  100
  8P GAIN WILD-TYPE   27  204
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               16                27
  YES             100               204
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    41  75
  8P GAIN WILD-TYPE  90 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     41   75
  8P GAIN WILD-TYPE   90  142
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              41                90
  MALE                75               142
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       4                         0   105
  8P GAIN WILD-TYPE     1                         1   221
D15V13, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 105               221
[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"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2 111
  8P GAIN WILD-TYPE   5 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2  111
  8P GAIN WILD-TYPE    5  223
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             111               223
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   82 76
  8Q GAIN WILD-TYPE 86 89
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              158               175 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               76                89 
$`8Q GAIN MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
        6.97         6.97        16.47       111.09        70.16        22.55 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
       81.24        10.29        85.32        88.50        86.76        44.19 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       56.19        64.44        59.57        15.25        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       13.32         6.31         9.34       103.59        26.37        29.23 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR 
       93.21        54.31        32.28        21.44        52.01        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D9-A6EC 
       17.72        23.11         4.18       142.45        87.62        13.22 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       14.60        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
        9.99         7.00        17.56        13.15         0.20        23.15 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A20B 
       19.00         0.20        10.55         6.31         1.12        60.23 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A5 
       37.97        62.79         8.55         8.84        30.44         9.67 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       17.98        60.00        47.21        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.69         5.42        13.02        98.27         2.70         6.18 
TCGA-EE-A2MH TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
        7.96        25.08        60.49       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       30.15        15.95         3.22        22.92        21.60        21.60 
TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       22.22        12.95         3.78       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       13.45        28.60        42.84         9.57        36.07         6.58 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A 
       11.80         1.87        13.08         6.58        22.49        85.74 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FS-A1YW 
        6.71         3.58         5.36        13.28         4.70        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD 
        3.45        11.01        23.80        15.52         7.33         8.22 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       40.64         8.68         0.82         3.22         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A265 
       14.20         2.27         0.20         0.16         9.90        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A8LL TCGA-GN-A9SD 
       10.13        16.24        12.16        14.70        14.50        14.50 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
       15.81        11.05         5.79        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      164.19         8.98        10.98        71.01         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-YG-AA3O 
       21.07         3.72         3.42        21.83         1.94         6.18 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

$`8Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        3.02         8.52        32.42       110.79        28.08        45.83 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
        8.38        21.14        68.22        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF 
        6.31        92.42       114.67        46.98        46.32        24.00 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       54.74        31.30        32.61        25.78       110.24        47.87 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL 
       29.72        22.06        10.22        15.19       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
       75.65       124.47        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I5 
       21.93         5.72         9.90        11.31        48.79        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 
       14.83         0.13        13.35        13.22        11.57         8.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        1.35        12.20         5.13         4.31         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H 
        9.21         1.18         7.99         9.90        11.15        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        1.08        39.62         9.50        12.03         8.09         9.99 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       36.33        51.12        34.29        30.08        19.43        16.01 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD 
        1.15        34.98        36.33         8.84        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46         2.73        44.25        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
      111.91        56.02        26.99        21.60        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB 
        5.56        51.62        13.81        12.72        16.14         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       38.40         5.72        76.41        25.18         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG 
       11.11        34.68        17.72        78.44         1.51        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P 
       11.74         9.04         1.71         5.62        18.41        15.72 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
        2.20         3.29        14.24         7.30         3.39        20.38 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW 
       19.53        11.08         7.17        30.87        12.92        27.39 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
        5.23        53.85        10.78         5.98         6.41         0.99 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
        0.13        17.33         7.23         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB 
       31.33        15.42        11.84        10.65        14.50         0.43 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       60.03         2.99       185.16        11.84         5.49         6.48 
TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3P 
       13.12         5.36         1.08        19.96        12.07         4.70 
TCGA-Z2-A8RT 
        8.22 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.16              0.13 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           164.19            185.16 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           14.975            14.560 
[1] "0.2 - 164.2 (15.0)" "0.1 - 185.2 (14.6)"
[1] "hr=" "1.1"
D16V2, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   83 76
  8Q GAIN WILD-TYPE 90 90
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              159               180 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               76                90 
$`8Q GAIN MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q9 
       61.02        12.99        16.57       112.04        71.80        31.59 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
       95.74        43.43       103.10       115.53        86.76        62.07 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC 
       56.19        66.08        59.57        58.06       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR 
      174.84       145.12        32.94        22.62       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D9-A1JW 
       18.18       125.19        58.52       228.99       137.79         3.65 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        22.95        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
      176.55        35.93        10.49       215.44        13.87        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
       68.25        54.02        12.20        27.22         8.65        33.73 
TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29T 
      133.81        47.84        63.78        72.07        14.47       369.93 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM 
       39.29       314.56       161.03       208.04        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       90.97       126.81        13.91        55.59       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB 
       19.76        16.96        47.54       134.40       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        54.51        23.47       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       64.08        53.19        13.94        48.89       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        61.05        44.05        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3EV 
        8.88        43.82        23.34        16.37        80.32        46.98 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
      174.21       210.08        15.16         7.00        38.27        29.46 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59       202.65        28.08         7.79 
TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 
      148.80        53.16        26.56        27.09        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT 
       28.73       174.84        77.88         0.20         0.16         9.90 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A8LL 
       84.72        10.13        64.44        32.48        39.58        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       59.41        65.88       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K6 
        0.69       212.22        63.02        42.08       105.04         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA3 
       90.28        56.98        52.34         3.75        22.68        10.36 
TCGA-YG-AA3O TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        93.07        11.74 

$`8Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       17.03        16.67       112.57       133.25        28.08        90.90 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       65.49        23.77       168.00        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF 
       12.10       171.58       130.72        46.98        46.32        24.53 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       55.73        56.35        63.81        26.89       125.79       137.92 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL 
       30.84        79.59        11.61        15.19       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       95.24       161.00        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         6.41        18.12        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        9.90        25.18        48.89       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5KH 
       65.92        23.44        68.09        28.60        15.68        17.85 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 
       17.29        52.01         6.35        29.82        94.98        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
       13.55        63.35        80.61        13.97        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       56.84        18.61        56.42        37.35        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      195.02        17.92        46.82       102.90        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR 
       59.28        67.43        48.72        89.33        54.74        14.30 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       44.88        94.82        21.67        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20       204.66        96.23       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90       248.65        43.23       162.48        71.21        53.26 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
       51.62        13.81       138.81        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       51.35       109.58       148.08        31.40        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        98.40        12.59        13.02        26.37 
TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
      162.08       148.18        79.99        20.15        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A8YC 
      247.04        33.21         6.77        92.98        15.72        34.82 
TCGA-FR-A8YE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       94.39        20.91        27.72        48.85       357.37        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       15.45         9.70        32.75        47.38        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
       77.82        12.43        26.73        49.45        22.92        47.54 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       19.30         7.23         2.04        11.74       139.89       117.93 
TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB TCGA-W3-A828 
       62.79        46.36        12.62        50.10       357.04       121.08 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZO 
        4.01       219.16        24.03        38.56        54.38        59.41 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT 
       43.73         2.20        30.18        15.16        14.43        23.64 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.16              2.04 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           369.93            357.37 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           53.520            48.785 
[1] "0.2 - 369.9 (53.5)" "2.0 - 357.4 (48.8)"
[1] "hr=" "1.2"
D16V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q GAIN MUTATED                   22             3
  8Q GAIN WILD-TYPE                 39             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8Q GAIN MUTATED                                          41
  8Q GAIN WILD-TYPE                                        31
                   vv
clus                REGIONAL LYMPH NODE
  8Q GAIN MUTATED                    95
  8Q GAIN WILD-TYPE                 114
D16V4, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     22                39
  PRIMARY TUMOR                                           3                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              41                31
  REGIONAL LYMPH NODE                                    95               114
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8Q GAIN MUTATED             5       1      15        7       12       12
  8Q GAIN WILD-TYPE           7       6      13       10       15       10
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8Q GAIN MUTATED           7         5         7        22         10
  8Q GAIN WILD-TYPE         7        14         5        13          5
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           14         23        9
  8Q GAIN WILD-TYPE         18         35       10
D16V5, multiclass
             clus
vv            8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  I OR II NOS               5                 7
  STAGE 0                   1                 6
  STAGE I                  15                13
  STAGE IA                  7                10
  STAGE IB                 12                15
  STAGE II                 12                10
  STAGE IIA                 7                 7
  STAGE IIB                 5                14
  STAGE IIC                 7                 5
  STAGE III                22                13
  STAGE IIIA               10                 5
  STAGE IIIB               14                18
  STAGE IIIC               23                35
  STAGE IV                  9                10
[1] 14  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                T0+T1 T2 T3 T4
  8Q GAIN MUTATED      37 37 30 29
  8Q GAIN WILD-TYPE    26 34 44 38
D16V6, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              37                26
  T2                 37                34
  T3                 30                44
  T4                 29                38
[1] 4 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                N0 N1 N2 N3
  8Q GAIN MUTATED   73 31 22 20
  8Q GAIN WILD-TYPE 95 30 16 27
D16V7, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              73                95
  N1              31                30
  N2              22                16
  N3              20                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"
                   vv
clus                 M0  M1 M1A M1B M1C
  8Q GAIN MUTATED   145   2   2   1   4
  8Q GAIN WILD-TYPE 161   2   1   3   5
D16V8, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              145               161
  M1                2                 2
  M1A               2                 1
  M1B               1                 3
  M1C               4                 5
[1] 5 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
  8Q GAIN MUTATED   56 39
  8Q GAIN WILD-TYPE 73 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     56   39
  8Q GAIN WILD-TYPE   73   48
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               56                73
  YES              39                48
[1] 2 2
[1] FALSE
D16V10, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    26 136
  8Q GAIN WILD-TYPE  17 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     26  136
  8Q GAIN WILD-TYPE   17  168
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               26                17
  YES             136               168
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    60 102
  8Q GAIN WILD-TYPE  71 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     60  102
  8Q GAIN WILD-TYPE   71  115
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              60                71
  MALE               102               115
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       4                         0   150
  8Q GAIN WILD-TYPE     1                         1   176
D16V13, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 150               176
[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"
D16V14, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3 156
  8Q GAIN WILD-TYPE   4 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  156
  8Q GAIN WILD-TYPE    4  178
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             156               178
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     8   8
  9P GAIN WILD-TYPE 160 157
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               317 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8               157 
$`9P GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A8GM 
       22.55        45.83        88.50        52.01        17.72        75.65 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A2M5 TCGA-ER-A19G TCGA-ER-A2NC TCGA-ER-A2NF 
       19.00         5.13         8.84       114.15        11.80        13.08 
TCGA-ER-A3ET TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A4F8 
        6.58        23.80        12.92        14.20 

$`9P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
       32.42        70.16       110.79        28.08        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       85.32         8.38        21.14        68.22        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        59.57       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.31        32.28        21.44        32.61        25.78       110.24 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       47.87        13.68        23.11        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       15.19         4.18       142.45       108.79        38.93       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        5.72         9.90        11.31        13.22        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13        23.15        13.35        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.84         9.99        30.44         2.43        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.11        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        17.72        78.44 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
        1.87         1.51        12.62        11.74         9.04        22.49 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        1.71         5.62        18.41        85.74        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        3.58         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47         3.45        11.01        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        30.87        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
        5.23        53.85         3.22         7.36        28.73        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        15.81         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       10.98       185.16        71.01        11.84         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        7.10        18.67        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       21.83         5.36         1.08        19.96         1.94        12.07 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         4.70         8.22         6.67         5.98 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             5.13              0.13 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           114.15            185.16 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            18.36             14.60 
[1] "5.1 - 114.2 (18.4)" "0.1 - 185.2 (14.6)"
[1] "hr=" "1.2"
D17V2, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     8   8
  9P GAIN WILD-TYPE 165 158
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               323 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8               158 
$`9P GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A8GM 
       31.59        90.90       115.53       135.75        18.18        95.24 
TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A2M5 TCGA-ER-A19G TCGA-ER-A2NC TCGA-ER-A2NF 
       54.02        68.15        21.67       268.93        43.82        16.37 
TCGA-ER-A3ET TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A4F8 
       80.32       202.65        47.38       174.84 

$`9P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
      112.57        71.80       133.25        28.08        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        65.49        23.77       168.00        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      137.92       178.32       125.19        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       15.19        58.52       228.99       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      137.79        29.06       129.63       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         6.41        18.12        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       215.44        15.68        13.87        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       68.25        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       133.81       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        80.61        47.84        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        55.92       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
       23.34        20.15        31.27        32.05       247.04        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       15.16         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
       27.02        77.82        50.14        66.67        28.73        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       32.48        39.58        46.36        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       59.41        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        38.56        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.61        90.28        56.98        59.41        52.34         3.75 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       22.68        43.73         2.20        30.18        10.36        15.16 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        23.64        93.07        11.74 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            16.37              0.16 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           268.93            369.93 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           74.235            49.480 
[1] "16.4 - 268.9 (74.2)" "0.2 - 369.9 (49.5)" 
[1] "hr=" "1.3"
D17V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P GAIN MUTATED                    3             1
  9P GAIN WILD-TYPE                 58             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9P GAIN MUTATED                                           2
  9P GAIN WILD-TYPE                                        70
                   vv
clus                REGIONAL LYMPH NODE
  9P GAIN MUTATED                    10
  9P GAIN WILD-TYPE                 199
D17V4, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  DISTANT METASTASIS                                      3                58
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                70
  REGIONAL LYMPH NODE                                    10               199
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  9P GAIN MUTATED             0       0       4        1        3        0
  9P GAIN WILD-TYPE          12       7      24       16       24       22
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9P GAIN MUTATED           0         1         0         1          2
  9P GAIN WILD-TYPE        14        18        12        34         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED            1          1        1
  9P GAIN WILD-TYPE         31         57       18
D17V5, multiclass
             clus
vv            9P GAIN MUTATED 9P GAIN WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   0                 7
  STAGE I                   4                24
  STAGE IA                  1                16
  STAGE IB                  3                24
  STAGE II                  0                22
  STAGE IIA                 0                14
  STAGE IIB                 1                18
  STAGE IIC                 0                12
  STAGE III                 1                34
  STAGE IIIA                2                13
  STAGE IIIB                1                31
  STAGE IIIC                1                57
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  9P GAIN MUTATED       4  6  2  3
  9P GAIN WILD-TYPE    59 65 72 64
D17V6, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               4                59
  T2                  6                65
  T3                  2                72
  T4                  3                64
[1] 4 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                 N0  N1  N2  N3
  9P GAIN MUTATED    11   3   1   1
  9P GAIN WILD-TYPE 157  58  37  46
D17V7, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              11               157
  N1               3                58
  N2               1                37
  N3               1                46
[1] 4 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                 M0  M1 M1A M1B M1C
  9P GAIN MUTATED    15   0   0   0   1
  9P GAIN WILD-TYPE 291   4   3   4   8
D17V8, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               15               291
  M1                0                 4
  M1A               0                 3
  M1B               0                 4
  M1C               1                 8
[1] 5 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
  9P GAIN MUTATED     9   4
  9P GAIN WILD-TYPE 120  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      9    4
  9P GAIN WILD-TYPE  120   83
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                9               120
  YES               4                83
[1] 2 2
[1] FALSE
D17V10, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  16
  9P GAIN WILD-TYPE  43 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   16
  9P GAIN WILD-TYPE   43  288
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                0                43
  YES              16               288
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     6  10
  9P GAIN WILD-TYPE 125 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6   10
  9P GAIN WILD-TYPE  125  207
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               6               125
  MALE                10               207
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         0    16
  9P GAIN WILD-TYPE     5                         1   310
D17V13, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16               310
[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"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  16
  9P GAIN WILD-TYPE   7 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   16
  9P GAIN WILD-TYPE    7  318
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              16               318
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     6  14
  9Q GAIN WILD-TYPE 162 151
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               313 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               14               151 
$`9Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JB TCGA-D3-A3ML TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       22.55        68.22         6.31        52.01        13.68        17.72 
TCGA-D3-A8GM TCGA-EE-A184 TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A3J3 TCGA-ER-A19G 
       75.65         5.13         8.84         9.53         3.22       114.15 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z0 
       11.80         1.87        13.08        85.74         3.45        23.80 
TCGA-FS-A1ZJ TCGA-FS-A4F8 
       12.92        14.20 

$`9Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       32.42        70.16       110.79        28.08        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       10.29        85.32         8.38        21.14        88.50        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        44.19         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        64.44        59.57       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.32        82.29        61.38        13.32        24.00         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.31        32.28        21.44        32.61        25.78       110.24 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       47.87        23.11        29.72        22.06        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
        4.18       142.45       108.79        38.93       124.47        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       11.44         5.56        24.07         4.01        21.93         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        11.31        13.22        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       23.15        19.00        13.35        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.84         9.99        30.44         2.43        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51        29.46         2.73        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       125.65       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       25.18         3.78         3.52        11.90        11.11        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG 
       36.07         6.58        17.72        78.44         1.51        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       18.41        15.72         6.71         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        2.20         4.70         3.29        64.47        11.01        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
       19.53        11.08         7.17        30.87        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       27.39         0.82         5.23        53.85         3.22         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       16.24        15.42        12.16        14.70        11.84        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       14.50        14.50        14.50        15.81         0.43        11.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        5.79        18.05         0.33         0.69       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
       60.03         2.99        10.98       185.16        71.01        11.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        5.49         6.48         7.10        18.67        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
        3.72         3.42        21.83         5.36         1.08        19.96 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        1.94        12.07         6.18         4.70         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.87              0.13 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           114.15            185.16 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            13.38             15.19 
[1] "1.9 - 114.2 (13.4)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1.4"
D18V2, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     6  14
  9Q GAIN WILD-TYPE 167 152
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               319 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               14               152 
$`9Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JB TCGA-D3-A3ML TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       31.59       168.00        13.87       135.75       178.32        18.18 
TCGA-D3-A8GM TCGA-EE-A184 TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A3J3 TCGA-ER-A19G 
       95.24        68.15        21.67        47.28       172.18       268.93 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z0 
       43.82        23.34        16.37       174.21        48.59       202.65 
TCGA-FS-A1ZJ TCGA-FS-A4F8 
       47.38       174.84 

$`9Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       43.43       103.10        65.49        23.77       115.53        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       46.32       166.52        86.93        60.23        24.53         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
      137.92       125.19        30.84        79.59        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       58.52       228.99       170.20        89.13       161.00       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        6.41        18.12        11.34        22.29        11.11         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       133.81       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        80.61        47.84        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        55.92       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       98.40        48.89        12.59        13.02        26.37       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NG 
       37.25         8.88       148.18        79.99        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       92.98        15.72       210.08        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       34.82        29.46        94.39       216.92       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
       40.27        15.45         9.70        32.75        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       64.44        62.79        32.48        39.58        46.36        12.62 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       50.10        21.37        59.41        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        6.67        18.05         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      121.08         4.01        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       38.56        54.38         8.61        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       52.34         3.75        22.68        43.73         2.20        30.18 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       10.36        15.16        36.03        14.43        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            13.87              0.16 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           268.93            369.93 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            58.37             50.14 
[1] "13.9 - 268.9 (58.4)" "0.2 - 369.9 (50.1)" 
[1] "hr=" "1.1"
D18V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q GAIN MUTATED                    4             1
  9Q GAIN WILD-TYPE                 57             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9Q GAIN MUTATED                                           2
  9Q GAIN WILD-TYPE                                        70
                   vv
clus                REGIONAL LYMPH NODE
  9Q GAIN MUTATED                    13
  9Q GAIN WILD-TYPE                 196
D18V4, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      4                57
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                70
  REGIONAL LYMPH NODE                                    13               196
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  9Q GAIN MUTATED             0       1       5        1        3        2
  9Q GAIN WILD-TYPE          12       6      23       16       24       20
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9Q GAIN MUTATED           0         1         0         1          1
  9Q GAIN WILD-TYPE        14        18        12        34         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED            1          2        1
  9Q GAIN WILD-TYPE         31         56       18
D18V5, multiclass
             clus
vv            9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   1                 6
  STAGE I                   5                23
  STAGE IA                  1                16
  STAGE IB                  3                24
  STAGE II                  2                20
  STAGE IIA                 0                14
  STAGE IIB                 1                18
  STAGE IIC                 0                12
  STAGE III                 1                34
  STAGE IIIA                1                14
  STAGE IIIB                1                31
  STAGE IIIC                2                56
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  9Q GAIN MUTATED       6  6  4  2
  9Q GAIN WILD-TYPE    57 65 70 65
D18V6, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               6                57
  T2                  6                65
  T3                  4                70
  T4                  2                65
[1] 4 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                 N0  N1  N2  N3
  9Q GAIN MUTATED    14   2   2   2
  9Q GAIN WILD-TYPE 154  59  36  45
D18V7, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              14               154
  N1               2                59
  N2               2                36
  N3               2                45
[1] 4 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                 M0  M1 M1A M1B M1C
  9Q GAIN MUTATED    19   0   0   0   1
  9Q GAIN WILD-TYPE 287   4   3   4   8
D18V8, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               19               287
  M1                0                 4
  M1A               0                 3
  M1B               0                 4
  M1C               1                 8
[1] 5 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
  9Q GAIN MUTATED    11   4
  9Q GAIN WILD-TYPE 118  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11    4
  9Q GAIN WILD-TYPE  118   83
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               11               118
  YES               4                83
[1] 2 2
[1] FALSE
D18V10, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  20
  9Q GAIN WILD-TYPE  43 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   20
  9Q GAIN WILD-TYPE   43  284
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                43
  YES              20               284
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     9  11
  9Q GAIN WILD-TYPE 122 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      9   11
  9Q GAIN WILD-TYPE  122  206
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               9               122
  MALE                11               206
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         1    19
  9Q GAIN WILD-TYPE     5                         0   307
D18V13, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  19               307
[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"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  20
  9Q GAIN WILD-TYPE   7 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   20
  9Q GAIN WILD-TYPE    7  314
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              20               314
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     6   6
  10P GAIN WILD-TYPE 162 159
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                321 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                159 
$`10P GAIN MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A51N TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1HY 
       15.25       103.59        21.44        75.65        13.22        51.12 
TCGA-EE-A29D TCGA-ER-A19C TCGA-ER-A19M TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-QB-AA9O 
       11.15         3.78        28.60         0.20        11.61        18.05 

$`10P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        86.76        11.41        44.19         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        59.57       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34        26.37        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       31.30        54.31        32.28        32.61        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       52.01        47.87        13.68        17.72        23.11        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       22.06        10.22        15.19         4.18       142.45       108.79 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       38.93       124.47        87.62        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
        4.01        21.93         5.72         9.90        11.31        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        35.80        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
        0.13        23.15        19.00        13.35        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        60.23         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        9.21         1.18         7.99         9.90        37.97        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        8.09         8.84         9.99        30.44         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        55.69 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       12.95        38.40         5.72        76.41        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74        15.72         6.71         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       13.28         2.20         4.70         3.29        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       30.87        12.92        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.81        49.15        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        5.23        53.85         3.22         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       10.78         5.98         6.41         2.27         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16        17.33         9.90         7.23         0.85        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       14.70        11.84        10.65        14.50        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.81         0.43        11.05         5.79         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
      164.19         8.98        60.03         2.99        10.98       185.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       71.01        11.84         5.49         6.48         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       21.07        13.12         3.72         3.42        21.83         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        1.08        19.96         1.94        12.07         6.18         4.70 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        8.22         6.67         5.98 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.20               0.13 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            103.59             185.16 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             16.65              14.60 
[1] "0.2 - 103.6 (16.6)" "0.1 - 185.2 (14.6)"
[1] "hr=" "1.1"
D19V2, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     6   6
  10P GAIN WILD-TYPE 167 160
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                327 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                160 
$`10P GAIN MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A51N TCGA-D3-A8GM TCGA-D9-A6EC TCGA-DA-A1HY 
       58.06       103.59        22.62        95.24        66.25       117.21 
TCGA-EE-A29D TCGA-ER-A19C TCGA-ER-A19M TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-QB-AA9O 
       13.97        48.89        61.05         0.20        11.74        18.05 

$`10P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        86.76        11.87        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        59.57       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       56.35       145.12        32.94        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      135.75       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        11.61        15.19        58.52       228.99       170.20 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       161.00       137.79        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        11.11         9.90        25.18        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       215.44        15.68        13.87        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       133.81       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      168.26        13.55        63.35        80.61        47.84        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       37.35        14.47        55.92       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       13.94        50.76         9.17        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        29.46        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16        19.30         9.90         7.23         2.04       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       39.58        46.36        12.62        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       65.88       357.04       294.77         6.67         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
      212.22        63.02       121.08         4.01        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      105.04        24.03        38.56        54.38         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       56.98        59.41        52.34         3.75        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        2.20        30.18        10.36        15.16        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.20               0.16 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            117.21             369.93 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            53.475             50.140 
[1] "0.2 - 117.2 (53.5)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.4"
D19V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10P GAIN MUTATED                    2             1
  10P GAIN WILD-TYPE                 59             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10P GAIN MUTATED                                           1
  10P GAIN WILD-TYPE                                        71
                    vv
clus                 REGIONAL LYMPH NODE
  10P GAIN MUTATED                     8
  10P GAIN WILD-TYPE                 201
D19V4, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  DISTANT METASTASIS                                       2                 59
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                1                 71
  REGIONAL LYMPH NODE                                      8                201
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  10P GAIN MUTATED             0       0       1        0        2        0
  10P GAIN WILD-TYPE          12       7      27       17       25       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10P GAIN MUTATED           0         1         0         1          1
  10P GAIN WILD-TYPE        14        18        12        34         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED            1          3        2
  10P GAIN WILD-TYPE         31         55       17
D19V5, multiclass
             clus
vv            10P GAIN MUTATED 10P GAIN WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    1                 27
  STAGE IA                   0                 17
  STAGE IB                   2                 25
  STAGE II                   0                 22
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  0                 12
  STAGE III                  1                 34
  STAGE IIIA                 1                 14
  STAGE IIIB                 1                 31
  STAGE IIIC                 3                 55
  STAGE IV                   2                 17
[1] 14  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                 T0+T1 T2 T3 T4
  10P GAIN MUTATED       2  4  3  1
  10P GAIN WILD-TYPE    61 67 71 66
D19V6, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1                2                 61
  T2                   4                 67
  T3                   3                 71
  T4                   1                 66
[1] 4 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                  N0  N1  N2  N3
  10P GAIN MUTATED     4   3   0   3
  10P GAIN WILD-TYPE 164  58  38  44
D19V7, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                4                164
  N1                3                 58
  N2                0                 38
  N3                3                 44
[1] 4 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                  M0  M1 M1A M1B M1C
  10P GAIN MUTATED     9   1   0   0   1
  10P GAIN WILD-TYPE 297   3   3   4   8
D19V8, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                 9                297
  M1                 1                  3
  M1A                0                  3
  M1B                0                  4
  M1C                1                  8
[1] 5 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
  10P GAIN MUTATED     4   3
  10P GAIN WILD-TYPE 125  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    3
  10P GAIN WILD-TYPE  125   84
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 4                125
  YES                3                 84
[1] 2 2
[1] FALSE
D19V10, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     5   7
  10P GAIN WILD-TYPE  38 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    7
  10P GAIN WILD-TYPE   38  297
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 5                 38
  YES                7                297
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4   8
  10P GAIN WILD-TYPE 127 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    8
  10P GAIN WILD-TYPE  127  209
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                4                127
  MALE                  8                209
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0    12
  10P GAIN WILD-TYPE     5                         1   314
D19V13, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   12                314
[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"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  12
  10P GAIN WILD-TYPE   7 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   12
  10P GAIN WILD-TYPE    7  322
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               12                322
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     2   1
  10Q GAIN WILD-TYPE 166 164
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                330 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                164 
$`10Q GAIN MUTATED`
TCGA-DA-A1HY TCGA-ER-A3ET TCGA-QB-AA9O 
       51.12         6.58        18.05 

$`10Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        86.76        11.41        44.19         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        59.57       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.61        25.78       110.24        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       17.72        23.11        29.72        22.06        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
        4.18       142.45       108.79        38.93        75.65       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        5.72         9.90        11.31        13.22        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       23.15        19.00        13.35        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        60.23         4.34        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        8.09         8.84         9.99        30.44         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        55.69 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       13.08        12.62        11.74         9.04        22.49         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        5.62        18.41        85.74        15.72         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
        0.82         5.23        53.85         3.22         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       16.24        15.42        12.16        14.70        11.84        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       14.50        14.50        14.50        15.81         0.43        11.05 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        5.79         0.33         0.69       164.19         8.98        60.03 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
        2.99        10.98       185.16        71.01        11.84         5.49 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        6.48         7.10        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        3.42        21.83         5.36         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         4.70         8.22         6.67         5.98 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              6.58               0.13 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             51.12             185.16 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             18.05              14.65 
[1] "6.6 - 51.1 (18.1)"  "0.1 - 185.2 (14.6)"
[1] "hr=" "1.5"
D20V2, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     2   1
  10Q GAIN WILD-TYPE 171 165
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                336 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                165 
$`10Q GAIN MUTATED`
TCGA-DA-A1HY TCGA-ER-A3ET TCGA-QB-AA9O 
      117.21        80.32        18.05 

$`10Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        86.76        11.87        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       18.18       125.19        30.84        79.59        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       58.52       228.99       170.20        89.13        95.24       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      137.79        29.06       129.63       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         6.41        18.12        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        66.25        22.95        48.89        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       37.35        14.47        55.92       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        8.88       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       16.37        31.27        32.05       247.04        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       210.08        15.16 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        7.00        38.27        34.82        29.46        94.39       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       64.44        62.79        32.48        39.58        46.36        12.62 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       50.10        21.37        59.41        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        6.67         0.33         0.69       212.22        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
        4.01        42.08       219.16       105.04        24.03        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       54.38         8.61        90.28        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        3.75        22.68        43.73         2.20        30.18        10.36 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        36.03        14.43        23.64        93.07        11.74 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             18.05               0.16 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            117.21             369.93 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             80.32              50.12 
[1] "18.1 - 117.2 (80.3)" "0.2 - 369.9 (50.1)" 
[1] "hr=" "1.5"
D20V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10Q GAIN MUTATED                    0             0
  10Q GAIN WILD-TYPE                 61             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10Q GAIN MUTATED                                           1
  10Q GAIN WILD-TYPE                                        71
                    vv
clus                 REGIONAL LYMPH NODE
  10Q GAIN MUTATED                     2
  10Q GAIN WILD-TYPE                 207
D20V4, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       0                 61
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                1                 71
  REGIONAL LYMPH NODE                                      2                207
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  10Q GAIN MUTATED             0       0       0        0        0        0
  10Q GAIN WILD-TYPE          12       7      28       17       27       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10Q GAIN MUTATED           0         0         0         0          1
  10Q GAIN WILD-TYPE        14        19        12        35         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED            0          2        0
  10Q GAIN WILD-TYPE         32         56       19
D20V5, multiclass
             clus
vv            10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    0                 28
  STAGE IA                   0                 17
  STAGE IB                   0                 27
  STAGE II                   0                 22
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  0                 12
  STAGE III                  0                 35
  STAGE IIIA                 1                 14
  STAGE IIIB                 0                 32
  STAGE IIIC                 2                 56
  STAGE IV                   0                 19
[1] 14  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                 T0+T1 T2 T3 T4
  10Q GAIN MUTATED       0  1  1  0
  10Q GAIN WILD-TYPE    63 70 73 67
D20V6, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                273 
        TCGA-3N-A9WB         TCGA-3N-A9WC         TCGA-3N-A9WD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q3         TCGA-D3-A1Q4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q6         TCGA-D3-A1Q7         TCGA-D3-A1Q8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A1QA         TCGA-D3-A1QB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J7         TCGA-D3-A2J8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2J9         TCGA-D3-A2JA         TCGA-D3-A2JC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JF         TCGA-D3-A2JG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JH         TCGA-D3-A2JK         TCGA-D3-A2JN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JP         TCGA-D3-A3BZ         TCGA-D3-A3C6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3C7         TCGA-D3-A3CB         TCGA-D3-A3CC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3CE         TCGA-D3-A3CF         TCGA-D3-A3ML 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3MR         TCGA-D3-A3MU         TCGA-D3-A3MV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A51E         TCGA-D3-A51F         TCGA-D3-A51H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A51J         TCGA-D3-A51N         TCGA-D3-A51R 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A51T         TCGA-D3-A5GL         TCGA-D3-A5GN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A5GO         TCGA-D3-A5GR         TCGA-D3-A5GS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A5GU         TCGA-D3-A8GB         TCGA-D3-A8GD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GI         TCGA-D3-A8GJ         TCGA-D3-A8GK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GL         TCGA-D3-A8GM         TCGA-D3-A8GO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GP         TCGA-D3-A8GQ         TCGA-D3-A8GS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A1JW         TCGA-D9-A1X3         TCGA-D9-A3Z1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-D9-A4Z6         TCGA-D9-A6E9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A6EA         TCGA-D9-A6EC         TCGA-D9-A6EG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1I0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EB-A5KH         TCGA-EB-A5SH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EB-A5UN         TCGA-EB-A5VV         TCGA-EE-A17X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A17Y         TCGA-EE-A17Z         TCGA-EE-A180 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A182         TCGA-EE-A184 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29B 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29G         TCGA-EE-A29H         TCGA-EE-A29L 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29Q 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GB         TCGA-EE-A2GC         TCGA-EE-A2GD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GE         TCGA-EE-A2GH         TCGA-EE-A2GI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GJ         TCGA-EE-A2GK         TCGA-EE-A2GL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GM         TCGA-EE-A2GN         TCGA-EE-A2GO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GP         TCGA-EE-A2GR         TCGA-EE-A2GS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GT         TCGA-EE-A2GU         TCGA-EE-A2M5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2M6         TCGA-EE-A2M7         TCGA-EE-A2M8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ME 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MF         TCGA-EE-A2MG         TCGA-EE-A2MH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MI         TCGA-EE-A2MJ         TCGA-EE-A2MK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2ML         TCGA-EE-A2MM         TCGA-EE-A2MN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MP         TCGA-EE-A2MQ         TCGA-EE-A2MR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A2MU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3AA         TCGA-EE-A3AB         TCGA-EE-A3AC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3AD         TCGA-EE-A3AE         TCGA-EE-A3AF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-EE-A3J3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3J4         TCGA-EE-A3J5         TCGA-EE-A3J7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3J8         TCGA-EE-A3JA         TCGA-EE-A3JB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3JE         TCGA-EE-A3JH         TCGA-EE-A3JI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A193         TCGA-ER-A197         TCGA-ER-A199 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19C         TCGA-ER-A19D         TCGA-ER-A19E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19M         TCGA-ER-A19O         TCGA-ER-A19T 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A2NC         TCGA-ER-A2ND         TCGA-ER-A2NF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A2NG         TCGA-ER-A2NH         TCGA-ER-A3EV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-ER-A42K         TCGA-FR-A3YN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A3YO         TCGA-FR-A44A         TCGA-FR-A729 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A7U9         TCGA-FR-A7UA         TCGA-FR-A8YC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A8YD         TCGA-FR-A8YE         TCGA-FS-A1YW 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1Z4         TCGA-FS-A1Z7         TCGA-FS-A1ZA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZB         TCGA-FS-A1ZD         TCGA-FS-A1ZE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZF         TCGA-FS-A1ZG         TCGA-FS-A1ZH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZJ         TCGA-FS-A1ZK         TCGA-FS-A1ZM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZR         TCGA-FS-A1ZS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZT         TCGA-FS-A1ZU         TCGA-FS-A1ZW 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZY         TCGA-FS-A1ZZ         TCGA-FS-A4F0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F2         TCGA-FS-A4F4         TCGA-FS-A4F5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F8         TCGA-FS-A4F9         TCGA-FS-A4FB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FS-A4FD         TCGA-FW-A3I3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FW-A3TV         TCGA-FW-A5DY         TCGA-GF-A3OT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GF-A4EO         TCGA-GF-A6C8         TCGA-GN-A267 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A4U9         TCGA-GN-A8LK         TCGA-GN-A8LL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A9SD         TCGA-HR-A2OH         TCGA-QB-A6FS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-A824         TCGA-W3-A825         TCGA-W3-A828 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-AA1V         TCGA-W3-AA1W         TCGA-W3-AA21 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8JZ         TCGA-WE-A8K1         TCGA-WE-A8K5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZN         TCGA-WE-A8ZO         TCGA-WE-A8ZQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZT         TCGA-WE-A8ZY         TCGA-WE-AA9Y 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-AAA0         TCGA-WE-AAA3         TCGA-YG-AA3P 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Z2-A8RT         TCGA-Z2-AA3S         TCGA-Z2-AA3V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED     0   1   0   2
  10Q GAIN WILD-TYPE 168  60  38  45
D20V7, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                0                168
  N1                1                 60
  N2                0                 38
  N3                2                 45
[1] 4 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                  M0  M1 M1A M1B M1C
  10Q GAIN MUTATED     3   0   0   0   0
  10Q GAIN WILD-TYPE 303   4   3   4   9
D20V8, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                 3                303
  M1                 0                  4
  M1A                0                  3
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  10Q GAIN MUTATED     0   1
  10Q GAIN WILD-TYPE 129  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    1
  10Q GAIN WILD-TYPE  129   86
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 0                129
  YES                1                 86
[1] 2 2
[1] FALSE
D20V10, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE  42 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE   42  302
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                 42
  YES                2                302
[1] 2 2
[1] FALSE
D20V11, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                255 
        TCGA-3N-A9WB         TCGA-3N-A9WC         TCGA-3N-A9WD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q3         TCGA-D3-A1Q4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q6         TCGA-D3-A1Q7         TCGA-D3-A1Q9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A1QA         TCGA-D3-A2J6         TCGA-D3-A2J7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JF         TCGA-D3-A2JG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A2JH         TCGA-D3-A2JK         TCGA-D3-A3BZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CB         TCGA-D3-A3CC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3ML         TCGA-D3-A3MU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-D3-A51E         TCGA-D3-A51F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A51G         TCGA-D3-A51H         TCGA-D3-A51K 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A51R         TCGA-D3-A51T         TCGA-D3-A5GL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A5GN         TCGA-D3-A5GO         TCGA-D3-A5GR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A5GS         TCGA-D3-A5GU         TCGA-D3-A8GB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GD         TCGA-D3-A8GI         TCGA-D3-A8GJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GK         TCGA-D3-A8GL         TCGA-D3-A8GM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GO         TCGA-D3-A8GP         TCGA-D3-A8GQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D3-A8GR         TCGA-D3-A8GS         TCGA-D9-A1X3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-D9-A6E9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D9-A6EA         TCGA-D9-A6EC         TCGA-D9-A6EG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1I0         TCGA-DA-A1I4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I8         TCGA-DA-A1IA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A1IB         TCGA-DA-A1IC         TCGA-DA-A3F2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A5SH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EB-A5UL         TCGA-EB-A5UN         TCGA-EB-A5VV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A17Y         TCGA-EE-A17Z 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A180         TCGA-EE-A181         TCGA-EE-A182 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A184         TCGA-EE-A185         TCGA-EE-A20B 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29B         TCGA-EE-A29C         TCGA-EE-A29D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29E         TCGA-EE-A29G         TCGA-EE-A29H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29M         TCGA-EE-A29P 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29W         TCGA-EE-A29X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2A0         TCGA-EE-A2A1         TCGA-EE-A2A2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2A5         TCGA-EE-A2A6         TCGA-EE-A2GB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GC         TCGA-EE-A2GD         TCGA-EE-A2GE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GI         TCGA-EE-A2GJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GK         TCGA-EE-A2GL         TCGA-EE-A2GM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GN         TCGA-EE-A2GO         TCGA-EE-A2GP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2GS         TCGA-EE-A2GT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2GU         TCGA-EE-A2M5         TCGA-EE-A2M6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2M7         TCGA-EE-A2M8         TCGA-EE-A2MC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MD         TCGA-EE-A2ME         TCGA-EE-A2MF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MG         TCGA-EE-A2MH         TCGA-EE-A2MI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MJ         TCGA-EE-A2MK         TCGA-EE-A2ML 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A2MP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MQ         TCGA-EE-A2MR         TCGA-EE-A2MS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A2MT         TCGA-EE-A2MU         TCGA-EE-A3AE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3AH         TCGA-EE-A3J3         TCGA-EE-A3J4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3J5         TCGA-EE-A3J7         TCGA-EE-A3J8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3JA         TCGA-EE-A3JB         TCGA-EE-A3JE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EE-A3JH         TCGA-EE-A3JI         TCGA-ER-A197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A198         TCGA-ER-A199         TCGA-ER-A19C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19E         TCGA-ER-A19F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19G         TCGA-ER-A19H         TCGA-ER-A19M 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A19Q         TCGA-ER-A19T         TCGA-ER-A19W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A2NC         TCGA-ER-A2ND         TCGA-ER-A2NF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A2NG         TCGA-ER-A2NH         TCGA-ER-A3EV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-ER-A42K         TCGA-FR-A3YN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FR-A729         TCGA-FR-A7U9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A7UA         TCGA-FR-A8YC         TCGA-FR-A8YD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FR-A8YE         TCGA-FS-A1YW         TCGA-FS-A1YX 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1YY         TCGA-FS-A1Z0         TCGA-FS-A1Z4 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1Z7         TCGA-FS-A1ZA         TCGA-FS-A1ZB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZD         TCGA-FS-A1ZE         TCGA-FS-A1ZF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZH         TCGA-FS-A1ZJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZK         TCGA-FS-A1ZM         TCGA-FS-A1ZP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A1ZS         TCGA-FS-A1ZT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZU         TCGA-FS-A1ZW         TCGA-FS-A1ZY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZZ         TCGA-FS-A4F0         TCGA-FS-A4F2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F4         TCGA-FS-A4F5         TCGA-FS-A4F8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FB         TCGA-FS-A4FC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FS-A4FD         TCGA-FW-A3TV         TCGA-GF-A6C8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A267 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A4U9         TCGA-GN-A8LK         TCGA-GN-A8LL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GN-A9SD         TCGA-HR-A2OH         TCGA-W3-A824 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-A825         TCGA-W3-A828         TCGA-W3-AA1V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-W3-AA1W         TCGA-W3-AA21         TCGA-WE-A8JZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8K1         TCGA-WE-A8K5         TCGA-WE-A8ZN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZO         TCGA-WE-A8ZQ         TCGA-WE-A8ZT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-A8ZY         TCGA-WE-AA9Y         TCGA-WE-AAA0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WE-AAA3         TCGA-YD-A9TB         TCGA-YG-AA3P 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Z2-A8RT         TCGA-Z2-AA3S         TCGA-Z2-AA3V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE 130 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE  130  215
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                130
  MALE                  2                215
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     3
  10Q GAIN WILD-TYPE     5                         1   323
D20V13, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                323
[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"
D20V14, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   3
  10Q GAIN WILD-TYPE   7 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    3
  10Q GAIN WILD-TYPE    7  331
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                3                331
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    17  15
  11P GAIN WILD-TYPE 151 150
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                32                301 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                150 
$`11P GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC 
       86.76        44.19        59.57        82.29        13.32        13.22 
TCGA-DA-A3F3 TCGA-EE-A180 TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GB TCGA-EE-A2GH 
        7.00         8.12        30.44        32.15        51.12        47.21 
TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19N 
        5.42         8.84        47.51         0.95        33.60        42.84 
TCGA-ER-A42K TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-FS-A4F2 
        5.62         3.45         3.39         8.22        49.15         3.22 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LL TCGA-W3-A825 TCGA-WE-A8K6 
       10.13        15.42        14.70        14.50         8.98         7.10 
TCGA-WE-A8ZQ TCGA-WE-A8ZX 
        3.72        21.83 

$`11P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       68.22        11.41         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        64.44       114.67        15.25        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       61.38        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       21.44        32.61        25.78       110.24        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       13.68        17.72        23.11        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19         4.18       142.45       108.79        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      124.47        87.62        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       21.93         5.72         9.90        11.31        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       19.36        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       23.15        19.00        13.35        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         2.43         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.30         9.67        36.33        34.29        17.98        60.00 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       55.69         1.15        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        2.70         6.18         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35        18.41        21.73 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
       34.88         4.21        13.45        28.60        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       22.49         1.71        18.41        85.74        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        3.58         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.30        20.38        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       84.72        16.24        12.16        11.84        10.65        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        15.81         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.33         0.69       164.19        60.03         2.99        10.98 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      185.16        71.01        11.84         5.49         6.48        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       21.07        13.12         3.42         5.36         1.08        19.96 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        1.94        12.07         6.18         4.70         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.95               0.13 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             86.76             185.16 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             13.91              15.19 
[1] "0.9 - 86.8 (13.9)"  "0.1 - 185.2 (15.2)"
[1] "hr=" "1"  
D21V2, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    17  15
  11P GAIN WILD-TYPE 156 151
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                32                307 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                151 
$`11P GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC 
       86.76        62.07        59.57       166.52        60.23        66.25 
TCGA-DA-A3F3 TCGA-EE-A180 TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GB TCGA-EE-A2GH 
       10.49        94.98       369.93       195.02        59.28       208.04 
TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19N 
       13.91        21.67        61.51       201.80       148.08        44.05 
TCGA-ER-A42K TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-FS-A4F2 
        6.77        48.59        48.85        53.52       148.80        50.14 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LL TCGA-W3-A825 TCGA-WE-A8K6 
       10.13        62.79        39.58        21.37        63.02         8.61 
TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       52.34        22.68 

$`11P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
      168.00        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        66.08       130.72        58.06        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      178.32        18.18       125.19        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19        58.52       228.99       170.20        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      161.00       137.79        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         6.41        18.12        11.34        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       11.11         9.90        25.18        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       27.22         8.65        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       133.81       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        80.61        47.84        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       14.47        55.92        25.87        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.82        39.29        86.14        67.43       314.56       161.03 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
      126.81        14.30        55.59        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       28.83        19.76        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        51.35       109.58 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98        33.21        92.98       174.21        15.72       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       15.16         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72       357.37        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       84.72        64.44        32.48        46.36        12.62        50.10 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       59.41        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.33         0.69       212.22       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      219.16       105.04        24.03        38.56        54.38        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       56.98        59.41         3.75        43.73         2.20        30.18 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       10.36        15.16        36.03        14.43        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              6.77               0.16 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            369.93             357.37 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            59.425             48.890 
[1] "6.8 - 369.9 (59.4)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.2"
D21V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P GAIN MUTATED                    4             1
  11P GAIN WILD-TYPE                 57             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11P GAIN MUTATED                                           5
  11P GAIN WILD-TYPE                                        67
                    vv
clus                 REGIONAL LYMPH NODE
  11P GAIN MUTATED                    24
  11P GAIN WILD-TYPE                 185
D21V4, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  DISTANT METASTASIS                                       4                 57
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                5                 67
  REGIONAL LYMPH NODE                                     24                185
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11P GAIN MUTATED             3       1       6        1        0        2
  11P GAIN WILD-TYPE           9       6      22       16       27       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11P GAIN MUTATED           2         1         3         4          1
  11P GAIN WILD-TYPE        12        18         9        31         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED            5          2        0
  11P GAIN WILD-TYPE         27         56       19
D21V5, multiclass
             clus
vv            11P GAIN MUTATED 11P GAIN WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    1                  6
  STAGE I                    6                 22
  STAGE IA                   1                 16
  STAGE IB                   0                 27
  STAGE II                   2                 20
  STAGE IIA                  2                 12
  STAGE IIB                  1                 18
  STAGE IIC                  3                  9
  STAGE III                  4                 31
  STAGE IIIA                 1                 14
  STAGE IIIB                 5                 27
  STAGE IIIC                 2                 56
  STAGE IV                   0                 19
[1] 14  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                 T0+T1 T2 T3 T4
  11P GAIN MUTATED       5  9  5  7
  11P GAIN WILD-TYPE    58 62 69 60
D21V6, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                5                 58
  T2                   9                 62
  T3                   5                 69
  T4                   7                 60
[1] 4 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                  N0  N1  N2  N3
  11P GAIN MUTATED    19   7   2   2
  11P GAIN WILD-TYPE 149  54  36  45
D21V7, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               19                149
  N1                7                 54
  N2                2                 36
  N3                2                 45
[1] 4 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                  M0  M1 M1A M1B M1C
  11P GAIN MUTATED    31   0   0   0   0
  11P GAIN WILD-TYPE 275   4   3   4   9
D21V8, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                31                275
  M1                 0                  4
  M1A                0                  3
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  11P GAIN MUTATED    10   7
  11P GAIN WILD-TYPE 119  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10    7
  11P GAIN WILD-TYPE  119   80
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                10                119
  YES                7                 80
[1] 2 2
[1] FALSE
D21V10, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     7  26
  11P GAIN WILD-TYPE  36 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7   26
  11P GAIN WILD-TYPE   36  278
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 7                 36
  YES               26                278
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    13  21
  11P GAIN WILD-TYPE 118 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     13   21
  11P GAIN WILD-TYPE  118  196
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               13                118
  MALE                 21                196
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0    32
  11P GAIN WILD-TYPE     5                         1   294
D21V13, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   32                294
[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"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  34
  11P GAIN WILD-TYPE   7 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   34
  11P GAIN WILD-TYPE    7  300
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               34                300
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    16  11
  11Q GAIN WILD-TYPE 152 154
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                306 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                154 
$`11Q GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC 
       86.76        44.19        59.57        82.29        13.32        13.22 
TCGA-DA-A3F3 TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC 
        7.00        32.15        47.21         5.42         8.84        47.51 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19N TCGA-ER-A42K TCGA-FR-A729 TCGA-FS-A1YX 
        0.95        33.60        42.84         5.62         6.71         3.45 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A268 
        3.39         8.22        49.15         3.22         7.23        15.42 
TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX 
        7.10         3.72        21.83 

$`11Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       68.22        11.41         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        64.44       114.67        15.25        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       61.38        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       21.44        32.61        25.78       110.24        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       13.68        17.72        23.11        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19         4.18       142.45       108.79        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      124.47        87.62        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       21.93         5.72         9.90        11.31        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       19.36        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       23.15        19.00        13.35        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        60.23         4.34        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
        8.09         8.84         9.99        30.44         2.43         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        28.31        33.83        55.69         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       34.98        36.33        98.27         2.70         6.18         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        18.41        21.73        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       28.60        34.68         9.57        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       85.74        15.72         3.58         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.70         3.29        64.47        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
       15.52         7.33         7.30        20.38        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65         8.81        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
        0.16        17.33         9.90         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        84.72        10.13        16.24        12.16        14.70 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       11.84        10.65        14.50        14.50        14.50        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
        0.43        11.05         5.79        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
      164.19         8.98        60.03         2.99        10.98       185.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       71.01        11.84         5.49         6.48        18.67        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       13.12         3.42         5.36         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         4.70         8.22         6.67         5.98 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.95               0.13 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             86.76             185.16 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.22              15.01 
[1] "0.9 - 86.8 (13.2)"  "0.1 - 185.2 (15.0)"
[1] "hr=" "1.1"
D22V2, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    16  11
  11Q GAIN WILD-TYPE 157 155
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                27                312 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                155 
$`11Q GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC 
       86.76        62.07        59.57       166.52        60.23        66.25 
TCGA-DA-A3F3 TCGA-EE-A29W TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC 
       10.49       195.02       208.04        13.91        21.67        61.51 
TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19N TCGA-ER-A42K TCGA-FR-A729 TCGA-FS-A1YX 
      201.80       148.08        44.05         6.77       210.08        48.59 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A268 
       48.85        53.52       148.80        50.14         7.23        62.79 
TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZX 
        8.61        52.34        22.68 

$`11Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
      168.00        11.87       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        66.08       130.72        58.06        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      178.32        18.18       125.19        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19        58.52       228.99       170.20        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      161.00       137.79        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         6.41        18.12        11.34        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       11.11         9.90        25.18        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
       37.35        14.47        55.92       369.93        25.87        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       161.03        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48        90.97       126.81        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       44.88        94.82       129.27        28.83        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        51.35       109.58        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       50.76         9.17        77.75        98.40        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       61.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      174.21        15.72        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       29.46        94.39       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
       28.08         7.79        27.72       357.37        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55        11.41        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
        0.16        19.30         9.90         2.04        11.74       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        10.13        64.44        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       46.36        12.62        50.10        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      357.04       294.77         6.67        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
      212.22        63.02       121.08         4.01        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      105.04        24.03        38.56        54.38        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.41         3.75        43.73         2.20        30.18        10.36 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        36.03        14.43        23.64        93.07        11.74 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              6.77               0.16 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            210.08             369.93 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             59.57              49.17 
[1] "6.8 - 210.1 (59.6)" "0.2 - 369.9 (49.2)"
[1] "hr=" "1.3"
D22V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q GAIN MUTATED                    2             1
  11Q GAIN WILD-TYPE                 59             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11Q GAIN MUTATED                                           4
  11Q GAIN WILD-TYPE                                        68
                    vv
clus                 REGIONAL LYMPH NODE
  11Q GAIN MUTATED                    22
  11Q GAIN WILD-TYPE                 187
D22V4, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       2                 59
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                4                 68
  REGIONAL LYMPH NODE                                     22                187
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11Q GAIN MUTATED             3       1       7        1        0        1
  11Q GAIN WILD-TYPE           9       6      21       16       27       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11Q GAIN MUTATED           2         1         1         3          1
  11Q GAIN WILD-TYPE        12        18        11        32         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED            4          3        0
  11Q GAIN WILD-TYPE         28         55       19
D22V5, multiclass
             clus
vv            11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    1                  6
  STAGE I                    7                 21
  STAGE IA                   1                 16
  STAGE IB                   0                 27
  STAGE II                   1                 21
  STAGE IIA                  2                 12
  STAGE IIB                  1                 18
  STAGE IIC                  1                 11
  STAGE III                  3                 32
  STAGE IIIA                 1                 14
  STAGE IIIB                 4                 28
  STAGE IIIC                 3                 55
  STAGE IV                   0                 19
[1] 14  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                 T0+T1 T2 T3 T4
  11Q GAIN MUTATED       7  8  4  4
  11Q GAIN WILD-TYPE    56 63 70 63
D22V6, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                7                 56
  T2                   8                 63
  T3                   4                 70
  T4                   4                 63
[1] 4 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                  N0  N1  N2  N3
  11Q GAIN MUTATED    17   6   2   3
  11Q GAIN WILD-TYPE 151  55  36  44
D22V7, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               17                151
  N1                6                 55
  N2                2                 36
  N3                3                 44
[1] 4 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                  M0  M1 M1A M1B M1C
  11Q GAIN MUTATED    28   0   0   0   0
  11Q GAIN WILD-TYPE 278   4   3   4   9
D22V8, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                28                278
  M1                 0                  4
  M1A                0                  3
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  11Q GAIN MUTATED    10   4
  11Q GAIN WILD-TYPE 119  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10    4
  11Q GAIN WILD-TYPE  119   83
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                10                119
  YES                4                 83
[1] 2 2
[1] FALSE
D22V10, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     7  21
  11Q GAIN WILD-TYPE  36 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7   21
  11Q GAIN WILD-TYPE   36  283
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 7                 36
  YES               21                283
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    11  18
  11Q GAIN WILD-TYPE 120 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     11   18
  11Q GAIN WILD-TYPE  120  199
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               11                120
  MALE                 18                199
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0    27
  11Q GAIN WILD-TYPE     5                         1   299
D22V13, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   27                299
[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"
D22V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  29
  11Q GAIN WILD-TYPE   7 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   29
  11Q GAIN WILD-TYPE    7  305
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               29                305
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    25  35
  12P GAIN WILD-TYPE 143 130
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                60                273 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                35                130 
$`12P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CC 
       16.47        70.16        22.55        56.19        15.25        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC 
       13.32        24.00        29.23        52.01        23.11        22.06 
TCGA-D3-A8GL TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A1IA 
       38.93         9.90        13.22        35.80        36.69         4.93 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 
       17.56        13.15         0.13        13.35        10.55         8.12 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        9.21        11.15         8.09         9.67        36.33        51.12 
TCGA-EE-A2GH TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A3AA TCGA-EE-A3AD 
       47.21        36.33         8.84        98.27       124.31         3.68 
TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C 
       21.60        18.41        33.60        12.95        25.18         3.78 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 
        4.21        13.45        28.60         6.58         1.71         6.71 
TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK 
       47.38         8.68         3.22        16.24        12.16        14.50 
TCGA-W3-A825 TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZX TCGA-YG-AA3O TCGA-YG-AA3P 
        8.98       185.16        71.01        21.83         6.18         4.70 

$`12P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      110.79        28.08        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       44.19         7.50        36.16         6.31        92.42        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3ML 
       59.57       114.67        46.98        46.32        82.29         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        26.37        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.31        32.28        21.44        32.61        25.78       110.24 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
       47.87        13.68        17.72        29.72        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
        4.18       142.45       108.79        75.65       124.47        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       11.44         5.56        24.07         4.01        21.93         5.72 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        14.60        48.79        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       13.68         9.99        44.52        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       19.36         7.00        14.83         0.20        23.15        19.00 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       13.22         0.20        11.57         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       12.20         5.13         4.31        60.23         4.34        15.85 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 
        8.84         9.99        30.44         2.43        32.15        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       49.22        36.30        34.29        17.98        60.00        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        55.69 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2M8 
        5.42         1.15        13.02        34.98         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       47.51         9.53        29.46         2.73        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       125.65       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        60.49        53.16        52.67         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
        3.22        22.92        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       27.35        21.73        31.40        18.61        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       76.41         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       11.74         9.04        22.49         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       15.72         3.58         5.36        13.28         2.20         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.29        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
       52.08         8.65         8.81        49.15        40.64        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       11.61        44.28        31.33        84.72        10.13        15.42 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       14.70        11.84        10.65        14.50        14.50        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
        0.43        11.05         5.79        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 
      164.19        60.03         2.99        10.98        11.84         5.49 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        6.48         7.10        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.42         5.36         1.08        19.96         1.94        12.07 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        8.22         6.67         5.98 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.13               0.13 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            185.16             164.19 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            15.745             14.600 
[1] "0.1 - 185.2 (15.7)" "0.1 - 164.2 (14.6)"
[1] "hr=" "1.2"
D23V2, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    25  35
  12P GAIN WILD-TYPE 148 131
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                60                279 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                35                131 
$`12P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CC 
       16.57        71.80        31.59        56.19        58.06        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D3-A8GC 
       60.23        24.53        45.30       135.75       125.19        79.59 
TCGA-D3-A8GL TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A1IA 
       89.13         9.90        66.25        36.03        61.18        65.92 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 
      215.44        13.87        17.85        17.29        27.22        94.98 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
      168.26        13.97        17.92        39.29        86.14        59.28 
TCGA-EE-A2GH TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A3AA TCGA-EE-A3AD 
      208.04        94.82        21.67       129.27       124.31         3.68 
TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19C 
       36.95        51.35       148.08        13.94        98.40        48.89 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 
        6.44       131.51        61.05        80.32        33.21       210.08 
TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK 
      101.26        26.56        50.14        64.44        32.48        50.10 
TCGA-W3-A825 TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8ZX TCGA-YG-AA3O TCGA-YG-AA3P 
       63.02       219.16       105.04        22.68        36.03        14.43 

$`12P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       62.07       113.52        42.08        12.10       171.58        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3ML 
       59.57       130.72        46.98        46.32       166.52        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        39.75       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
      137.92       178.32        18.18        30.84        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
       58.52       228.99       170.20        95.24       161.00       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA 
        6.41        18.12        11.34        22.29        11.11        25.18 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        48.89       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       107.34        53.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       10.49        15.68        10.16        68.25        54.02        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        6.35        12.20        29.82         8.65        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       26.89        68.15         4.96       133.81       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       13.55        63.35        80.61        47.84        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 
       14.47        55.92       369.93        25.87       195.02        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
      102.90        36.82        67.43       314.56       161.03        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       89.33        54.74        79.66        75.48        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.91        14.30        55.59        44.88        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       134.40       162.48        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      172.18       127.20        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       27.35       109.58        31.40        35.44        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       77.75        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        46.98         6.77        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       15.72        15.16         7.00        38.27        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       94.39       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
       74.73       133.55        11.41       148.80        53.16        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       11.74       139.89       117.93        84.72        10.13        62.79 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       39.58        46.36        12.62        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      357.04       294.77         6.67        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 
      212.22       121.08         4.01        42.08        24.03        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       54.38         8.61        90.28        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.75        43.73         2.20        30.18        10.36        15.16 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              3.68               0.16 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            219.16             369.93 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             58.67              48.85 
[1] "3.7 - 219.2 (58.7)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.2"
D23V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P GAIN MUTATED                    8             2
  12P GAIN WILD-TYPE                 53             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12P GAIN MUTATED                                          15
  12P GAIN WILD-TYPE                                        57
                    vv
clus                 REGIONAL LYMPH NODE
  12P GAIN MUTATED                    34
  12P GAIN WILD-TYPE                 175
D23V4, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  DISTANT METASTASIS                                       8                 53
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               15                 57
  REGIONAL LYMPH NODE                                     34                175
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12P GAIN MUTATED             0       0       9        2        6        2
  12P GAIN WILD-TYPE          12       7      19       15       21       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12P GAIN MUTATED           0         1         3        10          5
  12P GAIN WILD-TYPE        14        18         9        25         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           11          6        2
  12P GAIN WILD-TYPE         21         52       17
D23V5, multiclass
             clus
vv            12P GAIN MUTATED 12P GAIN WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    9                 19
  STAGE IA                   2                 15
  STAGE IB                   6                 21
  STAGE II                   2                 20
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  3                  9
  STAGE III                 10                 25
  STAGE IIIA                 5                 10
  STAGE IIIB                11                 21
  STAGE IIIC                 6                 52
  STAGE IV                   2                 17
[1] 14  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                 T0+T1 T2 T3 T4
  12P GAIN MUTATED      16 15 10 11
  12P GAIN WILD-TYPE    47 56 64 56
D23V6, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               16                 47
  T2                  15                 56
  T3                  10                 64
  T4                  11                 56
[1] 4 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                  N0  N1  N2  N3
  12P GAIN MUTATED    24  21   5   6
  12P GAIN WILD-TYPE 144  40  33  41
D23V7, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               24                144
  N1               21                 40
  N2                5                 33
  N3                6                 41
[1] 4 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                  M0  M1 M1A M1B M1C
  12P GAIN MUTATED    55   1   1   0   0
  12P GAIN WILD-TYPE 251   3   2   4   9
D23V8, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                55                251
  M1                 1                  3
  M1A                1                  2
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  12P GAIN MUTATED    26  13
  12P GAIN WILD-TYPE 103  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     26   13
  12P GAIN WILD-TYPE  103   74
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                26                103
  YES               13                 74
[1] 2 2
[1] FALSE
D23V10, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     8  52
  12P GAIN WILD-TYPE  35 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8   52
  12P GAIN WILD-TYPE   35  252
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 8                 35
  YES               52                252
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    23  37
  12P GAIN WILD-TYPE 108 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     23   37
  12P GAIN WILD-TYPE  108  180
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               23                108
  MALE                 37                180
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       3                         0    54
  12P GAIN WILD-TYPE     2                         1   272
D23V13, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   54                272
[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"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     2  57
  12P GAIN WILD-TYPE   5 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   57
  12P GAIN WILD-TYPE    5  277
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               57                277
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    15  21
  12Q GAIN WILD-TYPE 153 144
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                297 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                144 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CF 
       70.16        22.55        56.19        64.44        15.25        24.00 
TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GL TCGA-DA-A1HW TCGA-DA-A3F5 
       52.01        17.72        23.11        38.93        35.80        17.56 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
       13.15        13.35        10.55         8.12        11.15        36.33 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI 
       51.12        47.21         8.84        21.60        18.41        33.60 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19L TCGA-FR-A729 TCGA-FS-A1ZK TCGA-FS-A1ZM 
       25.18         3.78        13.45         6.71        12.89        47.38 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-W3-A825 TCGA-WE-A8ZX TCGA-YG-AA3O 
       16.24        12.16        14.50         8.98        21.83         6.18 

$`12Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       32.42       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        44.19         7.50        36.16         6.31        92.42 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       59.57       114.67        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       13.32         6.31         9.34       103.59        26.37        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GB 
       32.61        25.78       110.24        47.87        13.68        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       22.06        10.22        15.19         4.18       142.45       108.79 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       75.65       124.47        87.62        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        4.01        21.93         5.72         9.90        11.31        13.22 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       14.60        48.79        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH 
        6.64        19.36         7.00        14.83         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       23.15        19.00        13.22         0.20        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        62.79         8.55        36.85         1.08        39.62 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        9.50        12.03         8.09         8.84         9.99        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
        9.67        34.29        17.98        60.00        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 
       16.14        22.22         0.95        27.35        21.73        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
       18.61        12.95        38.40         5.72        76.41         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       11.90        11.11       114.15        34.88         4.21        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       18.41        85.74        15.72         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        2.20         4.70         3.29        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.92        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
        8.68        27.39         0.82         5.23        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        10.13        15.42        14.70        11.84        10.65 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.33         0.69       164.19        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       10.98       185.16        71.01        11.84         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        7.10        18.67        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P 
        5.36         1.08        19.96         1.94        12.07         4.70 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        8.22         6.67         5.98 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              3.78               0.13 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             70.16             185.16 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            18.065             14.500 
[1] "3.8 - 70.2 (18.1)"  "0.1 - 185.2 (14.5)"
[1] "hr=" "1.1"
D24V2, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    15  21
  12Q GAIN WILD-TYPE 158 145
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                303 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                145 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CF 
       71.80        31.59        56.19        66.08        58.06        24.53 
TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GL TCGA-DA-A1HW TCGA-DA-A3F5 
      135.75        18.18       125.19        89.13        36.03       215.44 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
       13.87        17.29        27.22        94.98        13.97        86.14 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI 
       59.28       208.04        21.67        36.95        51.35       148.08 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19L TCGA-FR-A729 TCGA-FS-A1ZK TCGA-FS-A1ZM 
       98.40        48.89       131.51       210.08        23.93       101.26 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A8LK TCGA-W3-A825 TCGA-WE-A8ZX TCGA-YG-AA3O 
       64.44        32.48        50.10        63.02        22.68        36.03 

$`12Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      112.57       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       59.57       130.72        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       60.23        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GB 
       63.81        26.89       125.79       137.92       178.32        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        11.61        15.19        58.52       228.99       170.20 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       95.24       161.00       137.79        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       22.29        11.11         9.90        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       28.60        10.49        15.68        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       54.02        52.01         6.35        12.20        29.82         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        91.56       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       47.84        63.78        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        37.35        14.47        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.29        67.43       314.56       161.03        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        23.47       138.81       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 
       34.32        53.19       201.80        27.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
       35.44        13.94        50.76         9.17        77.75        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       13.02        26.37       268.93       152.35         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       92.98       174.21        15.72        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        29.46        94.39       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        10.13        62.79        39.58        46.36        12.62 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       21.37        59.41        65.88       357.04       294.77         6.67 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.33         0.69       212.22       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        38.56        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.61        90.28        56.98        59.41        52.34         3.75 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P 
       43.73         2.20        30.18        10.36        15.16        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             13.87               0.16 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            215.44             369.93 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            57.125             49.450 
[1] "13.9 - 215.4 (57.1)" "0.2 - 369.9 (49.5)" 
[1] "hr=" "1.2"
D24V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q GAIN MUTATED                    4             0
  12Q GAIN WILD-TYPE                 57             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12Q GAIN MUTATED                                           9
  12Q GAIN WILD-TYPE                                        63
                    vv
clus                 REGIONAL LYMPH NODE
  12Q GAIN MUTATED                    23
  12Q GAIN WILD-TYPE                 186
D24V4, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       4                 57
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                9                 63
  REGIONAL LYMPH NODE                                     23                186
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12Q GAIN MUTATED             0       0       6        1        3        2
  12Q GAIN WILD-TYPE          12       7      22       16       24       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12Q GAIN MUTATED           0         0         0         6          2
  12Q GAIN WILD-TYPE        14        19        12        29         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED            7          5        1
  12Q GAIN WILD-TYPE         25         53       18
D24V5, multiclass
             clus
vv            12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    6                 22
  STAGE IA                   1                 16
  STAGE IB                   3                 24
  STAGE II                   2                 20
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  0                 12
  STAGE III                  6                 29
  STAGE IIIA                 2                 13
  STAGE IIIB                 7                 25
  STAGE IIIC                 5                 53
  STAGE IV                   1                 18
[1] 14  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                 T0+T1 T2 T3 T4
  12Q GAIN MUTATED       9  8  5  7
  12Q GAIN WILD-TYPE    54 63 69 60
D24V6, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                9                 54
  T2                   8                 63
  T3                   5                 69
  T4                   7                 60
[1] 4 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                  N0  N1  N2  N3
  12Q GAIN MUTATED    12  14   2   4
  12Q GAIN WILD-TYPE 156  47  36  43
D24V7, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               12                156
  N1               14                 47
  N2                2                 36
  N3                4                 43
[1] 4 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                  M0  M1 M1A M1B M1C
  12Q GAIN MUTATED    32   0   0   0   1
  12Q GAIN WILD-TYPE 274   4   3   4   8
D24V8, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                32                274
  M1                 0                  4
  M1A                0                  3
  M1B                0                  4
  M1C                1                  8
[1] 5 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
  12Q GAIN MUTATED    15   8
  12Q GAIN WILD-TYPE 114  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     15    8
  12Q GAIN WILD-TYPE  114   79
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                15                114
  YES                8                 79
[1] 2 2
[1] FALSE
D24V10, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  34
  12Q GAIN WILD-TYPE  41 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   34
  12Q GAIN WILD-TYPE   41  270
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 2                 41
  YES               34                270
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    10  26
  12Q GAIN WILD-TYPE 121 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     10   26
  12Q GAIN WILD-TYPE  121  191
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               10                121
  MALE                 26                191
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         0    32
  12Q GAIN WILD-TYPE     3                         1   294
D24V13, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   32                294
[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"
D24V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1  34
  12Q GAIN WILD-TYPE   6 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   34
  12Q GAIN WILD-TYPE    6  300
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               34                300
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    34  51
  13Q GAIN WILD-TYPE 134 114
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                85                248 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                51                114 
$`13Q GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JP 
        6.97        16.47         8.52        70.16        44.19        59.57 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU 
       15.25        61.38        13.32        25.78        47.87        23.11 
TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44R 
        4.18        38.93        75.65        36.69         7.00         0.20 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20H 
       23.15        13.35        10.55         8.12        60.23         9.21 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A5 
        7.99         9.90         8.55        12.03         8.84         9.67 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M7 
       51.12        47.21        28.31        33.83         5.42         2.70 
TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 
        2.73        26.99       124.31        13.81         3.22        21.60 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       22.22        33.60        12.95         5.72         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2NC 
       11.90        13.45        28.60        42.84        34.68        11.80 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX 
        1.71        15.72         6.71         2.20        64.47         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZJ 
       23.80        14.24        15.52         7.33        19.53        12.92 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-FW-A3TU 
        8.65        40.64         0.82         3.22         2.27         0.13 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-AA9O 
       84.72        16.24        15.42        10.65        11.05        18.05 
TCGA-W3-A824 TCGA-W3-A825 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-AAA3 
      164.19         8.98        11.84         7.10        21.83         1.94 
TCGA-Z2-A8RT 
        8.22 

$`13Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        3.02         6.97       111.09        32.42       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       22.55        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        86.76        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       36.16         6.31        92.42        56.19        64.44       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32        82.29        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61       110.24        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       13.68        17.72        29.72        22.06        10.22        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      142.45       108.79       124.47        87.62        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       24.07         4.01        21.93         5.72         9.90        11.31 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       13.22        14.60        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19        13.68         9.99        44.52        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36         6.64        19.36        17.56        14.83        13.15 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
        0.13        19.00        13.22         0.20        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
        1.12         1.35        12.20         5.13         4.31         4.34 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       15.85         1.18        37.97        11.15        62.79        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
        1.08        39.62         9.50         8.09         9.99        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       36.33        34.29        17.98        60.00        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       16.01        35.54        55.69         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       36.33         8.84        98.27         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      111.91        56.02        25.08        21.60        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67         5.56       122.73        51.62         3.68        30.15 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB 
       15.95        12.72        22.92        21.60        16.14         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        18.41        21.73        31.40        18.61        38.40 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       76.41        25.18        11.11       114.15        34.88         4.21 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
        9.57        36.07         6.58        17.72        78.44         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 
       22.49         5.62        18.41        85.74         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZB 
       13.28         4.70         3.29        11.01         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
       20.38         8.22        11.08         7.17        30.87        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
       47.38        52.08         8.81        49.15         8.68        27.39 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
        5.98         6.41         0.20         0.99         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        31.33 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
       10.13        12.16        14.70        11.84        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       14.50        15.81         0.43         5.79         0.33         0.69 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
       60.03         2.99        10.98       185.16        71.01         5.49 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        6.48        18.67        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        5.36         1.08        19.96        12.07         6.18         4.70 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.13               0.13 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            164.19             185.16 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             13.32              15.90 
[1] "0.1 - 164.2 (13.3)" "0.1 - 185.2 (15.9)"
[1] "hr=" "1.5"
D25V2, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    34  51
  13Q GAIN WILD-TYPE 139 115
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                85                254 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                51                115 
$`13Q GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JP 
       12.99        16.57        16.67        71.80        62.07        59.57 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU 
       58.06        86.93        60.23        26.89       137.92       125.19 
TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EB-A44R 
       58.52        89.13        95.24        61.18        10.49        10.16 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20H 
       68.25        17.29        27.22        94.98       133.81       168.26 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A5 
       63.35        80.61        72.07        56.42        14.47        39.29 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M7 
       59.28       208.04        75.48        90.97        13.91        28.83 
TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 
      268.73       248.65       124.31        13.81       172.18        64.08 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       53.19       148.08        13.94         9.17        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2NC 
       13.02       131.51        61.05        44.05       162.08        43.82 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX 
       33.21        15.72       210.08        34.82       216.92        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZJ 
      202.65        20.91        28.08         7.79        40.27        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-FW-A3TU 
      133.55        53.16        27.09        50.14        77.88        47.54 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-AA9O 
       84.72        64.44        62.79        12.62       294.77        18.05 
TCGA-W3-A824 TCGA-W3-A825 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-AAA3 
      212.22        63.02        24.03         8.61        22.68        10.36 
TCGA-Z2-A8RT 
       23.64 

$`13Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       17.03        61.02       112.04       112.57       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       31.59        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        86.76        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       42.08        12.10       171.58        56.19        66.08       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32       166.52        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81       125.79       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
      178.32        18.18        30.84        79.59        11.61        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      228.99       170.20       161.00       137.79        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       11.34        22.29        11.11         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55        35.93       107.34        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       68.09        28.60       215.44        15.68        13.87        17.85 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       54.02        52.01         6.35        12.20        29.82         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
       33.73        14.70        26.89        68.15         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       91.56        13.55        47.84        13.97        63.78        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
        2.60        56.84        18.61        37.35        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        67.43       314.56       161.03        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       54.74        79.66       126.81        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82        21.67       129.27        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      203.05       167.90        47.54        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21        53.26       122.73        51.62         3.68        54.51 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB 
       23.47       138.81       127.20        36.95        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        51.35       109.58        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       77.75        98.40        26.37       268.93       152.35         6.44 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
       50.89        37.25         8.88       148.18        79.99        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 
       46.98         6.77        92.98       174.21        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZB 
       38.27        29.46        94.39       228.59        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
      357.37        53.52        15.45         9.70        32.75        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
      101.26        74.73        11.41       148.80        26.56        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        49.45         0.20        22.92         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       117.93 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
       10.13        32.48        39.58        46.36        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       59.41        65.88       357.04         6.67         0.33         0.69 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      121.08         4.01        42.08       219.16       105.04        38.56 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       54.38        90.28        56.98        59.41        52.34         3.75 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
       43.73         2.20        30.18        15.16        36.03        14.43 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              7.79               0.16 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            294.77             369.93 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             58.06              48.87 
[1] "7.8 - 294.8 (58.1)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.3"
D25V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q GAIN MUTATED                   20             0
  13Q GAIN WILD-TYPE                 41             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  13Q GAIN MUTATED                                          19
  13Q GAIN WILD-TYPE                                        53
                    vv
clus                 REGIONAL LYMPH NODE
  13Q GAIN MUTATED                    51
  13Q GAIN WILD-TYPE                 158
D25V4, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      20                 41
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               19                 53
  REGIONAL LYMPH NODE                                     51                158
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  13Q GAIN MUTATED             3       1      12        3       10        4
  13Q GAIN WILD-TYPE           9       6      16       14       17       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  13Q GAIN MUTATED           1         6         6         6          4
  13Q GAIN WILD-TYPE        13        13         6        29         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           11         12        3
  13Q GAIN WILD-TYPE         21         46       16
D25V5, multiclass
             clus
vv            13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    1                  6
  STAGE I                   12                 16
  STAGE IA                   3                 14
  STAGE IB                  10                 17
  STAGE II                   4                 18
  STAGE IIA                  1                 13
  STAGE IIB                  6                 13
  STAGE IIC                  6                  6
  STAGE III                  6                 29
  STAGE IIIA                 4                 11
  STAGE IIIB                11                 21
  STAGE IIIC                12                 46
  STAGE IV                   3                 16
[1] 14  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                 T0+T1 T2 T3 T4
  13Q GAIN MUTATED      14 26 12 19
  13Q GAIN WILD-TYPE    49 45 62 48
D25V6, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               14                 49
  T2                  26                 45
  T3                  12                 62
  T4                  19                 48
[1] 4 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                  N0  N1  N2  N3
  13Q GAIN MUTATED    49  18   6   8
  13Q GAIN WILD-TYPE 119  43  32  39
D25V7, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               49                119
  N1               18                 43
  N2                6                 32
  N3                8                 39
[1] 4 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                  M0  M1 M1A M1B M1C
  13Q GAIN MUTATED    80   1   1   0   1
  13Q GAIN WILD-TYPE 226   3   2   4   8
D25V8, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                80                226
  M1                 1                  3
  M1A                1                  2
  M1B                0                  4
  M1C                1                  8
[1] 5 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
  13Q GAIN MUTATED    28  25
  13Q GAIN WILD-TYPE 101  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     28   25
  13Q GAIN WILD-TYPE  101   62
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                28                101
  YES               25                 62
[1] 2 2
[1] FALSE
D25V10, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    12  79
  13Q GAIN WILD-TYPE  31 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     12   79
  13Q GAIN WILD-TYPE   31  225
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                12                 31
  YES               79                225
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    34  57
  13Q GAIN WILD-TYPE  97 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     34   57
  13Q GAIN WILD-TYPE   97  160
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               34                 97
  MALE                 57                160
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       2                         0    85
  13Q GAIN WILD-TYPE     3                         1   241
D25V13, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   85                241
[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"
D25V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1  86
  13Q GAIN WILD-TYPE   6 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   86
  13Q GAIN WILD-TYPE    6  248
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               86                248
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    20  20
  14Q GAIN WILD-TYPE 148 145
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                40                293 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                20                145 
$`14Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A8GK TCGA-D3-A8GM 
       22.55        88.50        92.42        15.25       108.79        75.65 
TCGA-D9-A6E9 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H 
        9.90        13.68        36.69        19.00         8.12         9.21 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GO 
       11.15         1.08        39.62        47.21        28.31        55.69 
TCGA-EE-A2M5 TCGA-EE-A2MJ TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3JH TCGA-ER-A19C 
        8.84        63.42         5.56        30.15        21.73         3.78 
TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FR-A8YD 
       13.45        28.60        15.72         6.71         2.20         4.70 
TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A9SD 
       52.08        27.39         0.82        84.72        14.70        14.50 
TCGA-QB-AA9O TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-AAA3 
       18.05        60.03         2.99         1.94 

$`14Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       32.42        70.16       110.79        28.08        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       10.29        85.32         8.38        21.14        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       11.41        44.19         7.50        36.16         6.31        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       64.44        59.57       114.67        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       61.38        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.28        21.44        32.61        25.78       110.24        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       47.87        13.68        17.72        23.11        29.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GN 
       10.22        15.19         4.18       142.45        38.93       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        5.72        11.31        13.22        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       51.12        10.03        39.19         9.99        44.52        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL 
       14.83        13.15         0.20         0.13        23.15        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
       13.22         0.20        11.57        10.55         6.31         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       15.85         1.18         7.99         9.90        37.97        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        8.55        36.85         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        30.08        19.43        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
        2.73        44.25         7.96        14.56       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       52.67       124.31       122.73        51.62         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       16.14        22.22         0.95        27.35        18.41        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       25.18         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
        4.21        42.84        34.68         9.57        36.07         6.58 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       12.62        11.74         9.04         6.58        22.49         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
        5.62        18.41        85.74         3.58         5.36        13.28 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.29        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        5.23        53.85         3.22         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       11.61        44.28        31.33        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH 
       12.16        11.84        10.65        14.50        14.50        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.43        11.05         5.79         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
        8.98        10.98       185.16        71.01        11.84         5.49 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        6.48         7.10        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
        3.42        21.83         5.36         1.08        19.96        12.07 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         4.70         8.22         6.67         5.98 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.82               0.13 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            108.79             185.16 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            16.885             14.500 
[1] "0.8 - 108.8 (16.9)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.1"
D26V2, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    20  20
  14Q GAIN WILD-TYPE 153 146
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                40                299 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                20                146 
$`14Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A8GK TCGA-D3-A8GM 
       31.59       115.53       171.58        58.06       170.20        95.24 
TCGA-D9-A6E9 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H 
        9.90       176.55        61.18        54.02        94.98       168.26 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GO 
       13.97         2.60        56.84       208.04        75.48       126.81 
TCGA-EE-A2M5 TCGA-EE-A2MJ TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3JH TCGA-ER-A19C 
       21.67        96.23        53.26        54.51       109.58        48.89 
TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FR-A8YD 
      131.51        61.05        15.72       210.08        34.82        29.46 
TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A9SD 
       74.73        49.48        27.09        84.72        39.58        59.41 
TCGA-QB-AA9O TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-AAA3 
       18.05       121.08         4.01        10.36 

$`14Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       43.43       103.10        65.49        23.77       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       11.87        62.07       113.52        42.08        12.10        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.08        59.57       130.72        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       86.93        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      137.92       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GN 
       11.61        15.19        58.52       228.99        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      137.79        29.06       129.63       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         6.41        18.12        11.34        22.29        11.11 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
       20.38       194.83        35.93       107.34        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        17.85        68.25        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        6.35        12.20        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       91.56        13.55        63.35        80.61        47.84        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07        64.64        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       55.92       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03        48.72        89.33        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       71.21       124.31       122.73        51.62         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       23.47       138.81       172.18       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       34.32        53.19       201.80        27.35        51.35       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
        6.44        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
        6.77        92.98       174.21        15.16         7.00        38.27 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       94.39       216.92        48.59       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       11.74       139.89       117.93        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH 
       32.48        46.36        12.62        50.10        21.37        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      357.04       294.77         6.67         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
       63.02        42.08       219.16       105.04        24.03        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       54.38         8.61        90.28        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
        3.75        22.68        43.73         2.20        30.18        15.16 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        23.64        93.07        11.74 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              2.60               0.16 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            210.08             369.93 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            58.735             48.720 
[1] "2.6 - 210.1 (58.7)" "0.2 - 369.9 (48.7)"
[1] "hr=" "1.1"
D26V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q GAIN MUTATED                    7             1
  14Q GAIN WILD-TYPE                 54             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  14Q GAIN MUTATED                                           6
  14Q GAIN WILD-TYPE                                        66
                    vv
clus                 REGIONAL LYMPH NODE
  14Q GAIN MUTATED                    27
  14Q GAIN WILD-TYPE                 182
D26V4, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       7                 54
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                6                 66
  REGIONAL LYMPH NODE                                     27                182
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  14Q GAIN MUTATED             1       1       5        3        4        3
  14Q GAIN WILD-TYPE          11       6      23       14       23       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  14Q GAIN MUTATED           1         3         3         4          2
  14Q GAIN WILD-TYPE        13        16         9        31         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED            3          6        0
  14Q GAIN WILD-TYPE         29         52       19
D26V5, multiclass
             clus
vv            14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  I OR II NOS                1                 11
  STAGE 0                    1                  6
  STAGE I                    5                 23
  STAGE IA                   3                 14
  STAGE IB                   4                 23
  STAGE II                   3                 19
  STAGE IIA                  1                 13
  STAGE IIB                  3                 16
  STAGE IIC                  3                  9
  STAGE III                  4                 31
  STAGE IIIA                 2                 13
  STAGE IIIB                 3                 29
  STAGE IIIC                 6                 52
  STAGE IV                   0                 19
[1] 14  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                 T0+T1 T2 T3 T4
  14Q GAIN MUTATED       5 10  9 10
  14Q GAIN WILD-TYPE    58 61 65 57
D26V6, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                5                 58
  T2                  10                 61
  T3                   9                 65
  T4                  10                 57
[1] 4 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                  N0  N1  N2  N3
  14Q GAIN MUTATED    25   4   5   3
  14Q GAIN WILD-TYPE 143  57  33  44
D26V7, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               25                143
  N1                4                 57
  N2                5                 33
  N3                3                 44
[1] 4 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                  M0  M1 M1A M1B M1C
  14Q GAIN MUTATED    37   0   0   0   0
  14Q GAIN WILD-TYPE 269   4   3   4   9
D26V8, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                37                269
  M1                 0                  4
  M1A                0                  3
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  14Q GAIN MUTATED    15  13
  14Q GAIN WILD-TYPE 114  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15   13
  14Q GAIN WILD-TYPE  114   74
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                15                114
  YES               13                 74
[1] 2 2
[1] FALSE
D26V10, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5  36
  14Q GAIN WILD-TYPE  38 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   36
  14Q GAIN WILD-TYPE   38  268
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 5                 38
  YES               36                268
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    14  27
  14Q GAIN WILD-TYPE 117 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     14   27
  14Q GAIN WILD-TYPE  117  190
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               14                117
  MALE                 27                190
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0    40
  14Q GAIN WILD-TYPE     5                         1   286
D26V13, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   40                286
[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"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  41
  14Q GAIN WILD-TYPE   7 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   41
  14Q GAIN WILD-TYPE    7  293
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               41                293
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    37  40
  15Q GAIN WILD-TYPE 131 125
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                77                256 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                40                125 
$`15Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       32.42        22.55        21.14        88.50        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MV 
       44.19        92.42        56.19        82.29        13.32        29.23 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A6EA 
       10.22         4.18        38.93        75.65        11.44        11.31 
TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A183 TCGA-EE-A20B 
       35.80        36.69        17.56        10.55        12.20        60.23 
TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
        9.21        11.15        30.44        32.15         8.09        49.22 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 
       30.08        28.31        55.69         5.42        98.27         2.70 
TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
       63.42        25.08        26.99        60.49        53.16       124.31 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3JH TCGA-EE-A3JI 
       30.15        15.95         3.22        21.60        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T 
       31.40         3.78        28.60        34.68        36.07         6.58 
TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A8YC 
        5.62        85.74        15.72         6.71         5.36         2.20 
TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-GF-A4EO 
       14.24         8.22         0.82         3.22         2.27         7.23 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-A828 
       11.61        31.33        16.24        14.50         8.98        60.03 
TCGA-W3-AA1O TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX 
        2.99         7.10        18.67         3.72        21.83 

$`15Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       85.32         8.38        68.22         7.50        36.16         6.31 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        59.57       114.67        15.25        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       61.38        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.61        25.78       110.24        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ 
       17.72        23.11        29.72        22.06        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      108.79       124.47        87.62         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       21.93         5.72         9.90        13.22        14.60        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       14.83        13.15         0.20         0.13        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       13.35        13.22         0.20        11.57         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        1.12         1.35         5.13         4.31         4.34        15.85 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.84         9.99         2.43        11.31        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       19.43        16.01        35.54        33.83         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       34.98        36.33         8.84         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       29.46         2.73        44.25         7.96        14.56       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      111.91        56.02        21.60        52.67         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 
       51.62         3.68        13.81        12.72        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 
       16.14        22.22         0.95        27.35        18.41        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       12.95        38.40         5.72        76.41        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       42.84         9.57        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD 
       22.49         1.71        18.41         3.58        13.28         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        3.29        64.47         3.45        11.01        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         7.30         3.39        20.38        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
       17.33         9.90         0.85        44.28        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       15.42        12.16        14.70        11.84        10.65        14.50 
TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        15.81         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        0.33         0.69       164.19        10.98       185.16        71.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       11.84         5.49         6.48        21.07        13.12         3.42 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        5.36         1.08        19.96         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.82               0.13 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            124.31             185.16 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            21.600             13.745 
[1] "0.8 - 124.3 (21.6)" "0.1 - 185.2 (13.7)"
[1] "hr=" "1.1"
D27V2, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    38  40
  15Q GAIN WILD-TYPE 135 126
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                78                261 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                40                126 
$`15Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      112.57        31.59        23.77       115.53        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MV 
       62.07       171.58        56.19       166.52        60.23        45.30 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A149 
       11.61        58.52        89.13        95.24        29.06        54.67 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A183 
       25.18        36.03        61.18       215.44        27.22        26.89 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
      133.81       168.26        13.97       369.93       195.02        17.92 
TCGA-EE-A2A1 TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
      102.90        48.72        75.48       126.81        13.91       129.27 
TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
       28.83        96.23        47.54       248.65       134.40       162.48 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3JH 
      124.31        54.51        23.47       172.18        36.95       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S 
      148.08        31.40        48.89        61.05       162.08        37.25 
TCGA-ER-A19T TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 
        8.88         6.77       174.21        15.72       210.08         7.00 
TCGA-FR-A8YC TCGA-FS-A1Z3 TCGA-FS-A1ZD TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD 
       34.82        20.91        53.52        27.09        50.14        77.88 
TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A9SD TCGA-W3-A825 
        7.23        11.74       117.93        64.44        59.41        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX 
      121.08         4.01         8.61        90.28        52.34        22.68 

$`15Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      103.10        65.49       168.00       113.52        42.08        12.10 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        79.59        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      170.20       161.00       137.79       129.63       117.17       151.53 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         6.41        18.12        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        66.25        22.95        48.89       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
      194.83       176.55        35.93       107.34        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.16        17.85        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        6.35        12.20        29.82         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       14.70        68.15         4.96       151.27        91.56        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        63.78        72.07        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       55.92        25.87        46.82        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       59.28        67.43       314.56       161.03       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       54.74        79.66        90.97        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       94.82        21.67        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      167.90        43.23        71.21        53.26       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
        3.68        13.81       138.81       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 
       53.19       201.80        27.35        51.35        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       50.76         9.17        77.75        98.40        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       26.37       268.93       152.35         6.44       131.51        44.05 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       50.89       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
       33.21        92.98        15.16        38.27        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92        48.59       228.59       202.65        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       27.72        48.85       357.37        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       11.41       148.80        53.16        26.56        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        9.90         2.04       139.89        84.72        10.13        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       32.48        39.58        46.36        12.62        50.10        21.37 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       357.04       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        0.69       212.22        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY 
       38.56        54.38        56.98        59.41         3.75        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        2.20        30.18        10.36        15.16        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              4.01               0.16 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            369.93             357.37 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            57.355             48.590 
[1] "4.0 - 369.9 (57.4)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.1"
D27V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q GAIN MUTATED                   12             2
  15Q GAIN WILD-TYPE                 49             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  15Q GAIN MUTATED                                          15
  15Q GAIN WILD-TYPE                                        57
                    vv
clus                 REGIONAL LYMPH NODE
  15Q GAIN MUTATED                    54
  15Q GAIN WILD-TYPE                 155
D27V4, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      12                 49
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               15                 57
  REGIONAL LYMPH NODE                                     54                155
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  15Q GAIN MUTATED             6       2       8        5        5        8
  15Q GAIN WILD-TYPE           6       5      20       12       22       14
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  15Q GAIN MUTATED           2         4         2         8          2
  15Q GAIN WILD-TYPE        12        15        10        27         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           11         11        3
  15Q GAIN WILD-TYPE         21         47       16
D27V5, multiclass
             clus
vv            15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  I OR II NOS                6                  6
  STAGE 0                    2                  5
  STAGE I                    8                 20
  STAGE IA                   5                 12
  STAGE IB                   5                 22
  STAGE II                   8                 14
  STAGE IIA                  2                 12
  STAGE IIB                  4                 15
  STAGE IIC                  2                 10
  STAGE III                  8                 27
  STAGE IIIA                 2                 13
  STAGE IIIB                11                 21
  STAGE IIIC                11                 47
  STAGE IV                   3                 16
[1] 14  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                 T0+T1 T2 T3 T4
  15Q GAIN MUTATED      16 19 16 13
  15Q GAIN WILD-TYPE    47 52 58 54
D27V6, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1               16                 47
  T2                  19                 52
  T3                  16                 58
  T4                  13                 54
[1] 4 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                  N0  N1  N2  N3
  15Q GAIN MUTATED    43  15   7  10
  15Q GAIN WILD-TYPE 125  46  31  37
D27V7, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               43                125
  N1               15                 46
  N2                7                 31
  N3               10                 37
[1] 4 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                  M0  M1 M1A M1B M1C
  15Q GAIN MUTATED    75   1   1   0   1
  15Q GAIN WILD-TYPE 231   3   2   4   8
D27V8, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                75                231
  M1                 1                  3
  M1A                1                  2
  M1B                0                  4
  M1C                1                  8
[1] 5 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
  15Q GAIN MUTATED    29  16
  15Q GAIN WILD-TYPE 100  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     29   16
  15Q GAIN WILD-TYPE  100   71
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                29                100
  YES               16                 71
[1] 2 2
[1] FALSE
D27V10, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    13  69
  15Q GAIN WILD-TYPE  30 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13   69
  15Q GAIN WILD-TYPE   30  235
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                13                 30
  YES               69                235
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    30  53
  15Q GAIN WILD-TYPE 101 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     30   53
  15Q GAIN WILD-TYPE  101  164
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               30                101
  MALE                 53                164
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         0    78
  15Q GAIN WILD-TYPE     4                         1   248
D27V13, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   78                248
[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"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  80
  15Q GAIN WILD-TYPE   6 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   80
  15Q GAIN WILD-TYPE    6  254
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               80                254
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    24  26
  16P GAIN WILD-TYPE 144 139
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                50                283 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                26                139 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-D3-A8GI 
       70.16        22.55        15.25        13.32        13.68         4.18 
TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-EE-A17Y TCGA-EE-A20B 
      142.45        87.62         5.56        24.07        10.55        60.23 
TCGA-EE-A20H TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GB 
        9.21        12.03         8.84        49.22         9.67        51.12 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 
       47.21        30.08        28.31        33.83        98.27         2.70 
TCGA-EE-A2MP TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19C 
       26.99        30.15         3.22        21.60        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A69P 
        3.52        28.60        42.84        34.68         1.71        15.72 
TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1ZP TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 
        6.71         3.45        52.08         0.82         7.36        28.73 
TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-AA1V TCGA-WE-A8K6 
        2.27         7.23        14.50        18.05        10.98         7.10 
TCGA-WE-AAA3 TCGA-Z2-AA3V 
        1.94         5.98 

$`16P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       32.42       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        44.19         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        64.44        59.57       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        61.38        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.28        21.44        32.61        25.78       110.24        52.01 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       47.87        17.72        23.11        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ 
       15.19       108.79        38.93        75.65       124.47        11.44 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        4.01        21.93         5.72         9.90        11.31        13.22 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       14.60        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       13.15         0.20         0.13        23.15        19.00        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22         0.20        11.57         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        1.35        12.20         5.13         4.31         4.34        15.85 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
        8.55        36.85         1.08        39.62         9.50         8.09 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ 
       36.30        36.33        34.29        17.98        60.00        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        35.54        55.69         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       34.98        36.33         8.84         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      125.65       111.91        56.02        25.08        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        13.81        15.95        12.72        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       16.14        22.22         0.95        27.35        18.41        21.73 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       76.41        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       13.45         9.57        36.07         6.58        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         5.62        18.41        85.74 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        3.58         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        7.17        30.87        12.92        12.89        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
        8.81        49.15        40.64         8.68        27.39         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       53.85         3.22        14.20        10.78         5.98         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16        17.33         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       16.24        15.42        12.16        14.70        11.84        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      185.16        71.01        11.84         5.49         6.48        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       21.07        13.12         3.72         3.42        21.83         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
        1.08        19.96        12.07         6.18         4.70         8.22 
TCGA-Z2-AA3S 
        6.67 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.82               0.13 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            142.45             185.16 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            14.875             14.700 
[1] "0.8 - 142.4 (14.9)" "0.1 - 185.2 (14.7)"
[1] "hr=" "1.1"
D28V2, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    24  26
  16P GAIN WILD-TYPE 149 140
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                50                289 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                26                140 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-D3-A8GI 
       71.80        31.59        58.06        60.23       178.32        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-EE-A17Y TCGA-EE-A20B 
      228.99       137.79       129.63       117.17        27.22       133.81 
TCGA-EE-A20H TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GB 
      168.26        56.42        14.47       102.90        39.29        59.28 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 
      208.04        48.72        75.48        90.97       129.27        28.83 
TCGA-EE-A2MP TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19C 
      248.65        54.51       172.18        64.08        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A69P 
       12.59        61.05        44.05       162.08        33.21        15.72 
TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1ZP TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 
      210.08        48.59        74.73        27.09        66.67        28.73 
TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A9SD TCGA-QB-AA9O TCGA-W3-AA1V TCGA-WE-A8K6 
       77.88         7.23        59.41        18.05        42.08         8.61 
TCGA-WE-AAA3 TCGA-Z2-AA3V 
       10.36        11.74 

$`16P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      112.57       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        66.08        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      137.92        18.18       125.19        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ 
       15.19       170.20        89.13        95.24       161.00        29.06 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       22.29        11.11         9.90        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.16        17.85        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        6.35        12.20        29.82         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89        68.15         4.96       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       72.07        64.64         2.60        56.84        18.61        37.35 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       55.92       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ 
       36.82        86.14        67.43       314.56       161.03        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66       126.81        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        21.67        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      158.63       203.05       167.90        47.54        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        13.81        23.47       138.81       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       77.75        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      131.51        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98         6.77        92.98       174.21 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       15.16         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
      216.92       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        9.70        32.75        47.38        23.93       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       11.41       148.80        53.16        26.56        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        50.14       174.84        12.43        26.73        49.45 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16        19.30         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       64.44        62.79        32.48        39.58        46.36        12.62 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       50.10        21.37        65.88       357.04       294.77         6.67 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      219.16       105.04        24.03        38.56        54.38        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       56.98        59.41        52.34         3.75        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
        2.20        30.18        15.16        36.03        14.43        23.64 
TCGA-Z2-AA3S 
       93.07 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              7.23               0.16 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            248.65             369.93 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            59.345             48.850 
[1] "7.2 - 248.7 (59.3)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.1"
D28V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P GAIN MUTATED                    7             0
  16P GAIN WILD-TYPE                 54             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16P GAIN MUTATED                                          15
  16P GAIN WILD-TYPE                                        57
                    vv
clus                 REGIONAL LYMPH NODE
  16P GAIN MUTATED                    32
  16P GAIN WILD-TYPE                 177
D28V4, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  DISTANT METASTASIS                                       7                 54
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               15                 57
  REGIONAL LYMPH NODE                                     32                177
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16P GAIN MUTATED             2       2       9        5        7        5
  16P GAIN WILD-TYPE          10       5      19       12       20       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16P GAIN MUTATED           2         1         2         4          0
  16P GAIN WILD-TYPE        12        18        10        31         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED            4          6        1
  16P GAIN WILD-TYPE         28         52       18
D28V5, multiclass
             clus
vv            16P GAIN MUTATED 16P GAIN WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    2                  5
  STAGE I                    9                 19
  STAGE IA                   5                 12
  STAGE IB                   7                 20
  STAGE II                   5                 17
  STAGE IIA                  2                 12
  STAGE IIB                  1                 18
  STAGE IIC                  2                 10
  STAGE III                  4                 31
  STAGE IIIA                 0                 15
  STAGE IIIB                 4                 28
  STAGE IIIC                 6                 52
  STAGE IV                   1                 18
[1] 14  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                 T0+T1 T2 T3 T4
  16P GAIN MUTATED      11 19  9  5
  16P GAIN WILD-TYPE    52 52 65 62
D28V6, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1               11                 52
  T2                  19                 52
  T3                   9                 65
  T4                   5                 62
[1] 4 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                  N0  N1  N2  N3
  16P GAIN MUTATED    36   7   3   4
  16P GAIN WILD-TYPE 132  54  35  43
D28V7, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               36                132
  N1                7                 54
  N2                3                 35
  N3                4                 43
[1] 4 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                  M0  M1 M1A M1B M1C
  16P GAIN MUTATED    50   0   1   0   0
  16P GAIN WILD-TYPE 256   4   2   4   9
D28V8, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                50                256
  M1                 0                  4
  M1A                1                  2
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  16P GAIN MUTATED    16  12
  16P GAIN WILD-TYPE 113  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     16   12
  16P GAIN WILD-TYPE  113   75
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                16                113
  YES               12                 75
[1] 2 2
[1] FALSE
D28V10, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     5  49
  16P GAIN WILD-TYPE  38 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5   49
  16P GAIN WILD-TYPE   38  255
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 5                 38
  YES               49                255
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    22  32
  16P GAIN WILD-TYPE 109 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     22   32
  16P GAIN WILD-TYPE  109  185
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               22                109
  MALE                 32                185
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         0    51
  16P GAIN WILD-TYPE     4                         1   275
D28V13, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   51                275
[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"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  50
  16P GAIN WILD-TYPE   6 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   50
  16P GAIN WILD-TYPE    6  284
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               50                284
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    16  21
  16Q GAIN WILD-TYPE 152 144
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                37                296 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                21                144 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-D3-A8GP 
       70.16        22.55        15.25        13.32        13.68        87.62 
TCGA-D3-A8GR TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2A1 
        5.56        10.55        60.23         9.21         8.84        49.22 
TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 
       51.12        30.08        28.31        33.83        98.27         2.70 
TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       26.99         3.22        21.60         3.78         3.52        11.90 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX 
       28.60        34.68         1.71        15.72         6.71         3.45 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A9SD TCGA-W3-AA1V 
        0.82         7.36        28.73         7.23        14.50        10.98 
TCGA-WE-A8K6 
        7.10 

$`16Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       32.42       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        44.19         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        64.44        59.57       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        61.38        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.28        21.44        32.61        25.78       110.24        52.01 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       47.87        17.72        23.11        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19         4.18       142.45       108.79        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      124.47        11.44        24.07         4.01        21.93         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        11.31        13.22        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       23.15        19.00        13.35        13.22         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.31         4.34        15.85         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       39.62         9.50        12.03         8.09         9.99        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43        32.15         8.09        11.31        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       36.33        34.29        17.98        60.00        47.21        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        35.54        55.69         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       34.98        36.33         8.84         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      125.65       111.91        56.02        25.08        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
        3.68        30.15        13.81        15.95        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        5.72        76.41        25.18        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
        4.21        13.45        42.84         9.57        36.07         6.58 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       12.62        11.74         9.04         6.58        22.49         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       18.41        85.74         3.58         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.70         3.29        64.47        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       15.52         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       47.38        52.08         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
        8.68        27.39         5.23        53.85         3.22        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.13         0.16        17.33         9.90         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       15.81         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.69       164.19         8.98        60.03         2.99       185.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       71.01        11.84         5.49         6.48        18.67        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       13.12         3.72         3.42        21.83         5.36         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       19.96         1.94        12.07         6.18         4.70         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.82               0.13 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             98.27             185.16 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             13.68              15.01 
[1] "0.8 - 98.3 (13.7)"  "0.1 - 185.2 (15.0)"
[1] "hr=" "1.3"
D29V2, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    16  21
  16Q GAIN WILD-TYPE 157 145
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                37                302 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                21                145 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-D3-A8GP 
       71.80        31.59        58.06        60.23       178.32       137.79 
TCGA-D3-A8GR TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2A1 
      129.63        27.22       133.81       168.26        14.47       102.90 
TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 
       59.28        48.72        75.48        90.97       129.27        28.83 
TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
      248.65       172.18        64.08        48.89        12.59        13.02 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX 
       61.05       162.08        33.21        15.72       210.08        48.59 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A9SD TCGA-W3-AA1V 
       27.09        66.67        28.73         7.23        59.41        42.08 
TCGA-WE-A8K6 
        8.61 

$`16Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      112.57       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        66.08        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      137.92        18.18       125.19        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19        58.52       228.99       170.20        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      161.00        29.06       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        6.41        18.12        11.34        22.29        11.11         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        8.65        94.98        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.96       151.27        91.56        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        56.42        37.35        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87       195.02        17.92        46.82        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       86.14        67.43       314.56       161.03       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66       126.81        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        21.67        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      158.63       203.05       167.90        47.54        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
        3.68        54.51        13.81        23.47       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        9.17        77.75        98.40        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
        6.44       131.51        44.05        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       31.27        32.05       247.04        80.32        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       92.98       174.21        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       29.46        94.39       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
       26.56        49.48        27.02        77.82        50.14       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       47.54         0.16        19.30         9.90         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       32.48        39.58        46.36        12.62        50.10        21.37 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       357.04       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.69       212.22        63.02       121.08         4.01       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      105.04        24.03        38.56        54.38        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       59.41        52.34         3.75        22.68        43.73         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       30.18        10.36        15.16        36.03        14.43        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              7.23               0.16 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            248.65             369.93 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            59.410             49.465 
[1] "7.2 - 248.7 (59.4)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D29V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q GAIN MUTATED                    5             0
  16Q GAIN WILD-TYPE                 56             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16Q GAIN MUTATED                                          13
  16Q GAIN WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  16Q GAIN MUTATED                    24
  16Q GAIN WILD-TYPE                 185
D29V4, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       5                 56
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 59
  REGIONAL LYMPH NODE                                     24                185
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16Q GAIN MUTATED             2       2       7        2        7        3
  16Q GAIN WILD-TYPE          10       5      21       15       20       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16Q GAIN MUTATED           2         1         1         4          0
  16Q GAIN WILD-TYPE        12        18        11        31         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED            5          3        1
  16Q GAIN WILD-TYPE         27         55       18
D29V5, multiclass
             clus
vv            16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    2                  5
  STAGE I                    7                 21
  STAGE IA                   2                 15
  STAGE IB                   7                 20
  STAGE II                   3                 19
  STAGE IIA                  2                 12
  STAGE IIB                  1                 18
  STAGE IIC                  1                 11
  STAGE III                  4                 31
  STAGE IIIA                 0                 15
  STAGE IIIB                 5                 27
  STAGE IIIC                 3                 55
  STAGE IV                   1                 18
[1] 14  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                 T0+T1 T2 T3 T4
  16Q GAIN MUTATED       7 17  8  3
  16Q GAIN WILD-TYPE    56 54 66 64
D29V6, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                7                 56
  T2                  17                 54
  T3                   8                 66
  T4                   3                 64
[1] 4 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                  N0  N1  N2  N3
  16Q GAIN MUTATED    27   8   2   2
  16Q GAIN WILD-TYPE 141  53  36  45
D29V7, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               27                141
  N1                8                 53
  N2                2                 36
  N3                2                 45
[1] 4 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                  M0  M1 M1A M1B M1C
  16Q GAIN MUTATED    39   0   1   0   0
  16Q GAIN WILD-TYPE 267   4   2   4   9
D29V8, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                39                267
  M1                 0                  4
  M1A                1                  2
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  16Q GAIN MUTATED    13  10
  16Q GAIN WILD-TYPE 116  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     13   10
  16Q GAIN WILD-TYPE  116   77
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                13                116
  YES               10                 77
[1] 2 2
[1] FALSE
D29V10, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     3  39
  16Q GAIN WILD-TYPE  40 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   39
  16Q GAIN WILD-TYPE   40  265
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 3                 40
  YES               39                265
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    19  23
  16Q GAIN WILD-TYPE 112 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     19   23
  16Q GAIN WILD-TYPE  112  194
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               19                112
  MALE                 23                194
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         0    40
  16Q GAIN WILD-TYPE     4                         1   286
D29V13, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   40                286
[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"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  38
  16Q GAIN WILD-TYPE   6 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   38
  16Q GAIN WILD-TYPE    6  296
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               38                296
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    17  18
  17P GAIN WILD-TYPE 151 147
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                35                298 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                18                147 
$`17P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE 
       16.47        22.55        86.76       114.67        15.25        13.32 
TCGA-D3-A3MV TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A1IA 
       29.23        23.11        87.62        13.22        36.69         4.93 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P 
       10.55         1.35        15.85        11.15         9.50        12.03 
TCGA-EE-A29R TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 TCGA-EE-A3AG 
        8.84        36.33        47.21        28.31         2.70        15.95 
TCGA-EE-A3JA TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FS-A1ZD TCGA-FS-A1ZM 
       22.22         6.58         1.87         1.71         8.22        47.38 
TCGA-FS-A1ZS TCGA-GN-A26D TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-AA1O 
       49.15        14.70        14.50         8.98         2.99 

$`17P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD 
       85.32         8.38        21.14        88.50        68.22        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.44        59.57        46.98        46.32        82.29        61.38 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       24.00         6.31         9.34       103.59        26.37        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       25.78       110.24        52.01        47.87        13.68        17.72 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       29.72        22.06        10.22        15.19         4.18       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      108.79        38.93        75.65       124.47        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       24.07         4.01        21.93         5.72         9.90        11.31 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       14.60        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       13.68         9.99        44.52        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
        0.13        23.15        19.00        13.35        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       11.57         6.31         8.12         1.12        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        60.23         4.34         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        9.90        37.97        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       39.62         8.09         9.99        30.44         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.09        11.31        49.22        36.30         9.67        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        33.83        55.69         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
       34.98        36.33         8.84        98.27         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       125.65       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        51.62         3.68        30.15        13.81        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        3.22        22.92        21.60        21.60        16.14         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       12.95        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       17.72        78.44        11.80         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       11.74         9.04         6.58        22.49         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       85.74        15.72         6.71         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        2.20         4.70         3.29        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       20.38        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
       12.89        52.08         8.65         8.81        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       27.39         0.82         5.23        53.85         3.22         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        16.24        15.42        12.16        11.84        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V 
       18.05         0.33         0.69       164.19        60.03        10.98 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      185.16        71.01        11.84         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       18.67        21.07        13.12         3.72         3.42        21.83 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        5.36         1.08        19.96         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.35               0.13 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            114.67             185.16 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            14.700             14.715 
[1] "1.4 - 114.7 (14.7)" "0.1 - 185.2 (14.7)"
[1] "hr=" "1.1"
D30V2, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    17  18
  17P GAIN WILD-TYPE 156 148
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                35                304 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                18                148 
$`17P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JC TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE 
       16.57        31.59        86.76       130.72        58.06        60.23 
TCGA-D3-A3MV TCGA-D3-A5GU TCGA-D3-A8GP TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A1IA 
       45.30       125.19       137.79        66.25        61.18        65.92 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P 
       27.22        14.70        91.56        13.97        18.61        56.42 
TCGA-EE-A29R TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 TCGA-EE-A3AG 
       14.47        86.14       208.04        75.48        28.83        23.47 
TCGA-EE-A3JA TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FS-A1ZD TCGA-FS-A1ZM 
       53.19         8.88        23.34        33.21        53.52       101.26 
TCGA-FS-A1ZS TCGA-GN-A26D TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-AA1O 
      148.80        39.58        59.41        63.02         4.01 

$`17P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD 
      103.10        65.49        23.77       115.53       168.00        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.08        59.57        46.98        46.32       166.52        86.93 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E 
       24.53        13.87         9.34       103.59        39.75       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       30.84        79.59        11.61        15.19        58.52       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13        95.24       161.00        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       11.34        22.29        11.11         9.90        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       107.34        53.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       215.44        15.68        13.87        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       29.82         8.65        94.98        33.73        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.96       133.81       151.27       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       56.84        37.35        55.92       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
       17.92        46.82       102.90        36.82        39.29        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       161.03        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        90.97       126.81        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82        21.67       129.27        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       158.63       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        51.62         3.68        54.51        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
      172.18       127.20        36.95        64.08        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        43.82        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      174.21        15.72       210.08        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        29.46        94.39       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
       23.93        74.73       133.55        11.41        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         2.04        11.74       139.89       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        64.44        62.79        32.48        46.36        12.62 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       50.10        21.37        65.88       357.04       294.77         6.67 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V 
       18.05         0.33         0.69       212.22       121.08        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      219.16       105.04        24.03        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       90.28        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       43.73         2.20        30.18        10.36        15.16        36.03 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        23.64        93.07        11.74 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              4.01               0.16 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            208.04             369.93 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            56.420             49.465 
[1] "4.0 - 208.0 (56.4)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.2"
D30V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P GAIN MUTATED                    5             2
  17P GAIN WILD-TYPE                 56             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17P GAIN MUTATED                                           7
  17P GAIN WILD-TYPE                                        65
                    vv
clus                 REGIONAL LYMPH NODE
  17P GAIN MUTATED                    22
  17P GAIN WILD-TYPE                 187
D30V4, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  DISTANT METASTASIS                                       5                 56
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                7                 65
  REGIONAL LYMPH NODE                                     22                187
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17P GAIN MUTATED             2       0       3        2        3        2
  17P GAIN WILD-TYPE          10       7      25       15       24       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17P GAIN MUTATED           1         1         3         6          1
  17P GAIN WILD-TYPE        13        18         9        29         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED            5          5        2
  17P GAIN WILD-TYPE         27         53       17
D30V5, multiclass
             clus
vv            17P GAIN MUTATED 17P GAIN WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    0                  7
  STAGE I                    3                 25
  STAGE IA                   2                 15
  STAGE IB                   3                 24
  STAGE II                   2                 20
  STAGE IIA                  1                 13
  STAGE IIB                  1                 18
  STAGE IIC                  3                  9
  STAGE III                  6                 29
  STAGE IIIA                 1                 14
  STAGE IIIB                 5                 27
  STAGE IIIC                 5                 53
  STAGE IV                   2                 17
[1] 14  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                 T0+T1 T2 T3 T4
  17P GAIN MUTATED      10  9  7  7
  17P GAIN WILD-TYPE    53 62 67 60
D30V6, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1               10                 53
  T2                   9                 62
  T3                   7                 67
  T4                   7                 60
[1] 4 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                  N0  N1  N2  N3
  17P GAIN MUTATED    17   7   8   3
  17P GAIN WILD-TYPE 151  54  30  44
D30V7, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               17                151
  N1                7                 54
  N2                8                 30
  N3                3                 44
[1] 4 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                  M0  M1 M1A M1B M1C
  17P GAIN MUTATED    33   0   2   0   0
  17P GAIN WILD-TYPE 273   4   1   4   9
D30V8, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                33                273
  M1                 0                  4
  M1A                2                  1
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  17P GAIN MUTATED    11  11
  17P GAIN WILD-TYPE 118  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     11   11
  17P GAIN WILD-TYPE  118   76
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                11                118
  YES               11                 76
[1] 2 2
[1] FALSE
D30V10, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     5  31
  17P GAIN WILD-TYPE  38 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5   31
  17P GAIN WILD-TYPE   38  273
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 5                 38
  YES               31                273
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    16  20
  17P GAIN WILD-TYPE 115 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     16   20
  17P GAIN WILD-TYPE  115  197
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               16                115
  MALE                 20                197
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       1                         0    35
  17P GAIN WILD-TYPE     4                         1   291
D30V13, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   35                291
[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"
D30V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  34
  17P GAIN WILD-TYPE   6 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   34
  17P GAIN WILD-TYPE    6  300
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               34                300
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    32  30
  17Q GAIN WILD-TYPE 136 135
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                62                271 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                135 
$`17Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
       16.47         8.52        22.55        45.83        68.22        86.76 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D3-A5GS 
       92.42       114.67        15.25        13.32        29.23        17.72 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I7 
       75.65       124.47        87.62         9.90        48.79        36.69 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
        4.93         6.64        10.55         1.12         1.35         5.13 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
        4.31        15.85        11.15         1.08         9.50        12.03 
TCGA-EE-A29R TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 
        8.84        36.33        34.29        47.21        28.31         2.70 
TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3J5 TCGA-EE-A3JA 
        9.53        60.49        53.16        51.62        21.60        22.22 
TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX TCGA-FS-A1ZD 
        6.58        11.80         1.71        18.41         3.45         8.22 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
       47.38        49.15         8.68        84.72        15.42        14.70 
TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA1O TCGA-WE-A8JZ 
       14.50         5.79         0.69         8.98         2.99        11.84 
TCGA-WE-A8K1 TCGA-WE-AAA3 
        5.49         1.94 

$`17Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         6.97       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      110.79        28.08        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        88.50        11.41        44.19         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 
        6.31        56.19        64.44        59.57        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        61.38        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       21.44        32.61        25.78       110.24        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       13.68        23.11        29.72        22.06        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR 
        4.18       142.45       108.79        38.93        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
       24.07         4.01        21.93         5.72        11.31        13.22 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       14.60        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
        9.99        44.52        25.15        22.36        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       17.56        14.83        13.15         0.20         0.13        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       19.00        13.35        13.22         0.20        11.57         6.31 
TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I 
        8.12        12.20        60.23         4.34         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        62.79         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       39.62         8.09         9.99        30.44         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.09        11.31        49.22        36.30         9.67        51.12 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        30.08        19.43        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        55.69         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       36.33         8.84        98.27         6.18        47.51        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT 
      111.91        56.02        25.08        26.99        21.60        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31       122.73         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       36.07        17.72        78.44         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       12.62        11.74         9.04         6.58        22.49         5.62 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       85.74        15.72         6.71         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        2.20         4.70         3.29        64.47        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       52.08         8.65         8.81        40.64        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        5.23        53.85         3.22         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       11.61        44.28        31.33        10.13        16.24        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB 
       11.84        10.65        14.50        14.50        15.81         0.43 
TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V 
       11.05        18.05         0.33       164.19        60.03        10.98 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      185.16        71.01         6.48         7.10        18.67        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       13.12         3.72         3.42        21.83         5.36         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       19.96        12.07         6.18         4.70         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.69               0.13 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            124.47             185.16 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             14.60              14.83 
[1] "0.7 - 124.5 (14.6)" "0.1 - 185.2 (14.8)"
[1] "hr=" "1"  
D31V2, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    33  30
  17Q GAIN WILD-TYPE 140 136
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                63                276 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                136 
$`17Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
       16.57        16.67        31.59        90.90       168.00        86.76 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D3-A5GS 
      171.58       130.72        58.06        60.23        45.30        18.18 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-DA-A1HV 
       95.24       161.00       137.79         3.65         9.90        48.89 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
       61.18        65.92        68.09        27.22        33.73        14.70 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29N 
       68.15         4.96        91.56        13.97         2.60        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GM 
       56.42        14.47        86.14        67.43       208.04        75.48 
TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3J5 
       28.83        47.28       134.40       162.48        51.62        36.95 
TCGA-EE-A3JA TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX 
       53.19         8.88        43.82        33.21        92.98        48.59 
TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-GN-A265 TCGA-GN-A268 
       53.52       101.26       148.80        26.56        84.72        62.79 
TCGA-GN-A26D TCGA-GN-A9SD TCGA-QB-A6FS TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA1O 
       39.58        59.41         6.67         0.69        63.02         4.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-AAA3 
       24.03        38.56        10.36 

$`17Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        12.99       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        28.08        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53        11.87        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 
       12.10        56.19        66.08        59.57        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
      178.32       125.19        30.84        79.59        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR 
       58.52       228.99       170.20        89.13        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      117.17       151.53        54.67         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       22.29        11.11        25.18        66.25        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       53.92        23.44        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       13.87        10.16        17.85        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 
       52.01         6.35        12.20        29.82         8.65        94.98 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       26.89       133.81       151.27       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       80.61        47.84        63.78        72.07        64.64        56.84 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        55.92       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD 
       46.82       102.90        36.82        39.29        59.28       314.56 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      161.03        48.72        89.33        54.74        79.66        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
       21.67       129.27        19.76        61.51       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54       248.65        43.23        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
      138.81       172.18       127.20        64.08        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A 
       32.05       247.04        80.32        46.98         6.77       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       210.08        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       29.46        94.39       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       28.08         7.79        27.72        48.85       357.37        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       15.45         9.70        32.75        47.38        23.93        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      133.55        11.41        53.16        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 
      139.89       117.93        10.13        64.44        32.48        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       12.62        50.10        21.37        65.88       357.04       294.77 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W 
       18.05         0.33       212.22       121.08        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        54.38         8.61        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       52.34         3.75        22.68        43.73         2.20        30.18 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        36.03        14.43        23.64        93.07        11.74 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.69               0.16 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            208.04             369.93 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             51.62              50.12 
[1] "0.7 - 208.0 (51.6)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.1"
D31V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q GAIN MUTATED                    9             2
  17Q GAIN WILD-TYPE                 52             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17Q GAIN MUTATED                                          10
  17Q GAIN WILD-TYPE                                        62
                    vv
clus                 REGIONAL LYMPH NODE
  17Q GAIN MUTATED                    43
  17Q GAIN WILD-TYPE                 166
D31V4, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       9                 52
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               10                 62
  REGIONAL LYMPH NODE                                     43                166
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17Q GAIN MUTATED             4       1       5        2        6        5
  17Q GAIN WILD-TYPE           8       6      23       15       21       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17Q GAIN MUTATED           1         4         5         7          1
  17Q GAIN WILD-TYPE        13        15         7        28         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED            8          9        4
  17Q GAIN WILD-TYPE         24         49       15
D31V5, multiclass
             clus
vv            17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    1                  6
  STAGE I                    5                 23
  STAGE IA                   2                 15
  STAGE IB                   6                 21
  STAGE II                   5                 17
  STAGE IIA                  1                 13
  STAGE IIB                  4                 15
  STAGE IIC                  5                  7
  STAGE III                  7                 28
  STAGE IIIA                 1                 14
  STAGE IIIB                 8                 24
  STAGE IIIC                 9                 49
  STAGE IV                   4                 15
[1] 14  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                 T0+T1 T2 T3 T4
  17Q GAIN MUTATED      12 15 14 15
  17Q GAIN WILD-TYPE    51 56 60 52
D31V6, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1               12                 51
  T2                  15                 56
  T3                  14                 60
  T4                  15                 52
[1] 4 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                  N0  N1  N2  N3
  17Q GAIN MUTATED    33  10  12   6
  17Q GAIN WILD-TYPE 135  51  26  41
D31V7, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               33                135
  N1               10                 51
  N2               12                 26
  N3                6                 41
[1] 4 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                  M0  M1 M1A M1B M1C
  17Q GAIN MUTATED    58   0   2   0   2
  17Q GAIN WILD-TYPE 248   4   1   4   7
D31V8, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                58                248
  M1                 0                  4
  M1A                2                  1
  M1B                0                  4
  M1C                2                  7
[1] 5 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
  17Q GAIN MUTATED    21  21
  17Q GAIN WILD-TYPE 108  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     21   21
  17Q GAIN WILD-TYPE  108   66
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                21                108
  YES               21                 66
[1] 2 2
[1] FALSE
D31V10, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    10  54
  17Q GAIN WILD-TYPE  33 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     10   54
  17Q GAIN WILD-TYPE   33  250
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                10                 33
  YES               54                250
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    25  39
  17Q GAIN WILD-TYPE 106 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     25   39
  17Q GAIN WILD-TYPE  106  178
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               25                106
  MALE                 39                178
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       1                         1    60
  17Q GAIN WILD-TYPE     4                         0   266
D31V13, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   60                266
[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"
D31V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  61
  17Q GAIN WILD-TYPE   6 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   61
  17Q GAIN WILD-TYPE    6  273
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               61                273
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    25  24
  18P GAIN WILD-TYPE 143 141
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                49                284 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                24                141 
$`18P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J9 TCGA-D3-A2JN TCGA-D3-A3CC 
       32.42        22.55        45.83        21.14        56.19        61.38 
TCGA-D3-A3CE TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A8GP TCGA-D9-A6EA 
       13.32        93.21        32.28        21.44        87.62        11.31 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-EB-A5UL TCGA-EB-A6L9 
       13.22        35.80        10.03        39.19        13.35         0.20 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A2GB 
        8.12         1.12        62.79         1.08        12.03        51.12 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 
       47.21        28.31         8.84        26.99        21.60        12.95 
TCGA-ER-A19W TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1YX 
       17.72        22.49         1.71        18.41         6.71         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZT TCGA-FS-A1ZU 
       23.80        20.38        12.92        12.89        40.64         8.68 
TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-WE-A8K6 
        3.22         7.23        16.24        12.16        14.70         7.10 
TCGA-WE-AAA3 
        1.94 

$`18P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       70.16       110.79        28.08        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
        8.38        88.50        68.22        86.76        11.41        44.19 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
        7.50        36.16         6.31        92.42        64.44        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
      114.67        15.25        46.98        46.32        82.29        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
        6.31         9.34       103.59        26.37        29.23        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       31.30        54.31        32.61        25.78       110.24        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       47.87        13.68        17.72        23.11        29.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       10.22        15.19         4.18       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
       75.65       124.47        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       21.93         5.72         9.90        14.60        48.79        51.12 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       13.15         0.20         0.13        23.15        19.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       11.57        10.55         6.31         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       39.62         9.50         8.09         8.84         9.99        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
        9.67        36.33        34.29        17.98        60.00        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        35.54        33.83        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        21.60        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        18.61        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07         6.58        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42K 
       13.08        12.62        11.74         9.04         6.58         5.62 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       85.74        15.72         3.58         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.70         3.29        64.47        11.01        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         7.30         3.39         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        7.17        30.87        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       49.15        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20         0.99         0.13         0.16        17.33         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       15.42        11.84        10.65        14.50        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       15.81         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       164.19         8.98        60.03         2.99        10.98 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      185.16        71.01        11.84         5.49         6.48        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       21.07        13.12         3.72         3.42        21.83         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
        1.08        19.96        12.07         6.18         4.70         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.20               0.13 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             93.21             185.16 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             16.24              14.58 
[1] "0.2 - 93.2 (16.2)"  "0.1 - 185.2 (14.6)"
[1] "hr=" "1"  
D32V2, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    25  24
  18P GAIN WILD-TYPE 148 142
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                49                290 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                24                142 
$`18P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J9 TCGA-D3-A2JN TCGA-D3-A3CC 
      112.57        31.59        90.90        23.77        56.19        86.93 
TCGA-D3-A3CE TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A8GP TCGA-D9-A6EA 
       60.23       174.84        32.94        22.62       137.79        25.18 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-EB-A5UL TCGA-EB-A6L9 
       66.25        36.03        20.38       194.83        17.29        12.20 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A2GB 
       94.98        33.73        63.78         2.60        56.42        59.28 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 
      208.04        75.48        21.67       248.65        36.95        13.94 
TCGA-ER-A19W TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1YX 
      148.18        46.98        33.21        92.98       210.08        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZT TCGA-FS-A1ZU 
      202.65       357.37        47.38        23.93        53.16        26.56 
TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-WE-A8K6 
       50.14         7.23        64.44        32.48        39.58         8.61 
TCGA-WE-AAA3 
       10.36 

$`18P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       71.80       133.25        28.08        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       65.49       115.53       168.00        86.76        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08        12.10       171.58        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF 
      130.72        58.06        46.98        46.32       166.52        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       13.87         9.34       103.59        39.75        45.30        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       56.35       145.12        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      137.92       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       11.61        15.19        58.52       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       95.24       161.00        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         6.41        18.12        11.34        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 
       11.11         9.90        22.95        48.89       117.21       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV 
       10.16        17.85        68.25        54.02        52.01         6.35 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       29.82        27.22         8.65        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       133.81       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        13.97        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        37.35        14.47        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       39.29        86.14        67.43       314.56       161.03        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       89.33        54.74        79.66        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54        43.23       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        35.44        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25         8.88        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42K 
       16.37        31.27        32.05       247.04        80.32         6.77 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      174.21        15.72        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       29.46        94.39       216.92       228.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        27.72        48.85        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        32.75       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
      148.80        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16        19.30         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       62.79        46.36        12.62        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       357.04       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       212.22        63.02       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      219.16       105.04        24.03        38.56        54.38        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       56.98        59.41        52.34         3.75        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
        2.20        30.18        15.16        36.03        14.43        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              2.60               0.16 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            357.37             369.93 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            48.590             50.825 
[1] "2.6 - 357.4 (48.6)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.1"
D32V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P GAIN MUTATED                    9             2
  18P GAIN WILD-TYPE                 52             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18P GAIN MUTATED                                          11
  18P GAIN WILD-TYPE                                        61
                    vv
clus                 REGIONAL LYMPH NODE
  18P GAIN MUTATED                    28
  18P GAIN WILD-TYPE                 181
D32V4, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  DISTANT METASTASIS                                       9                 52
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               11                 61
  REGIONAL LYMPH NODE                                     28                181
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18P GAIN MUTATED             4       0       6        1        2        2
  18P GAIN WILD-TYPE           8       7      22       16       25       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18P GAIN MUTATED           0         0         6         8          3
  18P GAIN WILD-TYPE        14        19         6        27         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED            7          7        3
  18P GAIN WILD-TYPE         25         51       16
D32V5, multiclass
             clus
vv            18P GAIN MUTATED 18P GAIN WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    0                  7
  STAGE I                    6                 22
  STAGE IA                   1                 16
  STAGE IB                   2                 25
  STAGE II                   2                 20
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  6                  6
  STAGE III                  8                 27
  STAGE IIIA                 3                 12
  STAGE IIIB                 7                 25
  STAGE IIIC                 7                 51
  STAGE IV                   3                 16
[1] 14  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                 T0+T1 T2 T3 T4
  18P GAIN MUTATED       8 11  5 18
  18P GAIN WILD-TYPE    55 60 69 49
D32V6, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                8                 55
  T2                  11                 60
  T3                   5                 69
  T4                  18                 49
[1] 4 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                  N0  N1  N2  N3
  18P GAIN MUTATED    24  13   4   8
  18P GAIN WILD-TYPE 144  48  34  39
D32V7, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               24                144
  N1               13                 48
  N2                4                 34
  N3                8                 39
[1] 4 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                  M0  M1 M1A M1B M1C
  18P GAIN MUTATED    45   0   2   0   1
  18P GAIN WILD-TYPE 261   4   1   4   8
D32V8, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                45                261
  M1                 0                  4
  M1A                2                  1
  M1B                0                  4
  M1C                1                  8
[1] 5 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
  18P GAIN MUTATED    16  15
  18P GAIN WILD-TYPE 113  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     16   15
  18P GAIN WILD-TYPE  113   72
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                16                113
  YES               15                 72
[1] 2 2
[1] FALSE
D32V10, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     5  46
  18P GAIN WILD-TYPE  38 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5   46
  18P GAIN WILD-TYPE   38  258
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 5                 38
  YES               46                258
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    24  27
  18P GAIN WILD-TYPE 107 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     24   27
  18P GAIN WILD-TYPE  107  190
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               24                107
  MALE                 27                190
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       1                         0    48
  18P GAIN WILD-TYPE     4                         1   278
D32V13, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   48                278
[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"
D32V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1  49
  18P GAIN WILD-TYPE   6 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   49
  18P GAIN WILD-TYPE    6  285
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               49                285
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    24  16
  18Q GAIN WILD-TYPE 144 149
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                40                293 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                149 
$`18Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2J9 TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CC 
       32.42        45.83        21.14        56.19        59.57        61.38 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A8GP TCGA-D9-A6EA TCGA-DA-A1HW 
       93.21        32.28        21.44        87.62        11.31        35.80 
TCGA-DA-A1I1 TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A2GB 
       39.19        13.35         8.12         1.08        12.03        51.12 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 
       47.21        28.31         8.84        26.99        21.60        12.95 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZC 
        1.71        18.41         6.71         3.45        23.80        20.38 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A267 TCGA-GN-A26A 
       40.64         8.68         3.22         7.23        16.24        12.16 
TCGA-GN-A26D TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-AAA3 
       14.70        11.84         7.10         1.94 

$`18Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16       110.79        28.08        22.55        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       85.32         8.38        88.50        68.22        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       44.19         7.50        36.16         6.31        92.42        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
      114.67        15.25        46.98        46.32        82.29        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37        29.23 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.74        31.30        54.31        32.61        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       52.01        47.87        13.68        17.72        23.11        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       22.06        10.22        15.19         4.18       142.45       108.79 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       38.93        75.65       124.47        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01        21.93         5.72         9.90        13.22        14.60 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       48.79        51.12        10.03        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        19.00        13.22         0.20        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       60.23         4.34        15.85         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        62.79         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       39.62         9.50         8.09         8.84         9.99        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
        9.67        36.33        34.29        17.98        60.00        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        35.54        33.83        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        1.15        13.02        34.98        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        21.60        60.49        53.16        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       15.95        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        18.61        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       22.49         5.62        85.74        15.72         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       13.28         2.20         4.70         3.29        64.47        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD 
       14.24        15.52         7.33         7.30         3.39         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW 
       47.38        52.08         8.65         8.81        49.15        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.13         0.16        17.33         9.90         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U8 
       44.28        31.33        84.72        10.13        15.42        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       10.65        14.50        14.50        14.50        15.81         0.43 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       11.05         5.79        18.05         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        8.98        60.03         2.99        10.98       185.16        71.01 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        5.49         6.48        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
        3.42        21.83         5.36         1.08        19.96        12.07 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         4.70         8.22         6.67         5.98 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.08               0.13 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             93.21             185.16 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            19.395             14.500 
[1] "1.1 - 93.2 (19.4)"  "0.1 - 185.2 (14.5)"
[1] "hr=" "1.3"
D33V2, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    24  16
  18Q GAIN WILD-TYPE 149 150
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                40                299 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                150 
$`18Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2J9 TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CC 
      112.57        90.90        23.77        56.19        59.57        86.93 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A8GP TCGA-D9-A6EA TCGA-DA-A1HW 
      174.84        32.94        22.62       137.79        25.18        36.03 
TCGA-DA-A1I1 TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A2GB 
      194.83        17.29        94.98         2.60        56.42        59.28 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 
      208.04        75.48        21.67       248.65        36.95        13.94 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZC 
       33.21        92.98       210.08        48.59       202.65       357.37 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A267 TCGA-GN-A26A 
       53.16        26.56        50.14         7.23        64.44        32.48 
TCGA-GN-A26D TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-AAA3 
       39.58        24.03         8.61        10.36 

$`18Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        31.59        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        65.49       115.53       168.00        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       62.07       113.52        42.08        12.10       171.58        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
      130.72        58.06        46.98        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       55.73        56.35       145.12        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      135.75       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       79.59        11.61        15.19        58.52       228.99       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13        95.24       161.00        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        11.11         9.90        66.25        22.95        48.89 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       54.02        52.01         6.35        12.20        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      133.81       151.27        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       80.61        47.84        13.97        63.78        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        37.35        14.47        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       39.29        86.14        67.43       314.56       161.03        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       89.33        54.74        79.66        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54        43.23       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       23.47       138.81       172.18       127.20        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        35.44        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       46.98         6.77       174.21        15.72        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
       38.27        34.82        29.46        94.39       216.92       228.59 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD 
       20.91        28.08         7.79        27.72        48.85        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW 
      101.26        74.73       133.55        11.41       148.80        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.09        27.02        77.82        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
       47.54         0.16        19.30         9.90         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U8 
      139.89       117.93        84.72        10.13        62.79        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       12.62        50.10        21.37        59.41        65.88       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      294.77         6.67        18.05         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
       63.02       121.08         4.01        42.08       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       38.56        54.38        90.28        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
        3.75        22.68        43.73         2.20        30.18        15.16 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        23.64        93.07        11.74 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              2.60               0.16 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            357.37             369.93 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             51.65              50.10 
[1] "2.6 - 357.4 (51.6)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.4"
D33V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q GAIN MUTATED                    7             1
  18Q GAIN WILD-TYPE                 54             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18Q GAIN MUTATED                                          10
  18Q GAIN WILD-TYPE                                        62
                    vv
clus                 REGIONAL LYMPH NODE
  18Q GAIN MUTATED                    24
  18Q GAIN WILD-TYPE                 185
D33V4, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       7                 54
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               10                 62
  REGIONAL LYMPH NODE                                     24                185
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18Q GAIN MUTATED             4       1       5        1        2        0
  18Q GAIN WILD-TYPE           8       6      23       16       25       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18Q GAIN MUTATED           0         0         6         6          2
  18Q GAIN WILD-TYPE        14        19         6        29         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED            6          7        2
  18Q GAIN WILD-TYPE         26         51       17
D33V5, multiclass
             clus
vv            18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    1                  6
  STAGE I                    5                 23
  STAGE IA                   1                 16
  STAGE IB                   2                 25
  STAGE II                   0                 22
  STAGE IIA                  0                 14
  STAGE IIB                  0                 19
  STAGE IIC                  6                  6
  STAGE III                  6                 29
  STAGE IIIA                 2                 13
  STAGE IIIB                 6                 26
  STAGE IIIC                 7                 51
  STAGE IV                   2                 17
[1] 14  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                 T0+T1 T2 T3 T4
  18Q GAIN MUTATED       8 10  2 15
  18Q GAIN WILD-TYPE    55 61 72 52
D33V6, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                8                 55
  T2                  10                 61
  T3                   2                 72
  T4                  15                 52
[1] 4 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                  N0  N1  N2  N3
  18Q GAIN MUTATED    21  11   3   7
  18Q GAIN WILD-TYPE 147  50  35  40
D33V7, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               21                147
  N1               11                 50
  N2                3                 35
  N3                7                 40
[1] 4 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                  M0  M1 M1A M1B M1C
  18Q GAIN MUTATED    39   0   1   0   1
  18Q GAIN WILD-TYPE 267   4   2   4   8
D33V8, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                39                267
  M1                 0                  4
  M1A                1                  2
  M1B                0                  4
  M1C                1                  8
[1] 5 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
  18Q GAIN MUTATED    12  13
  18Q GAIN WILD-TYPE 117  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     12   13
  18Q GAIN WILD-TYPE  117   74
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                12                117
  YES               13                 74
[1] 2 2
[1] FALSE
D33V10, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5  38
  18Q GAIN WILD-TYPE  38 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5   38
  18Q GAIN WILD-TYPE   38  266
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 5                 38
  YES               38                266
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    19  24
  18Q GAIN WILD-TYPE 112 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     19   24
  18Q GAIN WILD-TYPE  112  193
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               19                112
  MALE                 24                193
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0    40
  18Q GAIN WILD-TYPE     5                         1   286
D33V13, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   40                286
[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"
D33V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1  40
  18Q GAIN WILD-TYPE   6 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   40
  18Q GAIN WILD-TYPE    6  294
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               40                294
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    28  25
  19P GAIN WILD-TYPE 140 140
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                53                280 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                25                140 
$`19P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JO 
       32.42        70.16        81.24        88.50        86.76        64.44 
TCGA-D3-A2JP TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EB-A5SH 
       59.57        23.11         4.18         9.90        13.22        19.00 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
       10.55         8.12        62.79         1.08        12.03         8.84 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MM 
       47.21        55.69        13.02        98.27         2.70        56.02 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL 
       33.60         5.72        11.90         1.87        12.62         1.71 
TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM 
        6.71         3.45        14.24        20.38         8.22        47.38 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 
       49.15         8.68         0.82         3.22        28.73         0.20 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-QB-AA9O TCGA-W3-AA21 TCGA-WE-A8ZQ 
       11.61        10.13        16.24        18.05        71.01         3.72 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
       21.83         5.36         1.08         1.94         6.18 

$`19P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 
      110.79        28.08        22.55        45.83        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
        8.38        21.14        68.22        11.41        44.19         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 
       36.16         6.31        92.42        56.19       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
        6.31         9.34       103.59        26.37        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       25.78       110.24        52.01        47.87        13.68        17.72 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       29.72        22.06        10.22        15.19       142.45       108.79 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       38.93        75.65       124.47        87.62        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG 
       24.07         4.01        21.93         5.72        11.31        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
        0.20         0.13        23.15        13.35        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       11.57         6.31         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       39.62         9.50         8.09         9.99        30.44         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       36.33        51.12        34.29        17.98        60.00        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       19.43        16.01        35.54        28.31        33.83         5.42 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
        1.15        34.98        36.33         8.84         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       63.42       125.65       111.91        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
        0.95        27.35        18.41        21.73        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       12.95        38.40        76.41        25.18         3.78         3.52 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       78.44        11.80         1.51        13.08        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         5.62        18.41        85.74        15.72 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        3.58         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       64.47        11.01        23.80        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        3.39        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW 
       12.89        52.08         8.65         8.81        40.64        27.39 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        5.23        53.85         7.36        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.99         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         0.85        44.28        31.33        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       15.42        12.16        14.70        11.84        10.65        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       10.98       185.16        11.84         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
       18.67        21.07        13.12         3.42        19.96        12.07 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.20               0.13 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             98.27             185.16 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            12.620             15.335 
[1] "0.2 - 98.3 (12.6)"  "0.1 - 185.2 (15.3)"
[1] "hr=" "1"  
D34V2, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    28  25
  19P GAIN WILD-TYPE 145 141
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                53                286 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                25                141 
$`19P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JO 
      112.57        71.80        95.74       115.53        86.76        66.08 
TCGA-D3-A2JP TCGA-D3-A5GU TCGA-D3-A8GI TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EB-A5SH 
       59.57       125.19        58.52         9.90        66.25        54.02 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
       27.22        94.98        63.78         2.60        56.42        14.47 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MM 
      208.04       126.81        55.59       129.27        28.83       167.90 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL 
      148.08         9.17        13.02        23.34        31.27        33.21 
TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM 
      210.08        48.59        20.91       357.37        53.52       101.26 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 
      148.80        26.56        27.09        50.14        28.73         0.20 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-QB-AA9O TCGA-W3-AA21 TCGA-WE-A8ZQ 
       11.74        10.13        64.44        18.05       105.04        52.34 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
       22.68        43.73         2.20        10.36        36.03 

$`19P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        31.59        90.90        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       65.49        23.77       168.00        11.87        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10       171.58        56.19       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       30.84        79.59        11.61        15.19       228.99       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13        95.24       161.00       137.79        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       11.34        22.29        11.11        25.18        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       17.85        68.25        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       29.82         8.65        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       133.81       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        13.97        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.84        18.61        37.35        55.92       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       86.14        59.28        67.43       314.56       161.03        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       89.33        54.74        79.66        75.48        90.97        13.91 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       14.30        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       158.63       203.05        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       109.58        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94        50.76        77.75        98.40        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       79.99        43.82        20.15        16.37        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98         6.77        92.98       174.21        15.72 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       15.16         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      216.92       228.59       202.65        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW 
       23.93        74.73       133.55        11.41        53.16        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.02        77.82        66.67       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       62.79        32.48        39.58        46.36        12.62        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       21.37        59.41        65.88       357.04       294.77         6.67 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       42.08       219.16        24.03        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
       90.28        56.98        59.41         3.75        30.18        15.16 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        23.64        93.07        11.74 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.20               0.16 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            357.37             369.93 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            53.520             49.465 
[1] "0.2 - 357.4 (53.5)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1"  
D34V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P GAIN MUTATED                    9             2
  19P GAIN WILD-TYPE                 52             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19P GAIN MUTATED                                          13
  19P GAIN WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  19P GAIN MUTATED                    30
  19P GAIN WILD-TYPE                 179
D34V4, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  DISTANT METASTASIS                                       9                 52
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 59
  REGIONAL LYMPH NODE                                     30                179
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19P GAIN MUTATED             2       0       8        1        4        2
  19P GAIN WILD-TYPE          10       7      20       16       23       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19P GAIN MUTATED           3         1         3         6          4
  19P GAIN WILD-TYPE        11        18         9        29         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED            4         10        3
  19P GAIN WILD-TYPE         28         48       16
D34V5, multiclass
             clus
vv            19P GAIN MUTATED 19P GAIN WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    0                  7
  STAGE I                    8                 20
  STAGE IA                   1                 16
  STAGE IB                   4                 23
  STAGE II                   2                 20
  STAGE IIA                  3                 11
  STAGE IIB                  1                 18
  STAGE IIC                  3                  9
  STAGE III                  6                 29
  STAGE IIIA                 4                 11
  STAGE IIIB                 4                 28
  STAGE IIIC                10                 48
  STAGE IV                   3                 16
[1] 14  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                 T0+T1 T2 T3 T4
  19P GAIN MUTATED       8 13 12 11
  19P GAIN WILD-TYPE    55 58 62 56
D34V6, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                8                 55
  T2                  13                 58
  T3                  12                 62
  T4                  11                 56
[1] 4 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                  N0  N1  N2  N3
  19P GAIN MUTATED    28   9   4   8
  19P GAIN WILD-TYPE 140  52  34  39
D34V7, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               28                140
  N1                9                 52
  N2                4                 34
  N3                8                 39
[1] 4 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                  M0  M1 M1A M1B M1C
  19P GAIN MUTATED    47   2   1   0   0
  19P GAIN WILD-TYPE 259   2   2   4   9
D34V8, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                47                259
  M1                 2                  2
  M1A                1                  2
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  19P GAIN MUTATED    21  14
  19P GAIN WILD-TYPE 108  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     21   14
  19P GAIN WILD-TYPE  108   73
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                21                108
  YES               14                 73
[1] 2 2
[1] FALSE
D34V10, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     9  45
  19P GAIN WILD-TYPE  34 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      9   45
  19P GAIN WILD-TYPE   34  259
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 9                 34
  YES               45                259
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    24  30
  19P GAIN WILD-TYPE 107 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     24   30
  19P GAIN WILD-TYPE  107  187
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               24                107
  MALE                 30                187
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         0    46
  19P GAIN WILD-TYPE     4                         1   280
D34V13, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   46                280
[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"
D34V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  51
  19P GAIN WILD-TYPE   6 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   51
  19P GAIN WILD-TYPE    6  283
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               51                283
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    27  26
  19Q GAIN WILD-TYPE 141 139
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                53                280 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                26                139 
$`19Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JO 
       16.47        32.42        70.16        88.50        86.76        64.44 
TCGA-D3-A2JP TCGA-D3-A3CE TCGA-D3-A8GI TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EB-A5SH 
       59.57        13.32         4.18         9.90        13.22        19.00 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
       10.55         8.12        62.79         1.08        12.03         8.84 
TCGA-EE-A29T TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       30.44        17.98        47.21        13.02        98.27         2.70 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2NG TCGA-ER-A3ET 
       33.60        12.95         5.72        11.90        12.62         6.58 
TCGA-ER-A3PL TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM 
        1.71         3.45        14.24        20.38         8.22        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F5 TCGA-FW-A3I3 
        8.65        49.15         8.68         0.82        28.73         0.20 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-QB-AA9O TCGA-WE-A8JZ TCGA-WE-A8ZQ 
       11.61        10.13        16.24        18.05        11.84         3.72 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
       21.83         5.36         1.08         1.94         6.18 

$`19Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 
        3.02         6.97         6.97         8.52       111.09       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
        8.38        21.14        68.22        11.41        44.19         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 
       36.16         6.31        92.42        56.19       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32        82.29        61.38        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        26.37        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      110.24        52.01        47.87        13.68        17.72        23.11 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       29.72        22.06        10.22        15.19       142.45       108.79 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       38.93        75.65       124.47        87.62        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG 
       24.07         4.01        21.93         5.72        11.31        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
        0.20         0.13        23.15        13.35        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       11.57         6.31         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        11.15         8.55        36.85 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       39.62         9.50         8.09         9.99         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       51.12        34.29        60.00        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        55.69         5.42         1.15 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       34.98        36.33         8.84         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.22        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
        0.95        27.35        18.41        21.73        31.40        18.61 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       38.40        76.41        25.18         3.78         3.52        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       11.80         1.87         1.51        13.08        11.74         9.04 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       22.49         5.62        18.41        85.74        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        3.58         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       64.47        11.01        23.80        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        3.39        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       12.89        52.08         8.81        40.64        27.39         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         3.22         7.36        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.99         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         0.85        44.28        31.33        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       15.42        12.16        14.70        11.84        10.65        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       10.98       185.16        71.01         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
       18.67        21.07        13.12         3.42        19.96        12.07 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.20               0.13 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             98.27             185.16 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             12.62              15.62 
[1] "0.2 - 98.3 (12.6)"  "0.1 - 185.2 (15.6)"
[1] "hr=" "1.2"
D35V2, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    27  26
  19Q GAIN WILD-TYPE 146 140
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                53                286 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                26                140 
$`19Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JO 
       16.57       112.57        71.80       115.53        86.76        66.08 
TCGA-D3-A2JP TCGA-D3-A3CE TCGA-D3-A8GI TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EB-A5SH 
       59.57        60.23        58.52         9.90        66.25        54.02 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
       27.22        94.98        63.78         2.60        56.42        14.47 
TCGA-EE-A29T TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
      369.93       314.56       208.04        55.59       129.27        28.83 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2NG TCGA-ER-A3ET 
      148.08        13.94         9.17        13.02        31.27        80.32 
TCGA-ER-A3PL TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM 
       33.21        48.59        20.91       357.37        53.52       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F5 TCGA-FW-A3I3 
      133.55       148.80        26.56        27.09        28.73         0.20 
TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A267 TCGA-QB-AA9O TCGA-WE-A8JZ TCGA-WE-A8ZQ 
       11.74        10.13        64.44        18.05        24.03        52.34 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
       22.68        43.73         2.20        10.36        36.03 

$`19Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 
       17.03        61.02        12.99        16.67       112.04       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       65.49        23.77       168.00        11.87        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10       171.58        56.19       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32       166.52        86.93        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       135.75       137.92       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       30.84        79.59        11.61        15.19       228.99       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13        95.24       161.00       137.79        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      117.17       151.53        54.67         3.65         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       11.34        22.29        11.11        25.18        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       17.85        68.25        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       29.82         8.65        33.73        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       133.81       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        47.84        13.97        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       56.84        18.61        37.35        55.92        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28        67.43       161.03        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       126.81        13.91        14.30 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        21.67        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      172.18       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
      201.80        27.35        51.35       109.58        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       50.76        77.75        98.40        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        32.05       247.04 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98         6.77        92.98       174.21        15.72       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       15.16         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      216.92       228.59       202.65        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       23.93        74.73        11.41        53.16        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       49.45        77.88        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23         2.04       139.89       117.93        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       62.79        32.48        39.58        46.36        12.62        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       21.37        59.41        65.88       357.04       294.77         6.67 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       42.08       219.16       105.04        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA4 
       90.28        56.98        59.41         3.75        30.18        15.16 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        23.64        93.07        11.74 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.20               0.16 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            369.93             357.04 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             52.34              50.12 
[1] "0.2 - 369.9 (52.3)" "0.2 - 357.0 (50.1)"
[1] "hr=" "1"  
D35V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q GAIN MUTATED                    9             2
  19Q GAIN WILD-TYPE                 52             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19Q GAIN MUTATED                                          13
  19Q GAIN WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  19Q GAIN MUTATED                    29
  19Q GAIN WILD-TYPE                 180
D35V4, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       9                 52
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 59
  REGIONAL LYMPH NODE                                     29                180
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19Q GAIN MUTATED             3       0       5        1        3        1
  19Q GAIN WILD-TYPE           9       7      23       16       24       21
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19Q GAIN MUTATED           3         2         2         6          5
  19Q GAIN WILD-TYPE        11        17        10        29         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED            6         10        3
  19Q GAIN WILD-TYPE         26         48       16
D35V5, multiclass
             clus
vv            19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    0                  7
  STAGE I                    5                 23
  STAGE IA                   1                 16
  STAGE IB                   3                 24
  STAGE II                   1                 21
  STAGE IIA                  3                 11
  STAGE IIB                  2                 17
  STAGE IIC                  2                 10
  STAGE III                  6                 29
  STAGE IIIA                 5                 10
  STAGE IIIB                 6                 26
  STAGE IIIC                10                 48
  STAGE IV                   3                 16
[1] 14  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                 T0+T1 T2 T3 T4
  19Q GAIN MUTATED       6 11 12 13
  19Q GAIN WILD-TYPE    57 60 62 54
D35V6, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                6                 57
  T2                  11                 60
  T3                  12                 62
  T4                  13                 54
[1] 4 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                  N0  N1  N2  N3
  19Q GAIN MUTATED    24  13   3   8
  19Q GAIN WILD-TYPE 144  48  35  39
D35V7, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               24                144
  N1               13                 48
  N2                3                 35
  N3                8                 39
[1] 4 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                  M0  M1 M1A M1B M1C
  19Q GAIN MUTATED    47   2   1   0   0
  19Q GAIN WILD-TYPE 259   2   2   4   9
D35V8, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                47                259
  M1                 2                  2
  M1A                1                  2
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  19Q GAIN MUTATED    17  16
  19Q GAIN WILD-TYPE 112  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     17   16
  19Q GAIN WILD-TYPE  112   71
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                17                112
  YES               16                 71
[1] 2 2
[1] FALSE
D35V10, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     9  45
  19Q GAIN WILD-TYPE  34 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9   45
  19Q GAIN WILD-TYPE   34  259
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 9                 34
  YES               45                259
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    24  30
  19Q GAIN WILD-TYPE 107 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     24   30
  19Q GAIN WILD-TYPE  107  187
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               24                107
  MALE                 30                187
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         0    45
  19Q GAIN WILD-TYPE     4                         1   281
D35V13, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   45                281
[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"
D35V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  50
  19Q GAIN WILD-TYPE   6 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   50
  19Q GAIN WILD-TYPE    6  284
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               50                284
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    66  69
  20P GAIN WILD-TYPE 102  96
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               135                198 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                69                 96 
$`20P GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JD 
        6.97        16.47        32.42        22.55        88.50        11.41 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
       44.19        36.16        56.19        15.25        82.29        13.32 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
      103.59        29.23        54.31        32.28        32.61        52.01 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM 
       13.68        23.11        22.06        10.22         4.18        75.65 
TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW 
       87.62        21.93         9.90        11.31        13.22        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5UL TCGA-EB-A6L9 
       10.03        13.68        36.69        17.56        13.35         0.20 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       10.55         8.12         1.12        60.23         9.21         7.99 
TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 
       11.15         8.84        30.44        32.15         8.09        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        9.67        36.33        51.12        60.00        47.21        30.08 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 
       28.31        33.83        55.69         5.42        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MU 
       98.27         2.70         6.18         7.96        26.99         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J5 
      124.31       122.73        51.62        30.15         3.22        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 
       21.60        22.22         0.95        21.73        33.60         5.72 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       25.18       114.15         4.21        13.45        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A42K 
        9.57         6.58        11.80         1.87        22.49         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YD TCGA-FS-A1YX 
       18.41        85.74        15.72         6.71         4.70         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
       23.80        15.52         7.33         7.30        20.38         8.22 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        7.17        12.92        12.89        47.38         8.65        49.15 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD 
        8.68         0.82         3.22        28.73        14.20         2.27 
TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        0.20        11.61        31.33        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X 
       14.70        10.65        14.50        14.50        15.81        11.05 
TCGA-QB-A6FS TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZQ 
        5.79         8.98        71.01        11.84         7.10         3.72 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 
       21.83         5.36         1.94 

$`20P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        3.02         6.97         8.52       111.09        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
       21.14        68.22        86.76         7.50         6.31        92.42 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC 
       64.44        59.57       114.67        46.98        46.32        61.38 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.00         6.31         9.34        26.37        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS 
       31.30        21.44        25.78       110.24        47.87        17.72 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       29.72        15.19       142.45       108.79        38.93       124.47 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG 
       11.44         5.56        24.07         4.01         5.72        14.60 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       48.79        51.12        39.19         9.99        44.52        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
        4.93        22.36         6.64        19.36         7.00        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       13.15         0.20         0.13        23.15        19.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       11.57         6.31         1.35        12.20         5.13         4.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        4.34        15.85         1.18         9.90        37.97        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC 
        8.09         9.99         2.43        11.31        36.30        34.29 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS 
       17.98        19.43        16.01        35.54         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       34.98        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       125.65       111.91        56.02        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF 
       21.60        60.49        53.16        52.67         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       15.95        12.72        22.92        16.14        27.35        18.41 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C 
       31.40        18.61        12.95        38.40        76.41         3.78 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S 
        3.52        11.90        11.11        34.88        42.84        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       17.72        78.44         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
        9.04         6.58         1.71         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB 
        2.20         3.29        64.47        11.01        14.24         3.39 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT 
       19.53        11.08        30.87        52.08         8.81        40.64 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.39         5.23        53.85         7.36        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         0.99         0.13         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 
        7.23         0.85        44.28        84.72        10.13        11.84 
TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       14.50         0.43        18.05         0.33         0.69       164.19 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 
       60.03         2.99        10.98       185.16         5.49         6.48 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       18.67        21.07        13.12         3.42         1.08        19.96 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         4.70         8.22         6.67         5.98 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.20               0.13 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            124.31             185.16 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            14.700             14.715 
[1] "0.2 - 124.3 (14.7)" "0.1 - 185.2 (14.7)"
[1] "hr=" "1.1"
D36V2, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    66  70
  20P GAIN WILD-TYPE 107  96
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               136                203 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                70                 96 
$`20P GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JD 
       12.99        16.57       112.57        31.59       115.53        11.87 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE 
       62.07        42.08        56.19        58.06       166.52        60.23 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
      103.59        45.30       145.12        32.94        63.81       135.75 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM 
      178.32       125.19        79.59        11.61        58.52        95.24 
TCGA-D3-A8GP TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
      137.79         6.41        22.29         9.90        25.18        66.25 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5UL 
       36.03        20.38       176.55        61.18       215.44        17.29 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H 
       12.20        27.22        94.98        33.73       133.81       168.26 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       63.35        13.97        14.47       369.93       195.02        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      102.90        39.29        86.14        59.28       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
       48.72        75.48        90.97       126.81        13.91        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MP 
       21.67       129.27        28.83        19.76        16.96       248.65 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J3 
       53.26       124.31       122.73        51.62        54.51       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       36.95        64.08        53.19       201.80       109.58       148.08 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        9.17        98.40       268.93         6.44       131.51        61.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3EV 
      162.08        50.89         8.88        43.82        23.34        46.98 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YD 
        6.77        92.98       174.21        15.72       210.08        29.46 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       48.59       202.65        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       53.52         9.70        47.38        23.93       101.26       133.55 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
      148.80        26.56        27.09        50.14        28.73       174.84 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       77.88         0.20        11.74       117.93        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH 
       32.48        39.58        12.62        50.10        59.41        65.88 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 
      294.77         6.67        63.02       105.04        24.03         8.61 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 
       52.34        22.68        43.73        10.36 

$`20P GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       17.03        61.02        16.67       112.04        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
       23.77       168.00        86.76       113.52        12.10       171.58 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC 
       66.08        59.57       130.72        46.98        46.32        86.93 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53        13.87         9.34        39.75       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS 
       56.35        22.62        26.89       125.79       137.92        18.18 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       30.84        15.19       228.99       170.20        89.13       161.00 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       18.12        11.34        11.11        22.95        48.89       117.21 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
      194.83        35.93       107.34        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       68.09        28.60        10.49        15.68        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       17.85        68.25        54.02        52.01         6.35        29.82 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
        8.65        14.70        26.89        68.15         4.96       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       91.56        13.55        80.61        47.84        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        18.61        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD 
       55.92        25.87        46.82        36.82        67.43       314.56 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       89.33        54.74        79.66        14.30        55.59        44.88 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       61.51        47.28       103.27       268.73       103.20       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       158.63       203.05       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      134.40       162.48        71.21         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 
      138.81       127.20        34.32        27.35        51.35        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       35.44        13.94        50.76        77.75        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19W 
       13.02        26.37       152.35        44.05        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       79.99        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       80.32        33.21        15.16         7.00        38.27        34.82 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE 
       94.39       216.92       228.59        20.91        48.85        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW 
       15.45        32.75        74.73        11.41        53.16        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       27.02        77.82        66.67        12.43        26.73        49.45 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A8LL 
        2.04       139.89        84.72        10.13        46.36        21.37 
TCGA-LH-A9QB TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
      357.04        18.05         0.33         0.69       212.22       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
        4.01        42.08       219.16        38.56        54.38        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       56.98        59.41         3.75         2.20        30.18        15.16 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        23.64        93.07        11.74 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.20               0.16 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            369.93             357.04 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             55.35              47.54 
[1] "0.2 - 369.9 (55.3)" "0.2 - 357.0 (47.5)"
[1] "hr=" "1.1"
D36V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P GAIN MUTATED                   24             4
  20P GAIN WILD-TYPE                 37             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20P GAIN MUTATED                                          27
  20P GAIN WILD-TYPE                                        45
                    vv
clus                 REGIONAL LYMPH NODE
  20P GAIN MUTATED                    87
  20P GAIN WILD-TYPE                 122
D36V4, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  DISTANT METASTASIS                                      24                 37
  PRIMARY TUMOR                                            4                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               27                 45
  REGIONAL LYMPH NODE                                     87                122
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20P GAIN MUTATED             8       2      16        9       14        7
  20P GAIN WILD-TYPE           4       5      12        8       13       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20P GAIN MUTATED           5         3         5        17          7
  20P GAIN WILD-TYPE         9        16         7        18          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           15         20        4
  20P GAIN WILD-TYPE         17         38       15
D36V5, multiclass
             clus
vv            20P GAIN MUTATED 20P GAIN WILD-TYPE
  I OR II NOS                8                  4
  STAGE 0                    2                  5
  STAGE I                   16                 12
  STAGE IA                   9                  8
  STAGE IB                  14                 13
  STAGE II                   7                 15
  STAGE IIA                  5                  9
  STAGE IIB                  3                 16
  STAGE IIC                  5                  7
  STAGE III                 17                 18
  STAGE IIIA                 7                  8
  STAGE IIIB                15                 17
  STAGE IIIC                20                 38
  STAGE IV                   4                 15
[1] 14  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                 T0+T1 T2 T3 T4
  20P GAIN MUTATED      31 35 22 28
  20P GAIN WILD-TYPE    32 36 52 39
D36V6, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               31                 32
  T2                  35                 36
  T3                  22                 52
  T4                  28                 39
[1] 4 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                 N0 N1 N2 N3
  20P GAIN MUTATED   74 28 14 16
  20P GAIN WILD-TYPE 94 33 24 31
D36V7, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               74                 94
  N1               28                 33
  N2               14                 24
  N3               16                 31
[1] 4 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                  M0  M1 M1A M1B M1C
  20P GAIN MUTATED   131   2   2   0   0
  20P GAIN WILD-TYPE 175   2   1   4   9
D36V8, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               131                175
  M1                 2                  2
  M1A                2                  1
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  20P GAIN MUTATED   58 31
  20P GAIN WILD-TYPE 71 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     58   31
  20P GAIN WILD-TYPE   71   56
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                58                 71
  YES               31                 56
[1] 2 2
[1] FALSE
D36V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    15 126
  20P GAIN WILD-TYPE  28 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     15  126
  20P GAIN WILD-TYPE   28  178
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                15                 28
  YES              126                178
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    55  87
  20P GAIN WILD-TYPE  76 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     55   87
  20P GAIN WILD-TYPE   76  130
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               55                 76
  MALE                 87                130
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       2                         0   134
  20P GAIN WILD-TYPE     3                         1   192
D36V13, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  134                192
[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"
D36V14, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 136
  20P GAIN WILD-TYPE   5 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  136
  20P GAIN WILD-TYPE    5  198
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              136                198
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   83 82
  20Q GAIN WILD-TYPE 85 83
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               165                168 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                82                 83 
$`20Q GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JA 
        3.02         6.97        16.47        32.42        22.55        88.50 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       86.76        11.41        44.19        36.16        92.42        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
       59.57        15.25        82.29        13.32       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       29.23        54.31        32.28        32.61        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL 
       13.68        23.11        22.06        10.22         4.18        38.93 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       75.65        87.62        11.44        21.93         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 
       13.22        48.79        35.80        10.03        13.68        36.69 
TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y 
        4.93        17.56        19.00        13.35         0.20        10.55 
TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
        8.12        12.20         5.13        60.23         9.21         7.99 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T 
       11.15        62.79         1.08        12.03         8.84        30.44 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       32.15         8.09        49.22         9.67        36.33        51.12 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       60.00        47.21        30.08        28.31        33.83        55.69 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        5.42        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       44.25         7.96        26.99        53.16         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 
      122.73        51.62         3.68        30.15        15.95         3.22 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        21.60        22.22         0.95        21.73        33.60 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       12.95         5.72        25.18       114.15         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC 
       28.60        34.68         9.57         6.58        17.72        11.80 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        1.87        12.62        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 
       85.74        15.72         6.71         4.70         3.45        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
       15.52         7.33         7.30        20.38         8.22         7.17 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.92        12.89        47.38         8.65        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD 
        8.68         0.82         3.22        28.73        14.20         2.27 
TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.20         7.23        11.61        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       15.42        12.16        14.70        10.65        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A825 
       14.50        15.81        11.05         5.79        18.05         8.98 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       71.01        11.84         7.10        18.67         3.72        21.83 
TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YG-AA3O 
        5.36         1.94         6.18 

$`20Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        6.97         8.52       111.09        70.16       110.79        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       45.83        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 
       68.22         7.50         6.31        64.44       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E 
       46.32        61.38        24.00         6.31         9.34        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS 
       54.74        31.30        21.44        25.78       110.24        17.72 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GR 
       29.72        15.19       142.45       108.79       124.47         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
       24.07         4.01         5.72        14.60        51.12        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        44.52        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
        7.00        14.83        13.15         0.20         0.13        23.15 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
       13.22        11.57         6.31         1.12         1.35         4.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
        4.34        15.85         1.18         9.90        37.97         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       36.85        39.62         9.50         8.09         9.99         2.43 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK 
       11.31        36.30        34.29        17.98        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MC TCGA-EE-A2MD 
       35.54         1.15        13.02        34.98        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46         2.73        14.56        63.42       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AF 
       56.02        25.08        21.60        60.49        52.67        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 
       12.72        22.92        16.14        27.35        18.41        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       18.61        38.40        76.41         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE 
       11.11        34.88        42.84        36.07        78.44         1.51 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7U9 
       13.08        11.74         9.04         6.58         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
       13.28         2.20         3.29        64.47        11.01        14.24 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR 
        3.39        19.53        11.08        30.87        52.08         8.81 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB 
       27.39         5.23        53.85         7.36        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         0.99         0.13         0.16        17.33         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-RP-A693 
        0.85        44.28        10.13        11.84         0.43         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
        0.69       164.19        60.03         2.99        10.98       185.16 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y 
        5.49         6.48        21.07        13.12         3.42         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       19.96        12.07         4.70         8.22         6.67         5.98 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.20               0.13 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            124.31             185.16 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             15.42              14.40 
[1] "0.2 - 124.3 (15.4)" "0.1 - 185.2 (14.4)"
[1] "hr=" "1"  
D37V2, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   84 83
  20Q GAIN WILD-TYPE 89 83
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               167                172 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                83                 83 
$`20Q GAIN MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JA 
       17.03        12.99        16.57       112.57        31.59       115.53 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       86.76        11.87        62.07        42.08       171.58        56.19 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
       59.57        58.06       166.52        60.23       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       45.30       145.12        32.94        63.81       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL 
      178.32       125.19        79.59        11.61        58.52        89.13 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z3 
       95.24       137.79        29.06       151.53         6.41        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
        9.90        25.18        66.25        48.89        36.03        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A5UL 
      176.55        61.18        65.92       215.44        54.02        17.29 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B 
       12.20        27.22        94.98        26.89        68.15       133.81 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P 
      168.26        63.35        13.97        63.78         2.60        56.42 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 
       14.47       369.93       195.02        17.92       102.90        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
       86.14        59.28       161.03       208.04        48.72        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       90.97       126.81        13.91        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MS 
       28.83        19.76       103.20        16.96       248.65       162.48 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB 
       23.47       172.18        36.95        64.08        53.19       201.80 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G 
      109.58       148.08        13.94         9.17        98.40       268.93 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T 
        6.44       131.51        61.05       162.08        50.89         8.88 
TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL 
      148.18        43.82        23.34        31.27        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YD 
        6.77        92.98       174.21        15.72       210.08        29.46 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       48.59       202.65        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       53.52         9.70        47.38        23.93       101.26       133.55 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 
      148.80        53.16        26.56        27.09        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
      174.84        77.88         0.20         7.23        11.74       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
       84.72        64.44        62.79        32.48        39.58        12.62 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS 
       50.10        21.37        59.41        65.88       294.77         6.67 
TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZM 
       18.05        63.02       105.04        24.03         8.61        90.28 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-YG-AA3O 
       52.34        22.68        43.73        10.36        36.03 

$`20Q GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       61.02        16.67       112.04        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 
      168.00       113.52        12.10        66.08       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E 
       46.32        86.93        24.53        13.87         9.34       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS 
       55.73        56.35        22.62        26.89       125.79        18.18 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GN TCGA-D3-A8GR 
       30.84        15.19       228.99       170.20       161.00       129.63 
TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
      117.17        54.67         3.65        18.12        11.34        11.11 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       22.95       117.21       194.83        35.93       107.34        53.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X 
       10.16        17.85        68.25        52.01         6.35        29.82 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        8.65        33.73        14.70         4.96       151.27        91.56 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       13.55        80.61        47.84        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 
       18.61        37.35        55.92        25.87        46.82        36.82 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR 
       67.43       314.56        89.33        54.74        79.66        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       55.59        44.88        61.51        47.28       103.27       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       203.05       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
       43.23       134.40        71.21        13.81       138.81       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       34.32        27.35        51.35        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       77.75        48.89        12.59        13.02        26.37       152.35 
TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       44.05        37.25        79.99        20.15        16.37        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
      247.04        80.32        15.16         7.00        38.27        34.82 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE 
       94.39       216.92       228.59        20.91        48.85        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       15.45        32.75        74.73        11.41        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
       77.82        66.67        12.43        26.73        49.45        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       47.54         0.16        19.30         9.90         2.04       139.89 
TCGA-GN-A266 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       10.13        46.36       357.04         0.33         0.69       212.22 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 
      121.08         4.01        42.08       219.16        38.56        54.38 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       56.98        59.41         3.75         2.20        30.18        15.16 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        23.64        93.07        11.74 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.20               0.16 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            369.93             357.04 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             54.51              46.90 
[1] "0.2 - 369.9 (54.5)" "0.2 - 357.0 (46.9)"
[1] "hr=" "1.1"
D37V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20Q GAIN MUTATED                   30             4
  20Q GAIN WILD-TYPE                 31             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20Q GAIN MUTATED                                          32
  20Q GAIN WILD-TYPE                                        40
                    vv
clus                 REGIONAL LYMPH NODE
  20Q GAIN MUTATED                   106
  20Q GAIN WILD-TYPE                 103
D37V4, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      30                 31
  PRIMARY TUMOR                                            4                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               32                 40
  REGIONAL LYMPH NODE                                    106                103
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20Q GAIN MUTATED             9       3      17       10       15        9
  20Q GAIN WILD-TYPE           3       4      11        7       12       13
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20Q GAIN MUTATED           5         3         7        22          8
  20Q GAIN WILD-TYPE         9        16         5        13          7
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           21         25        5
  20Q GAIN WILD-TYPE         11         33       14
D37V5, multiclass
             clus
vv            20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  I OR II NOS                9                  3
  STAGE 0                    3                  4
  STAGE I                   17                 11
  STAGE IA                  10                  7
  STAGE IB                  15                 12
  STAGE II                   9                 13
  STAGE IIA                  5                  9
  STAGE IIB                  3                 16
  STAGE IIC                  7                  5
  STAGE III                 22                 13
  STAGE IIIA                 8                  7
  STAGE IIIB                21                 11
  STAGE IIIC                25                 33
  STAGE IV                   5                 14
[1] 14  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                 T0+T1 T2 T3 T4
  20Q GAIN MUTATED      38 40 27 34
  20Q GAIN WILD-TYPE    25 31 47 33
D37V6, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               38                 25
  T2                  40                 31
  T3                  27                 47
  T4                  34                 33
[1] 4 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                 N0 N1 N2 N3
  20Q GAIN MUTATED   83 35 18 22
  20Q GAIN WILD-TYPE 85 26 20 25
D37V7, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               83                 85
  N1               35                 26
  N2               18                 20
  N3               22                 25
[1] 4 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                  M0  M1 M1A M1B M1C
  20Q GAIN MUTATED   157   2   3   1   0
  20Q GAIN WILD-TYPE 149   2   0   3   9
D37V8, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               157                149
  M1                 2                  2
  M1A                3                  0
  M1B                1                  3
  M1C                0                  9
[1] 5 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
  20Q GAIN MUTATED   67 38
  20Q GAIN WILD-TYPE 62 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     67   38
  20Q GAIN WILD-TYPE   62   49
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                67                 62
  YES               38                 49
[1] 2 2
[1] FALSE
D37V10, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    23 149
  20Q GAIN WILD-TYPE  20 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     23  149
  20Q GAIN WILD-TYPE   20  155
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                23                 20
  YES              149                155
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    65 108
  20Q GAIN WILD-TYPE  66 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     65  108
  20Q GAIN WILD-TYPE   66  109
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               65                 66
  MALE                108                109
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         0   163
  20Q GAIN WILD-TYPE     3                         1   163
D37V13, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  163                163
[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"
D37V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3 166
  20Q GAIN WILD-TYPE   4 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  166
  20Q GAIN WILD-TYPE    4  168
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              166                168
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    36  27
  21Q GAIN WILD-TYPE 132 138
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                63                270 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                27                138 
$`21Q GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3C6 
        8.52        22.55        85.32        44.19        59.57        15.25 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GU 
       82.29        61.38       103.59        29.23        52.01        23.11 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A6EC TCGA-EB-A6L9 
       22.06        10.22         4.18        75.65        13.22         0.20 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R 
        5.13         9.21         7.99        11.15         1.08         8.84 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN 
       11.31        49.22         9.67        47.21        28.31        33.83 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19B 
       26.99        21.60       124.31         3.22        21.60        25.18 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3PL 
        3.52        13.45        34.68        13.08        12.62         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1Z4 
        5.62        18.41        85.74         6.71         3.58        15.52 
TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GF-A4EO 
        8.22        12.92        49.15         3.22         0.20         7.23 
TCGA-GN-A26D TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K6 
       14.70        14.50         8.98       185.16        11.84         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-AAA3 
       18.67        21.83         1.94 

$`21Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97        16.47       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        86.76        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
        7.50        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
      114.67        46.98        46.32        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34        26.37        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78       110.24        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       13.68        17.72        29.72        15.19       142.45       108.79 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       38.93       124.47        87.62        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
        4.01        21.93         5.72         9.90        11.31        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
        0.20         0.13        23.15        19.00        13.35        13.22 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       12.20         4.31        60.23         4.34        15.85         1.18 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
        9.90        37.97        62.79         8.55        36.85        39.62 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        9.50        12.03         8.09         9.99        30.44         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       32.15         8.09        36.30        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        60.00        30.08        19.43        16.01        35.54 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       55.69         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS 
      125.65       111.91        56.02        25.08        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67         5.56       122.73        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        15.95        12.72        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.22         0.95        27.35        18.41        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.78        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       28.60        42.84         9.57        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES 
       78.44        11.80         1.87         1.51        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
        6.58        22.49        15.72         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.70         3.29        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       14.24         7.33         7.30         3.39        20.38        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65         8.81        40.64         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        5.23        53.85         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       17.33         9.90         0.85        11.61        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
       84.72        10.13        16.24        15.42        12.16        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       10.65        14.50        14.50        15.81         0.43        11.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        5.79        18.05         0.33         0.69       164.19        60.03 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
        2.99        10.98        71.01         5.49         6.48        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       13.12         3.72         3.42         5.36         1.08        19.96 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         4.70         8.22         6.67         5.98 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.20               0.13 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            185.16             164.19 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             14.50              15.01 
[1] "0.2 - 185.2 (14.5)" "0.1 - 164.2 (15.0)"
[1] "hr=" "1.2"
D38V2, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    36  27
  21Q GAIN WILD-TYPE 137 139
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                63                276 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                27                139 
$`21Q GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3C6 
       16.67        31.59       103.10        62.07        59.57        58.06 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GU 
      166.52        86.93       103.59        45.30       135.75       125.19 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A6EC TCGA-EB-A6L9 
       79.59        11.61        58.52        95.24        66.25        12.20 
TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R 
       68.15       168.26        63.35        13.97         2.60        14.47 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN 
       46.82       102.90        39.29       208.04        75.48        90.97 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A19B 
      248.65        43.23       124.31       172.18        64.08        98.40 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3PL 
       12.59       131.51       162.08        16.37        31.27        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1Z4 
        6.77        92.98       174.21       210.08        15.16        28.08 
TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GF-A4EO 
       53.52        47.38       148.80        50.14         0.20         7.23 
TCGA-GN-A26D TCGA-GN-A8LK TCGA-W3-A825 TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K6 
       39.58        50.10        63.02       219.16        24.03         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-AAA3 
       90.28        22.68        10.36 

$`21Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.57       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      113.52        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
      130.72        46.98        46.32        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34        39.75       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       125.79       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      178.32        18.18        30.84        15.19       228.99       170.20 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       161.00       137.79        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        11.11         9.90        25.18        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       17.85        68.25        54.02        17.29        52.01         6.35 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89         4.96       133.81       151.27        91.56        13.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       80.61        47.84        63.78        72.07        64.64        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        56.42        37.35        55.92       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      195.02        17.92        36.82        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03        48.72        89.33        54.74        79.66 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS 
      158.63       203.05       167.90        47.54       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21        53.26       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        23.47       138.81       127.20        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       53.19       201.80        27.35        51.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       61.05        44.05        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES 
       79.99        43.82        23.34        20.15        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       80.32        46.98        15.72         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       29.46        94.39       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
       20.91         7.79        27.72        48.85       357.37        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        32.75        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      133.55        11.41        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       19.30         9.90         2.04        11.74       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
       84.72        10.13        64.44        62.79        32.48        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       12.62        21.37        59.41        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        6.67        18.05         0.33         0.69       212.22       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZN 
        4.01        42.08       105.04        38.56        54.38        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       59.41        52.34         3.75        43.73         2.20        30.18 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        36.03        14.43        23.64        93.07        11.74 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.20               0.16 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            248.65             369.93 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             59.57              48.87 
[1] "0.2 - 248.7 (59.6)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.3"
D38V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q GAIN MUTATED                   11             2
  21Q GAIN WILD-TYPE                 50             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  21Q GAIN MUTATED                                          13
  21Q GAIN WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  21Q GAIN MUTATED                    41
  21Q GAIN WILD-TYPE                 168
D38V4, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      11                 50
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 59
  REGIONAL LYMPH NODE                                     41                168
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  21Q GAIN MUTATED             4       0       9        2        9        3
  21Q GAIN WILD-TYPE           8       7      19       15       18       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  21Q GAIN MUTATED           3         1         5         2          3
  21Q GAIN WILD-TYPE        11        18         7        33         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED            6         14        2
  21Q GAIN WILD-TYPE         26         44       17
D38V5, multiclass
             clus
vv            21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    0                  7
  STAGE I                    9                 19
  STAGE IA                   2                 15
  STAGE IB                   9                 18
  STAGE II                   3                 19
  STAGE IIA                  3                 11
  STAGE IIB                  1                 18
  STAGE IIC                  5                  7
  STAGE III                  2                 33
  STAGE IIIA                 3                 12
  STAGE IIIB                 6                 26
  STAGE IIIC                14                 44
  STAGE IV                   2                 17
[1] 14  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                 T0+T1 T2 T3 T4
  21Q GAIN MUTATED      11 19 13 13
  21Q GAIN WILD-TYPE    52 52 61 54
D38V6, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1               11                 52
  T2                  19                 52
  T3                  13                 61
  T4                  13                 54
[1] 4 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                  N0  N1  N2  N3
  21Q GAIN MUTATED    39  10   5  10
  21Q GAIN WILD-TYPE 129  51  33  37
D38V7, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               39                129
  N1               10                 51
  N2                5                 33
  N3               10                 37
[1] 4 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                  M0  M1 M1A M1B M1C
  21Q GAIN MUTATED    61   1   1   0   0
  21Q GAIN WILD-TYPE 245   3   2   4   9
D38V8, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                61                245
  M1                 1                  3
  M1A                1                  2
  M1B                0                  4
  M1C                0                  9
[1] 5 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
  21Q GAIN MUTATED    20  23
  21Q GAIN WILD-TYPE 109  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     20   23
  21Q GAIN WILD-TYPE  109   64
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                20                109
  YES               23                 64
[1] 2 2
[1] FALSE
D38V10, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     8  58
  21Q GAIN WILD-TYPE  35 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8   58
  21Q GAIN WILD-TYPE   35  246
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 8                 35
  YES               58                246
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    27  40
  21Q GAIN WILD-TYPE 104 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     27   40
  21Q GAIN WILD-TYPE  104  177
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               27                104
  MALE                 40                177
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       1                         0    62
  21Q GAIN WILD-TYPE     4                         1   264
D38V13, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   62                264
[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"
D38V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  64
  21Q GAIN WILD-TYPE   6 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   64
  21Q GAIN WILD-TYPE    6  270
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               64                270
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    63  52
  22Q GAIN WILD-TYPE 105 113
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               115                218 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                52                113 
$`22Q GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JO 
        6.97        16.47        22.55        85.32        88.50        64.44 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU 
       59.57        15.25        61.38        13.32         9.34        26.37 
TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GI 
       29.23        52.01        13.68        17.72        22.06         4.18 
TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       75.65        11.44         4.01         9.90        11.31        13.22 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 
       48.79        35.80        10.03        39.19        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
        4.93        22.36        17.56         0.13        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L 
       13.35         0.20        10.55         8.12         9.21         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A29X 
       39.62         9.50         8.09         8.84        32.15         8.09 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN 
        9.67        51.12        47.21        30.08        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MR 
       55.69        98.27         2.70        63.42        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       53.16         5.56       124.31       122.73         3.68        30.15 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-ER-A19C 
       15.95        21.60        21.60         0.95        27.35         3.78 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A2NG 
      114.15        13.45        28.60        17.72        13.08        12.62 
TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7UA 
        6.58        18.41        85.74        15.72         6.71        13.28 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM 
       11.01         7.33         7.30         8.22        30.87        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 
        8.65        49.15        40.64         8.68        27.39         3.22 
TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 
       28.73         2.27         0.20         0.13        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A8LK TCGA-HR-A2OH 
       16.24        15.42        12.16        14.70        14.50        15.81 
TCGA-QB-A6FS TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AAA3 
        5.79        11.84         6.48        18.67         5.36         1.94 
TCGA-YG-AA3O 
        6.18 

$`22Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         8.52       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      110.79        28.08        45.83        81.24        10.29         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        68.22        86.76        11.41        44.19         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C7 
       36.16         6.31        92.42        56.19       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E 
       46.32        82.29        24.00         6.31       103.59        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD 
       25.78       110.24        47.87        23.11        29.72        10.22 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       15.19       142.45       108.79        38.93       124.47        87.62 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY 
        5.56        24.07        21.93         5.72        14.60        51.12 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       13.68         9.99        44.52         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z 
       14.83        13.15         0.20        13.22        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.34        15.85         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S 
       11.15        62.79         8.55        36.85        12.03         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       30.44         2.43        11.31        49.22        36.30        36.33 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.29        17.98        60.00        19.43        16.01        35.54 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56       125.65       111.91        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       26.99        52.67        51.62        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       22.92        16.14        22.22        18.41        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       25.18         3.52        11.90        11.11        34.88         4.21 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07         6.58        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV 
       11.80         1.87         1.51        11.74         9.04        22.49 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD 
        1.71         5.62         3.58         5.36         2.20         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        3.29        64.47         3.45        23.80        14.24        15.52 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        3.39        20.38        19.53        11.08         7.17        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       12.89        52.08         8.81         0.82         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
        7.36        14.20        10.78         5.98         6.41         0.99 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       44.28        10.13        11.84        10.65        14.50        14.50 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.43        11.05        18.05         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        8.98        60.03         2.99        10.98       185.16        71.01 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        5.49         7.10        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT 
       21.83         1.08        19.96        12.07         4.70         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.13               0.16 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            124.31             185.16 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             15.81              14.37 
[1] "0.1 - 124.3 (15.8)" "0.2 - 185.2 (14.4)"
[1] "hr=" "1.2"
D39V2, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    64  52
  22Q GAIN WILD-TYPE 109 114
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               116                223 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                52                114 
$`22Q GAIN MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JO 
       12.99        16.57        31.59       103.10       115.53        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU 
       59.57        58.06        86.93        60.23         9.34        39.75 
TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GI 
       45.30       135.75       178.32        18.18        79.59        58.52 
TCGA-D3-A8GM TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
       95.24        29.06       151.53        11.34         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 
       66.25        48.89        36.03        20.38       194.83        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5SG 
       53.92        65.92        23.44       215.44        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H 
       54.02        17.29        12.20        27.22        94.98       168.26 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W 
        2.60        56.84        18.61        37.35        14.47       195.02 
TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
       17.92        39.29        59.28       208.04        48.72        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MQ 
       90.97       126.81       129.27        28.83        96.23        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      134.40       162.48        53.26       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD 
       54.51        23.47        36.95        64.08       201.80        27.35 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NF 
       48.89       268.93       131.51        61.05       148.18        16.37 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       31.27        80.32        92.98       174.21        15.72       210.08 
TCGA-FR-A7UA TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZH 
       38.27       228.59         7.79        27.72        53.52        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      101.26       133.55       148.80        53.16        26.56        49.48 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 
       50.14        28.73        77.88         0.20        47.54       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A8LK 
       84.72        64.44        62.79        32.48        39.58        50.10 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZY 
       65.88         6.67        24.03        54.38        90.28        43.73 
TCGA-WE-AAA3 TCGA-YG-AA3O 
       10.36        36.03 

$`22Q GAIN WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      133.25        28.08        90.90        95.74        43.43        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       168.00        86.76        11.87        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C7 
       42.08        12.10       171.58        56.19       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E 
       46.32       166.52        24.53        13.87       103.59       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD 
       26.89       125.79       137.92       125.19        30.84        11.61 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       15.19       228.99       170.20        89.13       161.00       137.79 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       117.17        54.67         3.65         6.41        18.12 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.29        11.11        22.95       117.21       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
      107.34        68.09        28.60        10.49        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       10.16        52.01         6.35        29.82         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       91.56        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T 
       63.78        72.07        64.64        56.42        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC 
       25.87        46.82       102.90        36.82        86.14        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP 
      314.56       161.03        89.33        54.74        79.66        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
       14.30        55.59        44.88        94.82        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66       158.63       203.05       167.90        47.54       248.65 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       71.21        51.62        13.81       138.81       172.18       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        53.19        51.35       109.58       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19N 
       12.59        13.02        26.37       152.35         6.44        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25         8.88        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       23.34        20.15        32.05       247.04        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        6.77        15.16         7.00        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB 
      216.92        48.59       202.65        20.91        28.08        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        40.27        15.45         9.70        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       74.73        11.41        27.09        27.02        77.82        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV 
      174.84        12.43        26.73        49.45        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB 
       10.13        46.36        12.62        21.37        59.41       357.04 
TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
      294.77        18.05         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
      121.08         4.01        42.08       219.16       105.04        38.56 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
        8.61        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        2.20        30.18        15.16        14.43        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.20               0.16 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            268.93             369.93 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             53.97              47.54 
[1] "0.2 - 268.9 (54.0)" "0.2 - 369.9 (47.5)"
[1] "hr=" "1.2"
D39V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q GAIN MUTATED                   16             4
  22Q GAIN WILD-TYPE                 45             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  22Q GAIN MUTATED                                          30
  22Q GAIN WILD-TYPE                                        42
                    vv
clus                 REGIONAL LYMPH NODE
  22Q GAIN MUTATED                    70
  22Q GAIN WILD-TYPE                 139
D39V4, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      16                 45
  PRIMARY TUMOR                                            4                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               30                 42
  REGIONAL LYMPH NODE                                     70                139
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  22Q GAIN MUTATED             3       2       9        4        9        5
  22Q GAIN WILD-TYPE           9       5      19       13       18       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  22Q GAIN MUTATED           4         3         5        17          9
  22Q GAIN WILD-TYPE        10        16         7        18          6
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           13         21        6
  22Q GAIN WILD-TYPE         19         37       13
D39V5, multiclass
             clus
vv            22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    2                  5
  STAGE I                    9                 19
  STAGE IA                   4                 13
  STAGE IB                   9                 18
  STAGE II                   5                 17
  STAGE IIA                  4                 10
  STAGE IIB                  3                 16
  STAGE IIC                  5                  7
  STAGE III                 17                 18
  STAGE IIIA                 9                  6
  STAGE IIIB                13                 19
  STAGE IIIC                21                 37
  STAGE IV                   6                 13
[1] 14  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                 T0+T1 T2 T3 T4
  22Q GAIN MUTATED      24 29 22 22
  22Q GAIN WILD-TYPE    39 42 52 45
D39V6, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1               24                 39
  T2                  29                 42
  T3                  22                 52
  T4                  22                 45
[1] 4 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                  N0  N1  N2  N3
  22Q GAIN MUTATED    46  26  17  19
  22Q GAIN WILD-TYPE 122  35  21  28
D39V7, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               46                122
  N1               26                 35
  N2               17                 21
  N3               19                 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"
                    vv
clus                  M0  M1 M1A M1B M1C
  22Q GAIN MUTATED   102   1   1   1   4
  22Q GAIN WILD-TYPE 204   3   2   3   5
D39V8, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               102                204
  M1                 1                  3
  M1A                1                  2
  M1B                1                  3
  M1C                4                  5
[1] 5 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
  22Q GAIN MUTATED   46 32
  22Q GAIN WILD-TYPE 83 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     46   32
  22Q GAIN WILD-TYPE   83   55
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                46                 83
  YES               32                 55
[1] 2 2
[1] FALSE
D39V10, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    15 105
  22Q GAIN WILD-TYPE  28 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     15  105
  22Q GAIN WILD-TYPE   28  199
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                15                 28
  YES              105                199
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    49  71
  22Q GAIN WILD-TYPE  82 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     49   71
  22Q GAIN WILD-TYPE   82  146
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               49                 82
  MALE                 71                146
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       3                         0   111
  22Q GAIN WILD-TYPE     2                         1   215
D39V13, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  111                215
[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"
D39V14, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1 116
  22Q GAIN WILD-TYPE   6 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1  116
  22Q GAIN WILD-TYPE    6  218
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              116                218
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    15  22
  XQ GAIN WILD-TYPE 153 143
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               37               296 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               22               143 
$`XQ GAIN MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A3MV 
        3.02         8.52        88.50        13.32        26.37        29.23 
TCGA-D3-A8GQ TCGA-DA-A3F3 TCGA-EB-A5KH TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29R 
       11.44         7.00         0.13         5.13         7.99         8.84 
TCGA-EE-A2GN TCGA-EE-A2MU TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC 
       33.83         5.56        15.95        21.60        28.60        11.80 
TCGA-ER-A2ND TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1ZG 
        1.87        18.41         6.71         2.20         4.70         7.17 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-FW-A3TV 
       12.89        52.08         8.68         0.82         2.27         0.16 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D TCGA-W3-AA1O TCGA-WE-A8K6 
       11.61        31.33        15.42        14.70         2.99         7.10 
TCGA-WE-A8ZT 
        3.42 

$`XQ GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        6.97         6.97        16.47       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.79        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       85.32         8.38        21.14        68.22        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       44.19         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        59.57       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        61.38        24.00         6.31         9.34       103.59 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.61        25.78       110.24        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       17.72        23.11        29.72        22.06        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
        4.18       142.45       108.79        38.93        75.65       124.47 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       87.62         5.56        24.07         4.01        21.93         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        11.31        13.22        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.20        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        8.12         1.12         1.35        12.20         4.31        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
        4.34        15.85         9.21         1.18         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       11.15        62.79         8.55        36.85         1.08        39.62 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        9.50        12.03         8.09         9.99        30.44         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       30.08        19.43        16.01        35.54        28.31        55.69 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       53.16        52.67       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        13.81        12.72         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       16.14        22.22         0.95        27.35        18.41        21.73 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
      114.15        34.88         4.21        13.45        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE 
        9.57        36.07         6.58        17.72        78.44         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
        1.71         5.62        85.74        15.72         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       13.28         3.29        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
        8.22        19.53        11.08        30.87        12.92        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
        8.65         8.81        49.15        40.64        27.39         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       53.85         3.22         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY 
        5.98         6.41         0.20         0.99         0.13        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         7.23         0.85        44.28        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       16.24        12.16        11.84        10.65        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        15.81         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
        0.33         0.69       164.19         8.98        60.03        10.98 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      185.16        71.01        11.84         5.49         6.48        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       21.07        13.12         3.72        21.83         5.36         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       19.96         1.94        12.07         6.18         4.70         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.13              0.13 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            88.50            185.16 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             8.68             15.93 
[1] "0.1 - 88.5 (8.7)"   "0.1 - 185.2 (15.9)"
[1] "hr=" "2"  
D40V2, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    15  22
  XQ GAIN WILD-TYPE 158 144
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               37               302 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               22               144 
$`XQ GAIN MUTATED`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A3MV 
       17.03        16.67       115.53        60.23        39.75        45.30 
TCGA-D3-A8GQ TCGA-DA-A3F3 TCGA-EB-A5KH TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29R 
       29.06        10.49        17.85        68.15        63.35        14.47 
TCGA-EE-A2GN TCGA-EE-A2MU TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC 
       90.97        53.26        23.47        64.08        61.05        43.82 
TCGA-ER-A2ND TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1ZG 
       23.34        92.98       210.08        34.82        29.46         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-FW-A3TV 
       23.93        74.73        26.56        27.09        77.88         0.16 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D TCGA-W3-AA1O TCGA-WE-A8K6 
       11.74       117.93        62.79        39.58         4.01         8.61 
TCGA-WE-A8ZT 
        3.75 

$`XQ GAIN WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       61.02        12.99        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        65.49        23.77       168.00        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       62.07       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        24.53        13.87         9.34       103.59 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       18.18       125.19        30.84        79.59        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       58.52       228.99       170.20        89.13        95.24       161.00 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      137.79       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        6.41        18.12        11.34        22.29        11.11         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       25.18        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       20.38       194.83       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       53.92        65.92        23.44        68.09        28.60       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        10.16        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       52.01         6.35        12.20        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        33.73        14.70        26.89         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56       168.26        13.55        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        63.78        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        56.42        37.35        55.92       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       48.72        89.33        54.74        79.66        75.48       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      162.48        71.21       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81       138.81       172.18       127.20        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       34.32        53.19       201.80        27.35        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P 
      268.93       152.35         6.44       131.51        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE 
       50.89        37.25         8.88       148.18        79.99        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       33.21         6.77       174.21        15.72        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       38.27        94.39       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       53.52        40.27        15.45        32.75        47.38       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
      133.55        11.41       148.80        53.16        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY 
       26.73        49.45         0.20        22.92        47.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         7.23         2.04       139.89        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       64.44        32.48        46.36        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       59.41        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
        0.33         0.69       212.22        63.02       121.08        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM 
      219.16       105.04        24.03        38.56        54.38        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       56.98        59.41        52.34        22.68        43.73         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       30.18        10.36        15.16        36.03        14.43        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.16              0.20 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           210.08            369.93 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           34.820            51.815 
[1] "0.2 - 210.1 (34.8)" "0.2 - 369.9 (51.8)"
[1] "hr=" "1.9"
D40V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ GAIN MUTATED                   12             0
  XQ GAIN WILD-TYPE                 49             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  XQ GAIN MUTATED                                           7
  XQ GAIN WILD-TYPE                                        65
                   vv
clus                REGIONAL LYMPH NODE
  XQ GAIN MUTATED                    19
  XQ GAIN WILD-TYPE                 190
D40V4, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  DISTANT METASTASIS                                     12                49
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               7                65
  REGIONAL LYMPH NODE                                    19               190
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XQ GAIN MUTATED             0       1       2        2        4        3
  XQ GAIN WILD-TYPE          12       6      26       15       23       19
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XQ GAIN MUTATED           1         3         4         5          3
  XQ GAIN WILD-TYPE        13        16         8        30         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED            4          4        1
  XQ GAIN WILD-TYPE         28         54       18
D40V5, multiclass
             clus
vv            XQ GAIN MUTATED XQ GAIN WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   1                 6
  STAGE I                   2                26
  STAGE IA                  2                15
  STAGE IB                  4                23
  STAGE II                  3                19
  STAGE IIA                 1                13
  STAGE IIB                 3                16
  STAGE IIC                 4                 8
  STAGE III                 5                30
  STAGE IIIA                3                12
  STAGE IIIB                4                28
  STAGE IIIC                4                54
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  XQ GAIN MUTATED       9  9  8  7
  XQ GAIN WILD-TYPE    54 62 66 60
D40V6, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1               9                54
  T2                  9                62
  T3                  8                66
  T4                  7                60
[1] 4 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                 N0  N1  N2  N3
  XQ GAIN MUTATED    19   7   7   2
  XQ GAIN WILD-TYPE 149  54  31  45
D40V7, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              19               149
  N1               7                54
  N2               7                31
  N3               2                45
[1] 4 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                 M0  M1 M1A M1B M1C
  XQ GAIN MUTATED    34   0   0   1   0
  XQ GAIN WILD-TYPE 272   4   3   3   9
D40V8, multiclass
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               34               272
  M1                0                 4
  M1A               0                 3
  M1B               1                 3
  M1C               0                 9
[1] 5 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
  XQ GAIN MUTATED    13  12
  XQ GAIN WILD-TYPE 116  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     13   12
  XQ GAIN WILD-TYPE  116   75
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               13               116
  YES              12                75
[1] 2 2
[1] FALSE
D40V10, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     5  33
  XQ GAIN WILD-TYPE  38 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5   33
  XQ GAIN WILD-TYPE   38  271
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                5                38
  YES              33               271
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    12  26
  XQ GAIN WILD-TYPE 119 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     12   26
  XQ GAIN WILD-TYPE  119  191
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              12               119
  MALE                26               191
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       1                         0    36
  XQ GAIN WILD-TYPE     4                         1   290
D40V13, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  36               290
[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"
D40V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  37
  XQ GAIN WILD-TYPE   7 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   37
  XQ GAIN WILD-TYPE    7  297
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              37               297
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    31  18
  1P LOSS WILD-TYPE 137 147
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               49               284 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               18               147 
$`1P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR 
      111.09        22.55        61.38        29.23        52.01        13.68 
TCGA-D3-A5GS TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       17.72         5.72        13.68        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2GE TCGA-EE-A2GH 
       14.83         0.20         9.21         8.84        60.00        47.21 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AD 
       55.69         1.15       125.65        26.99        53.16         3.68 
TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
        3.22        31.40        12.95         3.78         3.52        13.45 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 
        1.87        12.62        11.74        22.49        15.72         5.36 
TCGA-FS-A1Z7 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GN-A26D 
        7.33        40.64        27.39        14.20         0.16        14.70 
TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AA9Y TCGA-WE-AAA3 
       18.05         6.48        18.67         3.72         1.08         1.94 
TCGA-YG-AA3P 
        4.70 

$`1P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
        3.02         6.97         6.97        16.47         8.52        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        44.19         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        64.44        59.57       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        82.29        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        26.37        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       32.28        21.44        32.61        25.78       110.24        47.87 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       23.11        29.72        22.06        10.22        15.19         4.18 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
      142.45       108.79        38.93        75.65       124.47        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       11.44         5.56        24.07         4.01        21.93         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       11.31        13.22        14.60        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB 
       10.03        39.19         9.99        44.52         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
        6.64        19.36         7.00        13.15         0.13        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       19.00        13.35        13.22         0.20        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.31        60.23         4.34        15.85         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        9.90        37.97        11.15        62.79         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        1.08        39.62         9.50        12.03         8.09         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       30.44         2.43        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.30         9.67        36.33        51.12        34.29        17.98 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        5.42        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       44.25         7.96        14.56        63.42       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       25.08        21.60        60.49        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        51.62        30.15        13.81        15.95        12.72 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
       22.92        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       27.35        18.41        21.73        33.60        18.61        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        5.72        76.41        25.18        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       34.88         4.21        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
       36.07         6.58        17.72        78.44        11.80         1.51 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       13.08         9.04         6.58         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       85.74         6.71         3.58        13.28         2.20         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.29        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       52.08         8.65         8.81        49.15         8.68         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
        5.23        53.85         3.22         7.36        28.73        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       11.84        10.65        14.50        14.50        14.50        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.43        11.05         5.79         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        8.98        60.03         2.99        10.98       185.16        71.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
       11.84         5.49         7.10        21.07        13.12         3.42 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT 
       21.83         5.36        19.96        12.07         6.18         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.16              0.13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           125.65            185.16 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            14.20             15.22 
[1] "0.2 - 125.7 (14.2)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1.2"
D41V2, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    32  18
  1P LOSS WILD-TYPE 141 148
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               50               289 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               18               148 
$`1P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR 
      112.04        31.59        86.93        45.30       135.75       178.32 
TCGA-D3-A5GS TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 
       18.18        18.12        11.11       176.55        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2GE 
      215.44        15.68        10.16       168.26        14.47       161.03 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
      208.04       126.81        14.30       158.63       248.65       162.48 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19D 
        3.68       172.18        31.40        13.94        48.89        12.59 
TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A69P 
      131.51        23.34        31.27        32.05        46.98        15.72 
TCGA-FR-A7U9 TCGA-FS-A1Z7 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV 
        7.00         7.79        53.16        49.48       174.84         0.16 
TCGA-GN-A26D TCGA-QB-AA9O TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AA9Y 
       39.58        18.05        54.38        90.28        52.34         2.20 
TCGA-WE-AAA3 TCGA-YG-AA3P 
       10.36        14.43 

$`1P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.57        16.67       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       32.94        22.62        63.81        26.89       125.79       137.92 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
      125.19        30.84        79.59        11.61        15.19        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
      228.99       170.20        89.13        95.24       161.00       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34        22.29         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       107.34        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       10.49        13.87        17.85        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       52.01         6.35        12.20        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      133.81       151.27        91.56        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       47.84        13.97        63.78        72.07        64.64         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       56.84        18.61        56.42        37.35        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GI 
       39.29        86.14        59.28        67.43       314.56        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       89.33        54.74        79.66        75.48        90.97        13.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       16.96       204.66        96.23       203.05       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       134.40        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       51.62        54.51        13.81        23.47       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       51.35       109.58       148.08        35.44        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       77.75        98.40        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        33.21         6.77        92.98       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      210.08        15.16        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        9.70        32.75        47.38        23.93       101.26        74.73 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      133.55        11.41       148.80        26.56        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        50.14        66.67        28.73        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY 
       49.45        77.88         0.20        22.92        47.54        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
       84.72        10.13        64.44        62.79        32.48        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       12.62        50.10        21.37        59.41        65.88       357.04 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
      294.77         6.67         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      121.08         4.01        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
       38.56         8.61        56.98        59.41         3.75        22.68 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       43.73        30.18        15.16        36.03        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.16              0.20 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           248.65            369.93 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            46.14             51.35 
[1] "0.2 - 248.7 (46.1)" "0.2 - 369.9 (51.4)"
[1] "hr=" "1.4"
D41V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P LOSS MUTATED                    6             0
  1P LOSS WILD-TYPE                 55             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1P LOSS MUTATED                                          11
  1P LOSS WILD-TYPE                                        61
                   vv
clus                REGIONAL LYMPH NODE
  1P LOSS MUTATED                    33
  1P LOSS WILD-TYPE                 176
D41V4, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  DISTANT METASTASIS                                      6                55
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              11                61
  REGIONAL LYMPH NODE                                    33               176
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1P LOSS MUTATED             0       0       7        0        2        3
  1P LOSS WILD-TYPE          12       7      21       17       25       19
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1P LOSS MUTATED           1         2         2         6          0
  1P LOSS WILD-TYPE        13        17        10        29         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED            8         15        2
  1P LOSS WILD-TYPE         24         43       17
D41V5, multiclass
             clus
vv            1P LOSS MUTATED 1P LOSS WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   0                 7
  STAGE I                   7                21
  STAGE IA                  0                17
  STAGE IB                  2                25
  STAGE II                  3                19
  STAGE IIA                 1                13
  STAGE IIB                 2                17
  STAGE IIC                 2                10
  STAGE III                 6                29
  STAGE IIIA                0                15
  STAGE IIIB                8                24
  STAGE IIIC               15                43
  STAGE IV                  2                17
[1] 14  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                T0+T1 T2 T3 T4
  1P LOSS MUTATED       9 14  8 14
  1P LOSS WILD-TYPE    54 57 66 53
D41V6, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               9                54
  T2                 14                57
  T3                  8                66
  T4                 14                53
[1] 4 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                 N0  N1  N2  N3
  1P LOSS MUTATED    18  11   9  10
  1P LOSS WILD-TYPE 150  50  29  37
D41V7, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              18               150
  N1              11                50
  N2               9                29
  N3              10                37
[1] 4 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                 M0  M1 M1A M1B M1C
  1P LOSS MUTATED    44   0   0   0   2
  1P LOSS WILD-TYPE 262   4   3   4   7
D41V8, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               44               262
  M1                0                 4
  M1A               0                 3
  M1B               0                 4
  M1C               2                 7
[1] 5 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
  1P LOSS MUTATED    16  15
  1P LOSS WILD-TYPE 113  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     16   15
  1P LOSS WILD-TYPE  113   72
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               16               113
  YES              15                72
[1] 2 2
[1] FALSE
D41V10, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     4  47
  1P LOSS WILD-TYPE  39 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4   47
  1P LOSS WILD-TYPE   39  257
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                4                39
  YES              47               257
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    21  30
  1P LOSS WILD-TYPE 110 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     21   30
  1P LOSS WILD-TYPE  110  187
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              21               110
  MALE                30               187
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         0    45
  1P LOSS WILD-TYPE     4                         1   281
D41V13, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  45               281
[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"
D41V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1  50
  1P LOSS WILD-TYPE   6 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   50
  1P LOSS WILD-TYPE    6  284
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              50               284
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    13  12
  1Q LOSS WILD-TYPE 155 153
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               308 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               153 
$`1Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A4Z6 TCGA-DA-A1I2 
       22.55        61.38        13.68        17.72         5.72        13.68 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A20H TCGA-EE-A29X TCGA-EE-A2M6 
       36.69        25.15        14.83         9.21         8.09        98.27 
TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A2NG TCGA-ER-A3EV 
       26.99         3.22        31.40         3.78        12.62        22.49 
TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A4F8 TCGA-QB-AA9O TCGA-W3-AA1V TCGA-WE-A8ZQ 
       15.72         5.36        14.20        18.05        10.98         3.72 
TCGA-WE-AAA3 
        1.94 

$`1Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       32.42        70.16       110.79        28.08        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       10.29        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.41        44.19         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       92.42        56.19        64.44        59.57       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32        82.29        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        26.37        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      110.24        52.01        47.87        23.11        29.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       10.22        15.19         4.18       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       75.65       124.47        87.62        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01        21.93         9.90        11.31        13.22        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       48.79        35.80        51.12        10.03        39.19         9.99 
TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       44.52         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        13.15         0.20         0.13        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       60.23         4.34        15.85         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       37.97        11.15        62.79         8.55        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       30.44         2.43        32.15        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67        36.33        51.12        34.29        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        55.69         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       36.33         8.84         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      125.65       111.91        56.02        25.08        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
        3.68        30.15        13.81        15.95        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       18.41        21.73        33.60        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        5.72        76.41        25.18         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       11.80         1.87         1.51        13.08        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
        6.58         1.71         5.62        18.41        85.74         6.71 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        3.58        13.28         2.20         4.70         3.29        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
        7.17        30.87        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
        8.65         8.81        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
        0.82         5.23        53.85         3.22         7.36        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       15.42        12.16        14.70        11.84        10.65        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      185.16        71.01        11.84         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       18.67        21.07        13.12         3.42        21.83         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
        1.08        19.96        12.07         6.18         4.70         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.94              0.13 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            98.27            185.16 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           14.200            14.945 
[1] "1.9 - 98.3 (14.2)"  "0.1 - 185.2 (14.9)"
[1] "hr=" "1.1"
D42V2, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    14  12
  1Q LOSS WILD-TYPE 159 154
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               26               313 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               154 
$`1Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A1X3 TCGA-D9-A4Z6 
       31.59        86.93       178.32        18.18        18.12        11.11 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A20H TCGA-EE-A29X 
      176.55        61.18        53.92        15.68       168.26        17.92 
TCGA-EE-A2M6 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A2NG 
      129.27       248.65       172.18        31.40        48.89        31.27 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A4F8 TCGA-QB-AA9O TCGA-W3-AA1V 
       46.98        15.72         7.00       174.84        18.05        42.08 
TCGA-WE-A8ZQ TCGA-WE-AAA3 
       52.34        10.36 

$`1Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.87        62.07       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        56.19        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32       166.52        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      125.79       135.75       137.92       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       11.61        15.19        58.52       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       95.24       161.00       137.79        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      151.53        54.67         3.65         6.41        11.34        22.29 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA 
      117.21        20.38       194.83        35.93       107.34        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49       215.44        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.16        17.85        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        6.35        12.20        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.97        63.78        72.07        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        37.35        14.47        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.87       195.02        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      203.05       167.90        47.54        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       54.51        13.81        23.47       138.81       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      109.58       148.08        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       77.75        98.40        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       50.89        37.25         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        16.37        32.05       247.04        80.32 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       33.21         6.77        92.98       174.21       210.08        15.16 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        29.46        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 
       27.02        77.82        50.14        66.67        28.73        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       32.48        39.58        46.36        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       59.41        65.88       357.04       294.77         6.67         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.69       212.22        63.02       121.08         4.01       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      105.04        24.03        38.56        54.38         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       56.98        59.41         3.75        22.68        43.73         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       30.18        15.16        36.03        14.43        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             7.00              0.16 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           248.65            369.93 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            44.53             50.89 
[1] "7.0 - 248.7 (44.5)" "0.2 - 369.9 (50.9)"
[1] "hr=" "1.1"
D42V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q LOSS MUTATED                    2             0
  1Q LOSS WILD-TYPE                 59             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1Q LOSS MUTATED                                           5
  1Q LOSS WILD-TYPE                                        67
                   vv
clus                REGIONAL LYMPH NODE
  1Q LOSS MUTATED                    19
  1Q LOSS WILD-TYPE                 190
D42V4, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      2                59
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               5                67
  REGIONAL LYMPH NODE                                    19               190
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  1Q LOSS MUTATED             0       0       5        0        2        1
  1Q LOSS WILD-TYPE          12       7      23       17       25       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1Q LOSS MUTATED           1         1         1         2          0
  1Q LOSS WILD-TYPE        13        18        11        33         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED            3          8        1
  1Q LOSS WILD-TYPE         29         50       18
D42V5, multiclass
             clus
vv            1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   0                 7
  STAGE I                   5                23
  STAGE IA                  0                17
  STAGE IB                  2                25
  STAGE II                  1                21
  STAGE IIA                 1                13
  STAGE IIB                 1                18
  STAGE IIC                 1                11
  STAGE III                 2                33
  STAGE IIIA                0                15
  STAGE IIIB                3                29
  STAGE IIIC                8                50
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  1Q LOSS MUTATED       5  6  6  7
  1Q LOSS WILD-TYPE    58 65 68 60
D42V6, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               5                58
  T2                  6                65
  T3                  6                68
  T4                  7                60
[1] 4 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                 N0  N1  N2  N3
  1Q LOSS MUTATED    11   3   6   5
  1Q LOSS WILD-TYPE 157  58  32  42
D42V7, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              11               157
  N1               3                58
  N2               6                32
  N3               5                42
[1] 4 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                 M0  M1 M1A M1B M1C
  1Q LOSS MUTATED    23   0   0   0   1
  1Q LOSS WILD-TYPE 283   4   3   4   8
D42V8, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               23               283
  M1                0                 4
  M1A               0                 3
  M1B               0                 4
  M1C               1                 8
[1] 5 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
  1Q LOSS MUTATED     8   8
  1Q LOSS WILD-TYPE 121  79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8    8
  1Q LOSS WILD-TYPE  121   79
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                8               121
  YES               8                79
[1] 2 2
[1] FALSE
D42V10, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  23
  1Q LOSS WILD-TYPE  40 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   23
  1Q LOSS WILD-TYPE   40  281
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                3                40
  YES              23               281
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9  17
  1Q LOSS WILD-TYPE 122 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   17
  1Q LOSS WILD-TYPE  122  200
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               9               122
  MALE                17               200
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0    24
  1Q LOSS WILD-TYPE     5                         1   302
D42V13, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  24               302
[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"
D42V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  26
  1Q LOSS WILD-TYPE   7 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   26
  1Q LOSS WILD-TYPE    7  308
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              26               308
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    20  23
  2P LOSS WILD-TYPE 148 142
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               43               290 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               23               142 
$`2P LOSS MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
       86.76         7.50        15.25        24.00       103.59        26.37 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6EA 
       25.78        47.87        75.65        24.07        21.93        11.31 
TCGA-DA-A1I2 TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29P 
       13.68         8.12        60.23        15.85         1.18        12.03 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS 
       34.29        47.21         1.15        63.42       125.65        53.16 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A19C TCGA-ER-A19P 
        3.68         3.22        22.22        18.41         3.78        34.68 
TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-GN-A264 
        1.71         2.20        64.47        11.01        23.80        31.33 
TCGA-GN-A267 TCGA-GN-A26D TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-AA21 TCGA-WE-AA9Y 
       16.24        14.70        15.81        11.05        71.01         1.08 
TCGA-YG-AA3P 
        4.70 

$`2P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       68.22        11.41        44.19        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        64.44        59.57       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV 
       82.29        61.38        13.32         6.31         9.34        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       32.61       110.24        52.01        13.68        17.72        23.11 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       29.72        22.06        10.22        15.19         4.18       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      108.79        38.93       124.47        87.62        11.44         5.56 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        4.01         5.72         9.90        13.22        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        10.03        39.19         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       23.15        19.00        13.35        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.31         4.34         9.21         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       11.15        62.79         8.55        36.85         1.08        39.62 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        9.50         8.09         8.84         9.99        30.44         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       32.15         8.09        11.31        49.22        36.30         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       36.33        51.12        17.98        60.00        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        55.69         5.42 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
        7.96        14.56       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        60.49        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       51.62        30.15        13.81        15.95        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH 
       21.60        21.60        16.14         0.95        27.35        21.73 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.60        31.40        18.61        12.95        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       76.41        25.18         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
       34.88         4.21        13.45        28.60        42.84         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       22.49         5.62        18.41        85.74        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX 
        3.58         5.36        13.28         4.70         3.29         3.45 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        3.22         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        10.13        15.42        12.16        11.84        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        14.50        14.50         0.43         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       10.98       185.16        11.84         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       18.67        21.07        13.12         3.72         3.42        21.83 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT 
        5.36        19.96         1.94        12.07         6.18         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1.08              0.13 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           125.65            185.16 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            18.41             14.37 
[1] "1.1 - 125.7 (18.4)" "0.1 - 185.2 (14.4)"
[1] "hr=" "1"  
D43V2, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    22  23
  2P LOSS WILD-TYPE 151 143
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               45               294 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               23               143 
$`2P LOSS MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
       86.76       113.52        58.06        24.53       103.59        39.75 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1X3 
       26.89       137.92        95.24       117.17        54.67        18.12 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1I2 TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20F 
       22.29        25.18       176.55        94.98       133.81        91.56 
TCGA-EE-A20I TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ 
       13.55        56.42        67.43       208.04        14.30        96.23 
TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE 
      158.63       162.48         3.68       172.18        53.19        51.35 
TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
       48.89       162.08        33.21        34.82       216.92       228.59 
TCGA-FS-A1Z0 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D TCGA-HR-A2OH TCGA-OD-A75X 
      202.65       117.93        64.44        39.58        65.88       294.77 
TCGA-W3-AA21 TCGA-WE-AA9Y TCGA-YG-AA3P 
      105.04         2.20        14.43 

$`2P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
      168.00        11.87        62.07        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        66.08        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV 
      166.52        86.93        60.23        13.87         9.34        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       63.81       125.79       135.75       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       30.84        79.59        11.61        15.19        58.52       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       161.00       137.79        29.06       129.63 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 
      151.53         3.65         6.41        11.34        11.11         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       66.25        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      194.83        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       13.87        10.16        17.85        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       52.01         6.35        12.20        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
       33.73        14.70        26.89        68.15         4.96       151.27 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
      168.26        63.35        80.61        47.84        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       72.07        64.64         2.60        56.84        18.61        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        55.92       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48        90.97       126.81        13.91        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.28       103.27       268.73       103.20        16.96       204.66 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
       71.21        53.26       124.31       122.73        51.62        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        23.47       138.81       127.20        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32       201.80        27.35       109.58       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       35.44        13.94        50.76         9.17        77.75        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       12.59        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
      131.51        61.05        44.05        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       31.27        32.05       247.04        80.32        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       38.27        29.46        94.39        48.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       28.73       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        0.20        22.92        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        7.23         2.04        11.74       139.89        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       62.79        32.48        46.36        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
       59.41       357.04         6.67        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
      212.22        63.02       121.08         4.01        42.08       219.16 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        38.56        54.38         8.61        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 
       59.41        52.34         3.75        22.68        43.73        30.18 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       10.36        15.16        36.03        23.64        93.07        11.74 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.20              0.16 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           294.77            369.93 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           67.430            48.215 
[1] "2.2 - 294.8 (67.4)" "0.2 - 369.9 (48.2)"
[1] "hr=" "1.3"
D43V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P LOSS MUTATED                   12             1
  2P LOSS WILD-TYPE                 49             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2P LOSS MUTATED                                           9
  2P LOSS WILD-TYPE                                        63
                   vv
clus                REGIONAL LYMPH NODE
  2P LOSS MUTATED                    27
  2P LOSS WILD-TYPE                 182
D43V4, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  DISTANT METASTASIS                                     12                49
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               9                63
  REGIONAL LYMPH NODE                                    27               182
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2P LOSS MUTATED             1       0       5        1        4        4
  2P LOSS WILD-TYPE          11       7      23       16       23       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2P LOSS MUTATED           1         4         2         6          3
  2P LOSS WILD-TYPE        13        15        10        29         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED            3          5        3
  2P LOSS WILD-TYPE         29         53       16
D43V5, multiclass
             clus
vv            2P LOSS MUTATED 2P LOSS WILD-TYPE
  I OR II NOS               1                11
  STAGE 0                   0                 7
  STAGE I                   5                23
  STAGE IA                  1                16
  STAGE IB                  4                23
  STAGE II                  4                18
  STAGE IIA                 1                13
  STAGE IIB                 4                15
  STAGE IIC                 2                10
  STAGE III                 6                29
  STAGE IIIA                3                12
  STAGE IIIB                3                29
  STAGE IIIC                5                53
  STAGE IV                  3                16
[1] 14  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                T0+T1 T2 T3 T4
  2P LOSS MUTATED       7  8 12 14
  2P LOSS WILD-TYPE    56 63 62 53
D43V6, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               7                56
  T2                  8                63
  T3                 12                62
  T4                 14                53
[1] 4 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                 N0  N1  N2  N3
  2P LOSS MUTATED    27   8   5   3
  2P LOSS WILD-TYPE 141  53  33  44
D43V7, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              27               141
  N1               8                53
  N2               5                33
  N3               3                44
[1] 4 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                 M0  M1 M1A M1B M1C
  2P LOSS MUTATED    41   0   1   0   2
  2P LOSS WILD-TYPE 265   4   2   4   7
D43V8, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               41               265
  M1                0                 4
  M1A               1                 2
  M1B               0                 4
  M1C               2                 7
[1] 5 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
  2P LOSS MUTATED    21  13
  2P LOSS WILD-TYPE 108  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     21   13
  2P LOSS WILD-TYPE  108   74
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               21               108
  YES              13                74
[1] 2 2
[1] FALSE
D43V10, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3  46
  2P LOSS WILD-TYPE  40 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   46
  2P LOSS WILD-TYPE   40  258
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                3                40
  YES              46               258
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    19  30
  2P LOSS WILD-TYPE 112 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     19   30
  2P LOSS WILD-TYPE  112  187
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              19               112
  MALE                30               187
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0    45
  2P LOSS WILD-TYPE     5                         1   281
D43V13, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  45               281
[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"
D43V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2  45
  2P LOSS WILD-TYPE   5 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   45
  2P LOSS WILD-TYPE    5  289
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              45               289
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    17  26
  2Q LOSS WILD-TYPE 151 139
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               43               290 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               26               139 
$`2Q LOSS MUTATED`
TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51T 
        7.50        15.25        24.00       103.59        26.37        25.78 
TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A6EA TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C 
       75.65        24.07        11.31         8.12        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH 
       15.85         1.18        11.15        12.03        34.29        47.21 
TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3J3 
        1.15        63.42       125.65        53.16        13.81         3.22 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL 
       22.22        18.41         3.78        34.68         1.87         1.71 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZQ TCGA-GN-A267 
        2.20        64.47        11.01        23.80         8.65        16.24 
TCGA-GN-A26D TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-AA9Y 
       14.70        15.81        11.05        60.03        71.01         1.08 
TCGA-YG-AA3P 
        4.70 

$`2Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        86.76        11.41        44.19        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       92.42        56.19        64.44        59.57       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        82.29        61.38        13.32         6.31         9.34 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       21.44        32.61       110.24        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       17.72        23.11        29.72        22.06        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
        4.18       142.45       108.79        38.93       124.47        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
       11.44         5.56         4.01        21.93         5.72         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       13.22        14.60        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       14.83        13.15         0.20         0.13        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20H 
        1.12         1.35        12.20         5.13         4.31         9.21 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
        7.99         9.90        37.97        62.79         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08        39.62         9.50         8.09         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       30.44         2.43        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       36.30         9.67        36.33        51.12        17.98        60.00 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       55.69         5.42        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM 
        2.73        44.25         7.96        14.56       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
       25.08        26.99        21.60        60.49        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
      124.31       122.73        51.62         3.68        30.15        15.95 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
       12.72        22.92        21.60        21.60        16.14         0.95 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        21.73        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       38.40         5.72        76.41        25.18         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       42.84         9.57        36.07         6.58        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       11.80         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         5.62        18.41        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
        6.71         3.58         5.36        13.28         4.70         3.29 
TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        3.45        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        12.89        47.38        52.08         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        3.22         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
       31.33        84.72        10.13        15.42        12.16        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS 
       10.65        14.50        14.50        14.50         0.43         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O 
       18.05         0.33         0.69       164.19         8.98         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       10.98       185.16        11.84         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       18.67        21.07        13.12         3.72         3.42        21.83 
TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT 
        5.36        19.96         1.94        12.07         6.18         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             1.08              0.13 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           125.65            185.16 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            15.81             14.53 
[1] "1.1 - 125.7 (15.8)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.2"
D44V2, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    20  26
  2Q LOSS WILD-TYPE 153 140
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               46               293 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               26               140 
$`2Q LOSS MUTATED`
TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51T 
      113.52        58.06        24.53       103.59        39.75        26.89 
TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A6EA 
       95.24       117.17       151.53        54.67        18.12        25.18 
TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D 
       94.98       133.81       151.27        91.56        13.55        13.97 
TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK 
       56.42        67.43       208.04        14.30        96.23       158.63 
TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A19C 
      162.48        13.81       172.18        53.19        51.35        48.89 
TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
      162.08        23.34        33.21        34.82       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZQ TCGA-GN-A267 TCGA-GN-A26D TCGA-HR-A2OH TCGA-OD-A75X 
      202.65       133.55        64.44        39.58        65.88       294.77 
TCGA-W3-A828 TCGA-W3-AA21 TCGA-WE-AA9Y TCGA-YG-AA3P 
      121.08       105.04         2.20        14.43 

$`2Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        11.87        62.07        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
      171.58        56.19        66.08        59.57       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        86.93        60.23        13.87         9.34 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       22.62        63.81       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       18.18       125.19        30.84        79.59        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       58.52       228.99       170.20        89.13       161.00       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       29.06       129.63         3.65         6.41        11.34        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       11.11         9.90        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
      117.21        20.38       194.83       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       61.18        53.92        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       215.44        15.68        13.87        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       68.15         4.96       168.26        63.35        80.61        47.84 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       63.78        72.07        64.64         2.60        56.84        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       37.35        14.47        55.92       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28       314.56       161.03        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       79.66        75.48        90.97       126.81        13.91        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      204.66       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        54.51        23.47       138.81       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI 
       64.08        34.32       201.80        27.35       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       31.40        35.44        13.94        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        61.05        44.05        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       31.27        32.05       247.04        80.32        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       38.27        29.46        94.39        48.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       74.73        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       62.79        32.48        46.36        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
       59.41       357.04         6.67        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ 
      212.22        63.02         4.01        42.08       219.16        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       38.56        54.38         8.61        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 
       52.34         3.75        22.68        43.73        30.18        10.36 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        36.03        23.64        93.07        11.74 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.20              0.16 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           294.77            369.93 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           66.655            48.590 
[1] "2.2 - 294.8 (66.7)" "0.2 - 369.9 (48.6)"
[1] "hr=" "1.1"
D44V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q LOSS MUTATED                   15             1
  2Q LOSS WILD-TYPE                 46             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2Q LOSS MUTATED                                           9
  2Q LOSS WILD-TYPE                                        63
                   vv
clus                REGIONAL LYMPH NODE
  2Q LOSS MUTATED                    25
  2Q LOSS WILD-TYPE                 184
D44V4, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     15                46
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               9                63
  REGIONAL LYMPH NODE                                    25               184
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  2Q LOSS MUTATED             2       1       5        1        4        4
  2Q LOSS WILD-TYPE          10       6      23       16       23       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2Q LOSS MUTATED           1         4         2         4          3
  2Q LOSS WILD-TYPE        13        15        10        31         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED            2          7        3
  2Q LOSS WILD-TYPE         30         51       16
D44V5, multiclass
             clus
vv            2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   1                 6
  STAGE I                   5                23
  STAGE IA                  1                16
  STAGE IB                  4                23
  STAGE II                  4                18
  STAGE IIA                 1                13
  STAGE IIB                 4                15
  STAGE IIC                 2                10
  STAGE III                 4                31
  STAGE IIIA                3                12
  STAGE IIIB                2                30
  STAGE IIIC                7                51
  STAGE IV                  3                16
[1] 14  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                T0+T1 T2 T3 T4
  2Q LOSS MUTATED       7  8 13 12
  2Q LOSS WILD-TYPE    56 63 61 55
D44V6, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               7                56
  T2                  8                63
  T3                 13                61
  T4                 12                55
[1] 4 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                 N0  N1  N2  N3
  2Q LOSS MUTATED    29   7   3   6
  2Q LOSS WILD-TYPE 139  54  35  41
D44V7, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              29               139
  N1               7                54
  N2               3                35
  N3               6                41
[1] 4 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                 M0  M1 M1A M1B M1C
  2Q LOSS MUTATED    42   0   1   1   2
  2Q LOSS WILD-TYPE 264   4   2   3   7
D44V8, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               42               264
  M1                0                 4
  M1A               1                 2
  M1B               1                 3
  M1C               2                 7
[1] 5 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
  2Q LOSS MUTATED    21  13
  2Q LOSS WILD-TYPE 108  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     21   13
  2Q LOSS WILD-TYPE  108   74
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               21               108
  YES              13                74
[1] 2 2
[1] FALSE
D44V10, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  48
  2Q LOSS WILD-TYPE  41 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   48
  2Q LOSS WILD-TYPE   41  256
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2                41
  YES              48               256
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    19  31
  2Q LOSS WILD-TYPE 112 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     19   31
  2Q LOSS WILD-TYPE  112  186
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              19               112
  MALE                31               186
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0    46
  2Q LOSS WILD-TYPE     5                         1   280
D44V13, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  46               280
[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"
D44V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  46
  2Q LOSS WILD-TYPE   5 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   46
  2Q LOSS WILD-TYPE    5  288
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              46               288
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    30  26
  3P LOSS WILD-TYPE 138 139
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               56               277 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               26               139 
$`3P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JG 
      111.09        32.42       110.79        85.32        88.50         7.50 
TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D9-A4Z6 
       56.19        15.25        23.11        29.72        87.62         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 
        9.90        11.31        48.79        35.80        13.68        44.52 
TCGA-DA-A1I7 TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GC 
       36.69        10.55         4.34         8.55        12.03        34.29 
TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2MF TCGA-EE-A3AA TCGA-EE-A3AG TCGA-EE-A3J3 
       47.21        98.27         2.73       124.31        15.95         3.22 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19H TCGA-ER-A19S 
       21.60         0.95        18.61        12.95        34.88        36.07 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZM 
        1.87        12.62         5.36         2.20         3.45        47.38 
TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 
        8.65        14.20         2.27         0.13         0.85        44.28 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-WE-A8ZX TCGA-WE-AAA4 
       31.33        16.24        15.42        10.65        21.83        12.07 
TCGA-YG-AA3P TCGA-Z2-AA3S 
        4.70         6.67 

$`3P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
        3.02         6.97         6.97        16.47         8.52        70.16 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       28.08        22.55        45.83        81.24        10.29         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH 
       21.14        68.22        86.76        11.41        44.19        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
        6.31        92.42        64.44        59.57       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32        82.29        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        26.37        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC 
      110.24        52.01        47.87        13.68        17.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       10.22        15.19         4.18       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
       75.65       124.47        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       21.93        13.22        14.60        51.12        10.03        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       23.15        19.00        13.35        13.22         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31        60.23        15.85         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        9.90        37.97        11.15        62.79        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       39.62         9.50         8.09         8.84         9.99        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
        9.67        36.33        51.12        17.98        60.00        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       19.43        16.01        35.54        28.31        33.83        55.69 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       122.73        51.62         3.68        30.15        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       12.72        22.92        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 
       18.41        21.73        33.60        31.40        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       76.41        25.18         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      114.15         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
        9.57         6.58        17.72        78.44        11.80         1.51 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       13.08        11.74         9.04         6.58        22.49         1.71 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        5.62        18.41        85.74        15.72         6.71         3.58 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       13.28         4.70         3.29        64.47        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       12.89        52.08         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       27.39         0.82         5.23        53.85         3.22         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       28.73        10.78         5.98         6.41         0.20         0.99 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 
        0.16        17.33         9.90         7.23        11.61        84.72 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
       10.13        12.16        14.70        11.84        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        15.81         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       10.98       185.16        71.01        11.84         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        7.10        18.67        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-A8RT 
        5.36         1.08        19.96         1.94         6.18         8.22 
TCGA-Z2-AA3V 
        5.98 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.13              0.13 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           124.31            185.16 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           15.335            14.600 
[1] "0.1 - 124.3 (15.3)" "0.1 - 185.2 (14.6)"
[1] "hr=" "1.1"
D45V2, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    31  26
  3P LOSS WILD-TYPE 142 140
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               57               282 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               26               140 
$`3P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JG 
      112.04       112.57       133.25       103.10       115.53       113.52 
TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GP TCGA-D9-A1X3 
       56.19        58.06       125.19        30.84       137.79        18.12 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 
       11.11         9.90        25.18        48.89        36.03       176.55 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29P 
      107.34        61.18        27.22       151.27        72.07        56.42 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2MF TCGA-EE-A3AA TCGA-EE-A3AG 
       67.43       208.04       129.27       268.73       124.31        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19H 
      172.18        64.08       201.80        35.44        13.94       152.35 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YX 
       37.25        23.34        31.27         7.00        34.82        48.59 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A6C8 
      101.26       133.55       174.84        77.88        47.54         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-WE-A8ZX 
      139.89       117.93        64.44        62.79        12.62        22.68 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S 
       15.16        14.43        93.07 

$`3P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
       28.08        31.59        90.90        95.74        43.43        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH 
       23.77       168.00        86.76        11.87        62.07        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       12.10       171.58        66.08        59.57       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC 
      125.79       135.75       137.92       178.32        18.18        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       11.61        15.19        58.52       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       95.24       161.00        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC 
       54.67         3.65         6.41        11.34        22.29        66.25 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 
       22.95       117.21        20.38       194.83        35.93        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.16        17.85        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       17.29        52.01         6.35        12.20        29.82         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      133.81        91.56       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       47.84        13.97        63.78        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       18.61        37.35        14.47        55.92       369.93        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      195.02        17.92        46.82       102.90        36.82        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       86.14        59.28       314.56       161.03        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
       14.30        55.59        44.88        94.82        21.67        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       203.05       167.90        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      248.65        43.23       134.40       162.48        71.21        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        51.62         3.68        54.51        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        36.95        34.32        53.19        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      109.58       148.08        31.40        50.76         9.17        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA 
       92.98       174.21        15.72       210.08        15.16        38.27 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       29.46        94.39       216.92       228.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       28.08         7.79        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       74.73        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV 
       12.43        26.73        49.45         0.20        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 
       19.30         9.90         7.23        11.74        84.72        10.13 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       32.48        39.58        46.36        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       357.04       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       212.22        63.02       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      219.16       105.04        24.03        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       90.28        56.98        59.41        52.34         3.75        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
        2.20        30.18        10.36        36.03        23.64        11.74 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             2.04              0.16 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           268.73            369.93 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           64.080            48.785 
[1] "2.0 - 268.7 (64.1)" "0.2 - 369.9 (48.8)"
[1] "hr=" "1.3"
D45V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P LOSS MUTATED                    9             2
  3P LOSS WILD-TYPE                 52             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3P LOSS MUTATED                                          14
  3P LOSS WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  3P LOSS MUTATED                    32
  3P LOSS WILD-TYPE                 177
D45V4, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  DISTANT METASTASIS                                      9                52
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              14                58
  REGIONAL LYMPH NODE                                    32               177
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3P LOSS MUTATED             2       1       6        1        4        0
  3P LOSS WILD-TYPE          10       6      22       16       23       22
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3P LOSS MUTATED           0         5         1         6          5
  3P LOSS WILD-TYPE        14        14        11        29         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED            7         11        1
  3P LOSS WILD-TYPE         25         47       18
D45V5, multiclass
             clus
vv            3P LOSS MUTATED 3P LOSS WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   1                 6
  STAGE I                   6                22
  STAGE IA                  1                16
  STAGE IB                  4                23
  STAGE II                  0                22
  STAGE IIA                 0                14
  STAGE IIB                 5                14
  STAGE IIC                 1                11
  STAGE III                 6                29
  STAGE IIIA                5                10
  STAGE IIIB                7                25
  STAGE IIIC               11                47
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  3P LOSS MUTATED      13 12 12  9
  3P LOSS WILD-TYPE    50 59 62 58
D45V6, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              13                50
  T2                 12                59
  T3                 12                62
  T4                  9                58
[1] 4 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                 N0  N1  N2  N3
  3P LOSS MUTATED    22  14   9   7
  3P LOSS WILD-TYPE 146  47  29  40
D45V7, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              22               146
  N1              14                47
  N2               9                29
  N3               7                40
[1] 4 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                 M0  M1 M1A M1B M1C
  3P LOSS MUTATED    51   0   0   0   1
  3P LOSS WILD-TYPE 255   4   3   4   8
D45V8, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               51               255
  M1                0                 4
  M1A               0                 3
  M1B               0                 4
  M1C               1                 8
[1] 5 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
  3P LOSS MUTATED    20  14
  3P LOSS WILD-TYPE 109  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     20   14
  3P LOSS WILD-TYPE  109   73
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               20               109
  YES              14                73
[1] 2 2
[1] FALSE
D45V10, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     7  51
  3P LOSS WILD-TYPE  36 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      7   51
  3P LOSS WILD-TYPE   36  253
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                7                36
  YES              51               253
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    25  33
  3P LOSS WILD-TYPE 106 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     25   33
  3P LOSS WILD-TYPE  106  184
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              25               106
  MALE                33               184
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       1                         0    54
  3P LOSS WILD-TYPE     4                         1   272
D45V13, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  54               272
[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"
D45V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  56
  3P LOSS WILD-TYPE   6 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   56
  3P LOSS WILD-TYPE    6  278
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              56               278
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    24  25
  3Q LOSS WILD-TYPE 144 140
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               49               284 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               25               140 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A5GU 
      111.09        32.42       110.79         7.50        15.25        23.11 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       87.62         5.56         5.72         9.90        11.31        48.79 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y TCGA-EE-A20C 
       35.80        13.68        44.52        36.69        10.55         4.34 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GJ 
        8.55        36.85        12.03        34.29        47.21        19.43 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19H 
       15.95         3.22        33.60        18.61        12.95        34.88 
TCGA-ER-A19S TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       36.07         5.36         2.20         3.45        47.38         8.65 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
       14.20         2.27         0.13        44.28        31.33        16.24 
TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-WE-A8ZX TCGA-WE-AAA4 TCGA-YG-AA3P 
       15.42        10.65        14.50        21.83        12.07         4.70 
TCGA-Z2-AA3S 
        6.67 

$`3Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
        3.02         6.97         6.97        16.47         8.52        70.16 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       44.19        36.16         6.31        92.42        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       59.57       114.67        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       21.44        32.61        25.78       110.24        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       13.68        17.72        29.72        22.06        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
        4.18       142.45       108.79        38.93        75.65       124.47 
TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
       11.44        24.07         4.01        21.93        13.22        14.60 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA 
       51.12        10.03        39.19         9.99        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       13.15         0.20         0.13        23.15        19.00        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       13.22         0.20        11.57         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.35        12.20         5.13         4.31        60.23        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        9.21         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       62.79         1.08        39.62         9.50         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        36.30         9.67        36.33        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       60.00        30.08        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       55.69         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
       51.62         3.68        30.15        13.81        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       18.41        21.73        31.40        38.40         5.72        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       25.18         3.78         3.52        11.90        11.11       114.15 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        1.71         5.62        18.41        85.74        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY 
        3.58        13.28         4.70         3.29        64.47        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.92        12.89        52.08         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
        8.68        27.39         0.82         5.23        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
        7.36        28.73        10.78         5.98         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.99         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       11.61        84.72        10.13        12.16        14.70        11.84 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.33         0.69       164.19         8.98        60.03 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 
        2.99        10.98       185.16        71.01        11.84         5.49 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        6.48         7.10        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
        3.42         5.36         1.08        19.96         1.94         6.18 
TCGA-Z2-A8RT TCGA-Z2-AA3V 
        8.22         5.98 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.13              0.13 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           111.09            185.16 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            15.25             14.65 
[1] "0.1 - 111.1 (15.2)" "0.1 - 185.2 (14.6)"
[1] "hr=" "1.1"
D46V2, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    25  25
  3Q LOSS WILD-TYPE 148 141
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               50               289 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               25               141 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A5GU 
      112.04       112.57       133.25       113.52        58.06       125.19 
TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
      137.79       129.63        18.12        11.11         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y 
       48.89        36.03       176.55       107.34        61.18        27.22 
TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH 
      151.27        72.07        64.64        56.42        67.43       208.04 
TCGA-EE-A2GJ TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       89.33        23.47       172.18       148.08        35.44        13.94 
TCGA-ER-A19H TCGA-ER-A19S TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZM 
      152.35        37.25         7.00        34.82        48.59       101.26 
TCGA-FS-A1ZQ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 
      133.55       174.84        77.88        47.54       139.89       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-WE-A8ZX TCGA-WE-AAA4 
       64.44        62.79        12.62        21.37        22.68        15.16 
TCGA-YG-AA3P TCGA-Z2-AA3S 
       14.43        93.07 

$`3Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07        42.08        12.10       171.58        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       59.57       130.72        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       22.62        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
      178.32        18.18        30.84        79.59        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       58.52       228.99       170.20        89.13        95.24       161.00 
TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
       29.06       117.17       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
       11.34        22.29        66.25        22.95       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      194.83        35.93        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       28.60        10.49       215.44        15.68        13.87        10.16 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       17.85        68.25        54.02        17.29        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       12.20        29.82         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       133.81        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        63.78 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        2.60        56.84        18.61        37.35        14.47        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       36.82        39.29        86.14        59.28       314.56       161.03 
TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        54.74        79.66        75.48        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        54.51        13.81       138.81       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      109.58        31.40        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J 
       48.89        12.59        13.02        26.37       268.93         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T 
      131.51        61.05        44.05       162.08        50.89         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       210.08        15.16 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       38.27        29.46        94.39       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       23.93        74.73        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       28.73        12.43        26.73        49.45         0.20        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK 
       84.72        10.13        32.48        39.58        46.36        50.10 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       59.41        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        38.56        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.61        90.28        56.98        59.41        52.34         3.75 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-A8RT 
       43.73         2.20        30.18        10.36        36.03        23.64 
TCGA-Z2-AA3V 
       11.74 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             7.00              0.16 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           208.04            369.93 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            64.54             48.85 
[1] "7.0 - 208.0 (64.5)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.1"
D46V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q LOSS MUTATED                    8             2
  3Q LOSS WILD-TYPE                 53             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3Q LOSS MUTATED                                          11
  3Q LOSS WILD-TYPE                                        61
                   vv
clus                REGIONAL LYMPH NODE
  3Q LOSS MUTATED                    28
  3Q LOSS WILD-TYPE                 181
D46V4, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      8                53
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              11                61
  REGIONAL LYMPH NODE                                    28               181
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  3Q LOSS MUTATED             2       2       4        3        4        0
  3Q LOSS WILD-TYPE          10       5      24       14       23       22
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3Q LOSS MUTATED           0         4         2         3          4
  3Q LOSS WILD-TYPE        14        15        10        32         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED            6          8        1
  3Q LOSS WILD-TYPE         26         50       18
D46V5, multiclass
             clus
vv            3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   2                 5
  STAGE I                   4                24
  STAGE IA                  3                14
  STAGE IB                  4                23
  STAGE II                  0                22
  STAGE IIA                 0                14
  STAGE IIB                 4                15
  STAGE IIC                 2                10
  STAGE III                 3                32
  STAGE IIIA                4                11
  STAGE IIIB                6                26
  STAGE IIIC                8                50
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  3Q LOSS MUTATED      11 10  7 10
  3Q LOSS WILD-TYPE    52 61 67 57
D46V6, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1              11                52
  T2                 10                61
  T3                  7                67
  T4                 10                57
[1] 4 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                 N0  N1  N2  N3
  3Q LOSS MUTATED    23   9   8   5
  3Q LOSS WILD-TYPE 145  52  30  42
D46V7, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              23               145
  N1               9                52
  N2               8                30
  N3               5                42
[1] 4 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                 M0  M1 M1A M1B M1C
  3Q LOSS MUTATED    44   0   0   0   1
  3Q LOSS WILD-TYPE 262   4   3   4   8
D46V8, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               44               262
  M1                0                 4
  M1A               0                 3
  M1B               0                 4
  M1C               1                 8
[1] 5 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
  3Q LOSS MUTATED    18  11
  3Q LOSS WILD-TYPE 111  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     18   11
  3Q LOSS WILD-TYPE  111   76
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               18               111
  YES              11                76
[1] 2 2
[1] FALSE
D46V10, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5  45
  3Q LOSS WILD-TYPE  38 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   45
  3Q LOSS WILD-TYPE   38  259
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                5                38
  YES              45               259
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    21  29
  3Q LOSS WILD-TYPE 110 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     21   29
  3Q LOSS WILD-TYPE  110  188
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              21               110
  MALE                29               188
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         0    46
  3Q LOSS WILD-TYPE     4                         1   280
D46V13, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  46               280
[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"
D46V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  48
  3Q LOSS WILD-TYPE   6 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   48
  3Q LOSS WILD-TYPE    6  286
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              48               286
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    37  34
  4P LOSS WILD-TYPE 131 131
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               71               262 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               34               131 
$`4P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO 
       16.47       111.09        10.29        88.50        56.19        64.44 
TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51N TCGA-D3-A8GC 
       61.38       103.59        29.23        54.74        21.44        22.06 
TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC 
        4.18        75.65        21.93         5.72         9.90        13.22 
TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A180 TCGA-EE-A20B 
       35.80        14.83         0.20         0.13         8.12        60.23 
TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29T 
        4.34         9.90        37.97        11.15        39.62        30.44 
TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 
       32.15         9.67        47.21        28.31        55.69         8.84 
TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AG TCGA-EE-A3J8 
       98.27        56.02        21.60        53.16        15.95        16.14 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       18.41        31.40        12.95        25.18         3.52        11.90 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV 
       36.07         6.58         1.87        12.62        11.74        22.49 
TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A4F8 TCGA-FW-A3TU 
        3.58        23.80        15.52         7.30        14.20         0.13 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ 
        0.85        11.61        10.13         8.98        10.98        11.84 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-A8RT 
       21.83         1.08         1.94         6.18         8.22 

$`4P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         6.97         8.52        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
      110.79        28.08        22.55        45.83        81.24        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
        8.38        21.14        68.22        86.76        11.41        44.19 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ 
        7.50        36.16         6.31        92.42        59.57       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       15.25        46.98        46.32        82.29        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J 
        6.31         9.34        26.37        93.21        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        32.61        25.78       110.24        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
       13.68        17.72        23.11        29.72        10.22        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      142.45       108.79        38.93       124.47        87.62        11.44 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
        5.56        24.07         4.01        11.31        14.60        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
        7.00        17.56        13.15        23.15        19.00        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
       13.22         0.20        11.57        10.55         6.31         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H 
        1.35        12.20         5.13         4.31        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        1.18         7.99        62.79         8.55        36.85         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        36.30        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       35.54        33.83         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       36.33         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
      111.91        25.08        26.99        60.49        52.67         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        51.62         3.68        30.15        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
       12.72         3.22        22.92        21.60        21.60        22.22 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
        0.95        27.35        21.73        33.60        18.61        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        5.72        76.41         3.78        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
       17.72        78.44        11.80         1.51        13.08         9.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58         1.71         5.62        18.41        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        6.71         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
       64.47         3.45        11.01        14.24         7.33         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       20.38         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         3.22         7.36        28.73        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.20         0.99         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        9.90         7.23        44.28        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       15.42        12.16        14.70        11.84        10.65        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
       18.05         0.33         0.69       164.19        60.03         2.99 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      185.16        71.01         5.49         6.48         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 
       21.07        13.12         3.72         3.42         5.36        19.96 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         4.70         6.67         5.98 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.16 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           111.09            185.16 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            15.52             14.58 
[1] "0.1 - 111.1 (15.5)" "0.2 - 185.2 (14.6)"
[1] "hr=" "1"  
D47V2, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    39  34
  4P LOSS WILD-TYPE 134 132
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               73               266 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               34               132 
$`4P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO 
       16.57       112.04        43.43       115.53        56.19        66.08 
TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51N TCGA-D3-A8GC 
       86.93       103.59        45.30        55.73        22.62        79.59 
TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       58.52        95.24       151.53        54.67        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH 
        9.90        66.25        36.03        15.68        10.16        17.85 
TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       94.98       133.81       151.27        80.61        47.84        13.97 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GM 
       56.84       369.93       195.02        39.29       208.04        75.48 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS 
      126.81        21.67       129.27       167.90        43.23       162.48 
TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B 
       23.47        34.32        51.35        31.40        13.94        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG 
       12.59        13.02        37.25         8.88        23.34        31.27 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA 
       32.05        46.98        15.16       202.65        28.08        27.72 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-W3-A825 
      174.84        47.54         2.04        11.74        10.13        63.02 
TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O 
       42.08        24.03        22.68         2.20        10.36        36.03 
TCGA-Z2-A8RT 
       23.64 

$`4P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.67       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
      133.25        28.08        31.59        90.90        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       65.49        23.77       168.00        86.76        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10       171.58        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF 
       58.06        46.98        46.32       166.52        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J 
       13.87         9.34        39.75       174.84        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
      178.32        18.18       125.19        30.84        11.61        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      228.99       170.20        89.13       161.00       137.79        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      129.63       117.17         3.65         6.41        18.12        11.34 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        22.95        48.89       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49       215.44        13.87 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       68.15         4.96        91.56       168.26        13.55        63.35 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       63.78        72.07        64.64         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       37.35        14.47        55.92        25.87        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        36.82        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      161.03        48.72        89.33        54.74        79.66        90.97 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 
       13.91        14.30        55.59        44.88        94.82        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
       16.96       204.66        96.23       158.63       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      248.65       134.40        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        54.51        13.81       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        53.19       201.80        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      109.58       148.08        35.44        50.76         9.17        77.75 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       48.89        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05       162.08        50.89       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       43.82        20.15        16.37       247.04        80.32        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 
        6.77        92.98       174.21        15.72       210.08         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        29.46        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59        20.91         7.79        48.85       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
      101.26        74.73       133.55        11.41       148.80        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67        28.73        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        22.92         0.16        19.30         9.90         7.23 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       39.58        46.36        12.62        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       357.04       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 
        0.69       212.22       121.08         4.01       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       38.56        54.38         8.61        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3P 
       52.34         3.75        43.73        30.18        15.16        14.43 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2.04              0.16 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           369.93            357.37 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            43.23             52.75 
[1] "2.0 - 369.9 (43.2)" "0.2 - 357.4 (52.8)"
[1] "hr=" "1.1"
D47V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P LOSS MUTATED                   13             3
  4P LOSS WILD-TYPE                 48             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4P LOSS MUTATED                                          17
  4P LOSS WILD-TYPE                                        55
                   vv
clus                REGIONAL LYMPH NODE
  4P LOSS MUTATED                    41
  4P LOSS WILD-TYPE                 168
D47V4, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  DISTANT METASTASIS                                     13                48
  PRIMARY TUMOR                                           3                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              17                55
  REGIONAL LYMPH NODE                                    41               168
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4P LOSS MUTATED             1       2       6        2        5        5
  4P LOSS WILD-TYPE          11       5      22       15       22       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4P LOSS MUTATED           0         6         2         6          5
  4P LOSS WILD-TYPE        14        13        10        29         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           11         13        3
  4P LOSS WILD-TYPE         21         45       16
D47V5, multiclass
             clus
vv            4P LOSS MUTATED 4P LOSS WILD-TYPE
  I OR II NOS               1                11
  STAGE 0                   2                 5
  STAGE I                   6                22
  STAGE IA                  2                15
  STAGE IB                  5                22
  STAGE II                  5                17
  STAGE IIA                 0                14
  STAGE IIB                 6                13
  STAGE IIC                 2                10
  STAGE III                 6                29
  STAGE IIIA                5                10
  STAGE IIIB               11                21
  STAGE IIIC               13                45
  STAGE IV                  3                16
[1] 14  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                T0+T1 T2 T3 T4
  4P LOSS MUTATED      13 14 19 12
  4P LOSS WILD-TYPE    50 57 55 55
D47V6, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              13                50
  T2                 14                57
  T3                 19                55
  T4                 12                55
[1] 4 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                 N0  N1  N2  N3
  4P LOSS MUTATED    31  18   7  11
  4P LOSS WILD-TYPE 137  43  31  36
D47V7, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              31               137
  N1              18                43
  N2               7                31
  N3              11                36
[1] 4 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                 M0  M1 M1A M1B M1C
  4P LOSS MUTATED    66   0   1   1   2
  4P LOSS WILD-TYPE 240   4   2   3   7
D47V8, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               66               240
  M1                0                 4
  M1A               1                 2
  M1B               1                 3
  M1C               2                 7
[1] 5 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
  4P LOSS MUTATED   30 18
  4P LOSS WILD-TYPE 99 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     30   18
  4P LOSS WILD-TYPE   99   69
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               30                99
  YES              18                69
[1] 2 2
[1] FALSE
D47V10, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    10  65
  4P LOSS WILD-TYPE  33 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10   65
  4P LOSS WILD-TYPE   33  239
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               10                33
  YES              65               239
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    33  42
  4P LOSS WILD-TYPE  98 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     33   42
  4P LOSS WILD-TYPE   98  175
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              33                98
  MALE                42               175
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       2                         0    68
  4P LOSS WILD-TYPE     3                         1   258
D47V13, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  68               258
[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"
D47V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  73
  4P LOSS WILD-TYPE   6 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   73
  4P LOSS WILD-TYPE    6  261
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              73               261
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    39  37
  4Q LOSS WILD-TYPE 129 128
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               76               257 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               37               128 
$`4Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO 
       16.47       111.09        28.08        88.50        56.19        64.44 
TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51N 
       46.98        61.38       103.59        29.23        54.74        21.44 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
       22.06         4.18        75.65        21.93         5.72         9.90 
TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A180 
       35.80        14.83         0.20         0.13        10.55         8.12 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T 
        1.12        60.23         4.34        37.97        39.62        30.44 
TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO 
       32.15         9.67        47.21        30.08        28.31        55.69 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AG 
        8.84        98.27        56.02        21.60        53.16        15.95 
TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D 
       16.14        18.41        31.40        12.95        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
       11.90        36.07         6.58         1.87        12.62        11.74 
TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A4F8 
       22.49         3.58        23.80        15.52         7.30        14.20 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 TCGA-GN-A8LK TCGA-HR-A2OH 
        0.13         0.85        11.61        10.13        14.50        15.81 
TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZX 
       18.05         8.98        10.98        11.84         7.10        21.83 
TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-A8RT 
        1.08         1.94         6.18         8.22 

$`4Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         6.97         8.52        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      110.79        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
        8.38        21.14        68.22        86.76        11.41        44.19 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ 
        7.50        36.16         6.31        92.42        59.57       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       15.25        46.32        82.29        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        9.34        26.37        93.21        31.30        54.31        32.28 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.61        25.78       110.24        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       17.72        23.11        29.72        10.22        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      108.79        38.93       124.47        87.62        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       24.07         4.01        11.31        13.22        14.60        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
        7.00        17.56        13.15        23.15        19.00        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       13.22         0.20        11.57         6.31         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        5.13         4.31        15.85         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        9.90        11.15        62.79         8.55        36.85         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        36.30        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.29        17.98        60.00        19.43        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       125.65       111.91 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       25.08        26.99        60.49        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        51.62         3.68        30.15        13.81        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB 
        3.22        22.92        21.60        21.60        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       27.35        21.73        33.60        18.61        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       76.41         3.78        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       13.45        28.60        42.84        34.68         9.57        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       78.44        11.80         1.51        13.08         9.04         6.58 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        1.71         5.62        18.41        85.74        15.72         6.71 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
        3.45        11.01        14.24         7.33         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        3.22         7.36        28.73        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.99         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        7.23        44.28        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.43        11.05         5.79         0.33         0.69       164.19 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       60.03         2.99       185.16        71.01         5.49         6.48 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY 
       18.67        21.07        13.12         3.72         3.42         5.36 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       19.96        12.07         4.70         6.67         5.98 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.13              0.16 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           111.09            185.16 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           16.045            14.500 
[1] "0.1 - 111.1 (16.0)" "0.2 - 185.2 (14.5)"
[1] "hr=" "1"  
D48V2, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    41  37
  4Q LOSS WILD-TYPE 132 129
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               78               261 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               37               129 
$`4Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A2JN TCGA-D3-A2JO 
       16.57       112.04        28.08       115.53        56.19        66.08 
TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51N 
       46.98        86.93       103.59        45.30        55.73        22.62 
TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 
       79.59        58.52        95.24       151.53        54.67        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH 
       11.11         9.90        36.03        15.68        10.16        17.85 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29C 
       27.22        94.98        33.73       133.81       151.27        47.84 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GI 
       56.84       369.93       195.02        39.29       208.04        48.72 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ 
       75.48       126.81        21.67       129.27       167.90        43.23 
TCGA-EE-A2MS TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 
      162.48        23.47        34.32        51.35        31.40        13.94 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND 
       98.40        12.59        13.02        37.25         8.88        23.34 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       31.27        32.05        46.98        15.16       202.65        28.08 
TCGA-FS-A1ZA TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A266 
       27.72       174.84        47.54         2.04        11.74        10.13 
TCGA-GN-A8LK TCGA-HR-A2OH TCGA-QB-AA9O TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ 
       50.10        65.88        18.05        63.02        42.08        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-A8RT 
        8.61        22.68         2.20        10.36        36.03        23.64 

$`4Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.67       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       65.49        23.77       168.00        86.76        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10       171.58        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.32       166.52        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        9.34        39.75       174.84        56.35       145.12        32.94 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ 
       18.18       125.19        30.84        11.61        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
      170.20        89.13       161.00       137.79        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EA 
      117.17         3.65         6.41        18.12        11.34        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       66.25        22.95        48.89       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       23.44        68.09        28.60        10.49       215.44        13.87 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       29.82         8.65        14.70        26.89        68.15         4.96 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       91.56       168.26        13.55        63.35        80.61        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       63.78        72.07        64.64         2.60        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       37.35        14.47        55.92        25.87        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        36.82        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
      161.03        89.33        54.74        79.66        90.97        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
       14.30        55.59        44.88        94.82        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH 
       61.51        47.28       103.27       268.73       103.20        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66        96.23       158.63       203.05        47.54       248.65 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JH 
       36.95        64.08        53.19       201.80        27.35       109.58 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
      148.08        35.44        50.76         9.17        77.75        48.89 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       44.05       162.08        50.89       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K 
       20.15        16.37       247.04        80.32        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA 
       92.98       174.21        15.72       210.08         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        29.46        94.39       216.92        48.59       228.59 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       20.91         7.79        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       74.73       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       49.48        27.09        27.02        77.82        50.14        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       28.73        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 
       22.92         0.16        19.30         9.90         7.23       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        64.44        62.79        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-OD-A75X 
       46.36        12.62        21.37        59.41       357.04       294.77 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
        6.67         0.33         0.69       212.22       121.08         4.01 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        38.56        54.38        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA4 
       59.41        52.34         3.75        43.73        30.18        15.16 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        93.07        11.74 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2.04              0.16 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           369.93            357.37 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           40.685            53.520 
[1] "2.0 - 369.9 (40.7)" "0.2 - 357.4 (53.5)"
[1] "hr=" "1.1"
D48V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q LOSS MUTATED                   13             2
  4Q LOSS WILD-TYPE                 48             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4Q LOSS MUTATED                                          18
  4Q LOSS WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  4Q LOSS MUTATED                    45
  4Q LOSS WILD-TYPE                 164
D48V4, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     13                48
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              18                54
  REGIONAL LYMPH NODE                                    45               164
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  4Q LOSS MUTATED             0       2       6        3        6        6
  4Q LOSS WILD-TYPE          12       5      22       14       21       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4Q LOSS MUTATED           0         4         2         7          4
  4Q LOSS WILD-TYPE        14        15        10        28         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           14         13        4
  4Q LOSS WILD-TYPE         18         45       15
D48V5, multiclass
             clus
vv            4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   2                 5
  STAGE I                   6                22
  STAGE IA                  3                14
  STAGE IB                  6                21
  STAGE II                  6                16
  STAGE IIA                 0                14
  STAGE IIB                 4                15
  STAGE IIC                 2                10
  STAGE III                 7                28
  STAGE IIIA                4                11
  STAGE IIIB               14                18
  STAGE IIIC               13                45
  STAGE IV                  4                15
[1] 14  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                T0+T1 T2 T3 T4
  4Q LOSS MUTATED      17 13 18 12
  4Q LOSS WILD-TYPE    46 58 56 55
D48V6, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              17                46
  T2                 13                58
  T3                 18                56
  T4                 12                55
[1] 4 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                 N0  N1  N2  N3
  4Q LOSS MUTATED    30  19   8  13
  4Q LOSS WILD-TYPE 138  42  30  34
D48V7, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              30               138
  N1              19                42
  N2               8                30
  N3              13                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"
                   vv
clus                 M0  M1 M1A M1B M1C
  4Q LOSS MUTATED    68   0   1   2   2
  4Q LOSS WILD-TYPE 238   4   2   2   7
D48V8, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               68               238
  M1                0                 4
  M1A               1                 2
  M1B               2                 2
  M1C               2                 7
[1] 5 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
  4Q LOSS MUTATED   31 17
  4Q LOSS WILD-TYPE 98 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     31   17
  4Q LOSS WILD-TYPE   98   70
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               31                98
  YES              17                70
[1] 2 2
[1] FALSE
D48V10, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    13  66
  4Q LOSS WILD-TYPE  30 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     13   66
  4Q LOSS WILD-TYPE   30  238
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               13                30
  YES              66               238
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    34  45
  4Q LOSS WILD-TYPE  97 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     34   45
  4Q LOSS WILD-TYPE   97  172
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              34                97
  MALE                45               172
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       3                         0    70
  4Q LOSS WILD-TYPE     2                         1   256
D48V13, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  70               256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     1  75
  4Q LOSS WILD-TYPE   6 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   75
  4Q LOSS WILD-TYPE    6  259
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              75               259
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    36  35
  5P LOSS WILD-TYPE 132 130
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               71               262 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               35               130 
$`5P LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
        6.97        16.47        68.22        11.41         7.50        92.42 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GO TCGA-D3-A8GB 
       64.44        61.38        24.00        29.23        47.87        29.72 
TCGA-D3-A8GN TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-EB-A5KH 
      124.47         5.72        48.79        35.80        17.56         0.13 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A29C 
       13.35        11.57        10.55         5.13         4.31        37.97 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD 
       62.79        39.62        12.03        36.30        51.12        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GR TCGA-EE-A2GT 
       60.00        47.21        30.08        19.43         1.15        34.98 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J5 
       56.02        21.60         5.56         3.68        12.72        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
       21.60         0.95         5.72         1.51        12.62        11.74 
TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZW 
       15.72         8.22         7.17        47.38        40.64        27.39 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 
        0.82         3.22         7.36        14.20         5.98         0.85 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-HR-A2OH 
       44.28        10.13        16.24        15.42        14.50        15.81 
TCGA-OD-A75X TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       11.05        18.67        21.83         5.36        12.07 

$`5P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         8.52       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.79        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
       85.32         8.38        21.14        88.50        86.76        44.19 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       36.16         6.31        56.19        59.57       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32        82.29        13.32         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        26.37        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.28        21.44        32.61        25.78       110.24        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       13.68        17.72        23.11        22.06        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
        4.18       142.45       108.79        38.93        75.65        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       11.44         5.56        24.07         4.01        21.93         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       11.31        13.22        14.60        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Z 
        0.20        23.15        19.00        13.22         0.20         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C 
        8.12         1.12         1.35        12.20        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       15.85         9.21         1.18         7.99         9.90        11.15 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
        8.55        36.85         1.08         9.50         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL 
       49.22         9.67        36.33        34.29        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       28.31        33.83        55.69         5.42        13.02        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        8.84        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      125.65       111.91        25.08        26.99        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       52.67       124.31       122.73        51.62        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       15.95         3.22        22.92        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       38.40        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       78.44        11.80         1.87        13.08         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
       22.49         1.71         5.62        18.41        85.74         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        3.58         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         7.30         3.39        20.38        19.53        11.08 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        12.92        12.89        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F9 
       49.15         8.68         5.23        53.85        28.73        10.78 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
       17.33         9.90         7.23        11.61        31.33        84.72 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
        0.43         5.79        18.05         0.33         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
        8.98        60.03         2.99        10.98       185.16        71.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
       11.84         5.49         6.48         7.10        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O 
        3.72         3.42         1.08        19.96         1.94         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.13              0.13 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           124.47            185.16 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            15.81             14.53 
[1] "0.1 - 124.5 (15.8)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1"  
D49V2, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    37  35
  5P LOSS WILD-TYPE 136 131
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               72               267 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               35               131 
$`5P LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
       12.99        16.57       168.00        11.87       113.52       171.58 
TCGA-D3-A2JO TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GO TCGA-D3-A8GB 
       66.08        86.93        24.53        45.30       137.92        30.84 
TCGA-D3-A8GN TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F5 
      161.00        18.12        11.11        48.89        36.03       215.44 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 TCGA-EE-A185 
       17.85        17.29        29.82        27.22        68.15         4.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB 
       47.84        63.78        56.84        56.42        36.82        59.28 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GR 
      314.56       161.03       208.04        48.72        89.33        14.30 
TCGA-EE-A2GT TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AH 
       44.88       167.90        43.23        53.26         3.68       138.81 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A2NE TCGA-ER-A2NG 
       36.95        64.08       201.80         9.17        20.15        31.27 
TCGA-ER-A2NH TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT 
       32.05        15.72        53.52         9.70       101.26        53.16 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB 
       49.48        27.09        50.14        66.67       174.84        26.73 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK 
        2.04       139.89        10.13        64.44        62.79        50.10 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       65.88       294.77        90.28        22.68        43.73        15.16 

$`5P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
      103.10        65.49        23.77       115.53        86.76        62.07 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10        56.19        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.98        46.32       166.52        60.23        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        39.75       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       32.94        22.62        63.81        26.89       125.79       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
      178.32        18.18       125.19        79.59        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP 
       58.52       228.99       170.20        89.13        95.24       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        6.41        11.34        22.29         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       28.60        10.49        15.68        13.87        10.16        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 
       54.02        52.01         6.35        12.20         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       33.73        14.70        26.89       133.81       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
      168.26        13.55        63.35        80.61        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       64.64         2.60        18.61        37.35        14.47        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      369.93        25.87       195.02        17.92        46.82       102.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       39.29        86.14        67.43        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
       90.97       126.81        13.91        55.59        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      203.05        47.54       248.65       134.40       162.48        71.21 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        51.62        54.51        13.81        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      172.18       127.20        34.32        53.19        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       77.75        98.40        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
      162.08        50.89        37.25         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       43.82        23.34        16.37       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       33.21         6.77        92.98       174.21       210.08        15.16 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        7.00        38.27        34.82        29.46        94.39       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH 
       27.72        48.85       357.37        40.27        15.45        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC 
       26.56        27.02        77.82        28.73        12.43        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A 
        9.90         7.23        11.74       117.93        84.72        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB 
       39.58        46.36        12.62        21.37        59.41       357.04 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
        6.67        18.05         0.33         0.69       212.22        63.02 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      121.08         4.01        42.08       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       38.56        54.38         8.61        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
        3.75         2.20        30.18        10.36        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2.04              0.16 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           314.56            369.93 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           49.185            51.350 
[1] "2.0 - 314.6 (49.2)" "0.2 - 369.9 (51.4)"
[1] "hr=" "1"  
D49V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P LOSS MUTATED                   12             0
  5P LOSS WILD-TYPE                 49             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5P LOSS MUTATED                                          19
  5P LOSS WILD-TYPE                                        53
                   vv
clus                REGIONAL LYMPH NODE
  5P LOSS MUTATED                    45
  5P LOSS WILD-TYPE                 164
D49V4, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  DISTANT METASTASIS                                     12                49
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              19                53
  REGIONAL LYMPH NODE                                    45               164
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5P LOSS MUTATED             4       2       5        4        4        3
  5P LOSS WILD-TYPE           8       5      23       13       23       19
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5P LOSS MUTATED           4         4         3         8          4
  5P LOSS WILD-TYPE        10        15         9        27         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           11         14        0
  5P LOSS WILD-TYPE         21         44       19
D49V5, multiclass
             clus
vv            5P LOSS MUTATED 5P LOSS WILD-TYPE
  I OR II NOS               4                 8
  STAGE 0                   2                 5
  STAGE I                   5                23
  STAGE IA                  4                13
  STAGE IB                  4                23
  STAGE II                  3                19
  STAGE IIA                 4                10
  STAGE IIB                 4                15
  STAGE IIC                 3                 9
  STAGE III                 8                27
  STAGE IIIA                4                11
  STAGE IIIB               11                21
  STAGE IIIC               14                44
  STAGE IV                  0                19
[1] 14  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                T0+T1 T2 T3 T4
  5P LOSS MUTATED      12 17 14 17
  5P LOSS WILD-TYPE    51 54 60 50
D49V6, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              12                51
  T2                 17                54
  T3                 14                60
  T4                 17                50
[1] 4 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                 N0  N1  N2  N3
  5P LOSS MUTATED    30  21   7  10
  5P LOSS WILD-TYPE 138  40  31  37
D49V7, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              30               138
  N1              21                40
  N2               7                31
  N3              10                37
[1] 4 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                 M0  M1 M1A M1B M1C
  5P LOSS MUTATED    69   0   0   0   0
  5P LOSS WILD-TYPE 237   4   3   4   9
D49V8, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               69               237
  M1                0                 4
  M1A               0                 3
  M1B               0                 4
  M1C               0                 9
[1] 5 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
  5P LOSS MUTATED    24  23
  5P LOSS WILD-TYPE 105  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     24   23
  5P LOSS WILD-TYPE  105   64
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               24               105
  YES              23                64
[1] 2 2
[1] FALSE
D49V10, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     6  70
  5P LOSS WILD-TYPE  37 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6   70
  5P LOSS WILD-TYPE   37  234
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                6                37
  YES              70               234
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    32  44
  5P LOSS WILD-TYPE  99 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     32   44
  5P LOSS WILD-TYPE   99  173
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              32                99
  MALE                44               173
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       2                         1    67
  5P LOSS WILD-TYPE     3                         0   259
D49V13, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  67               259
[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"
D49V14, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  71
  5P LOSS WILD-TYPE   7 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   71
  5P LOSS WILD-TYPE    7  263
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              71               263
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    42  46
  5Q LOSS WILD-TYPE 126 119
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               88               245 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               46               119 
$`5Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
        6.97        28.08        68.22        11.41         7.50         6.31 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV 
       92.42        64.44        15.25        61.38        24.00        29.23 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GI TCGA-D9-A3Z1 TCGA-D9-A4Z6 
      110.24        52.01        47.87         4.18         4.01         5.72 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
       13.22        48.79        35.80        10.03        44.52        36.69 
TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A185 
       17.56         0.13        13.35        11.57        10.55         4.31 
TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29V 
        9.21        37.97        62.79        39.62        12.03         2.43 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       36.30        51.12        17.98        60.00        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2MJ 
       19.43        28.31         1.15        34.98        98.27        63.42 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J5 
       56.02        21.60       122.73         3.68        12.72        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A2NE TCGA-ER-A2NH 
       21.60         0.95         5.72        25.18         1.51        11.74 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZM 
       85.74        15.72         3.45         3.39         7.17        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 
        8.65        40.64        27.39         0.82         3.22         7.36 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 
       14.20         5.98         0.85        44.28        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A8LK TCGA-HR-A2OH TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1V 
       15.42        14.50        15.81        11.05         8.98        10.98 
TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       18.67        21.83         5.36        12.07 

$`5Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97        16.47         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16       110.79        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
       85.32         8.38        21.14        88.50        86.76        44.19 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       36.16        56.19        59.57       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       82.29        13.32         6.31         9.34       103.59        26.37 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       32.61        25.78        13.68        17.72        23.11        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       22.06        10.22        15.19       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       75.65       124.47        87.62        11.44         5.56        24.07 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
       21.93         9.90        11.31        14.60        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       13.68         9.99        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       19.36         7.00        14.83        13.15         0.20        23.15 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       19.00        13.22         0.20         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
        1.35        12.20         5.13        60.23         4.34        15.85 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        1.18         7.99         9.90        11.15         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        1.08         9.50         8.09         8.84         9.99        30.44 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
       32.15         8.09        11.31        49.22         9.67        36.33 
TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       34.29        16.01        35.54        33.83        55.69         5.42 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       13.02        36.33         8.84         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      125.65       111.91        25.08        26.99        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       52.67         5.56       124.31        51.62        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       15.95         3.22        22.92        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       38.40        76.41         3.78         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       34.68         9.57        36.07         6.58        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       11.80         1.87        13.08        12.62         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 
       22.49         1.71         5.62        18.41         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       20.38         8.22        19.53        11.08        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ 
       12.89        52.08         8.81        49.15         8.68         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       53.85        28.73        10.78         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       11.61        31.33        84.72        12.16        14.70        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       10.65        14.50        14.50         0.43         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.33         0.69       164.19        60.03         2.99       185.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
       71.01        11.84         5.49         6.48         7.10        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       13.12         3.72         3.42         1.08        19.96         1.94 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.18         4.70         8.22         6.67         5.98 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.13              0.13 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           122.73            185.16 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           15.765            14.500 
[1] "0.1 - 122.7 (15.8)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.1"
D50V2, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    43  47
  5Q LOSS WILD-TYPE 130 119
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               90               249 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               47               119 
$`5Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       12.99        28.08       168.00        11.87       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV 
      171.58        66.08        58.06        86.93        24.53        45.30 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A8GI TCGA-D9-A1JX TCGA-D9-A1X3 
      125.79       135.75       137.92        58.52         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
       11.34        11.11        66.25        48.89        36.03        20.38 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17X 
      107.34        61.18       215.44        17.85        17.29        29.82 
TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M 
       27.22         4.96       168.26        47.84        63.78        56.84 
TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       56.42        25.87        36.82        59.28       314.56       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT 
      208.04        48.72        89.33        75.48        14.30        44.88 
TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A3AB TCGA-EE-A3AD 
      129.27        96.23       167.90        43.23       122.73         3.68 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-ER-A199 TCGA-ER-A19B 
      138.81        36.95        64.08       201.80         9.17        98.40 
TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZB 
       20.15        32.05       174.21        15.72        48.59        48.85 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
        9.70       101.26       133.55        53.16        49.48        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 
       50.14        66.67       174.84        26.73         2.04       139.89 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A8LK TCGA-HR-A2OH TCGA-OD-A75X 
       10.13        64.44        62.79        50.10        65.88       294.77 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 
       63.02        42.08        90.28        22.68        43.73        15.16 

$`5Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
      103.10        65.49        23.77       115.53        86.76        62.07 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       42.08        56.19        59.57       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        60.23        13.87         9.34       103.59        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       63.81        26.89       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        11.61        15.19       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       95.24       161.00       137.79        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
      151.53        54.67         3.65        22.29         9.90        25.18 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 
       22.95       117.21       194.83       176.55        35.93        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       65.92        23.44        68.09        28.60        10.49        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.16        68.25        54.02        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       12.20         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
       68.15       133.81       151.27        91.56        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       80.61        13.97        72.07        64.64         2.60        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       37.35        14.47        55.92       369.93       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GK 
       46.82       102.90        39.29        86.14        67.43        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU 
       79.66        90.97       126.81        13.91        55.59        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       21.67        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      268.73       103.20        16.96       204.66       158.63       203.05 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       47.54       248.65       134.40       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
      124.31        51.62        54.51        13.81        23.47       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        34.32        53.19        27.35        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
      148.08        31.40        35.44        13.94        50.76        77.75 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       16.37        31.27       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
        6.77        92.98       210.08        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       34.82        29.46        94.39       216.92       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
       20.91        28.08         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       40.27        15.45        32.75        47.38        23.93        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 
       11.41       148.80        26.56        27.02        77.82        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 
        0.16        19.30         9.90         7.23        11.74       117.93 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL 
       84.72        32.48        39.58        46.36        12.62        21.37 
TCGA-GN-A9SD TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
       59.41       357.04         6.67        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      212.22       121.08         4.01       219.16       105.04        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       38.56        54.38         8.61        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
        3.75         2.20        30.18        10.36        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2.04              0.16 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           314.56            369.93 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            51.65             49.45 
[1] "2.0 - 314.6 (51.6)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.1"
D50V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q LOSS MUTATED                   16             1
  5Q LOSS WILD-TYPE                 45             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5Q LOSS MUTATED                                          24
  5Q LOSS WILD-TYPE                                        48
                   vv
clus                REGIONAL LYMPH NODE
  5Q LOSS MUTATED                    54
  5Q LOSS WILD-TYPE                 155
D50V4, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     16                45
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              24                48
  REGIONAL LYMPH NODE                                    54               155
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  5Q LOSS MUTATED             4       3       9        4        5        7
  5Q LOSS WILD-TYPE           8       4      19       13       22       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5Q LOSS MUTATED           3         4         4        10          5
  5Q LOSS WILD-TYPE        11        15         8        25         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           11         15        3
  5Q LOSS WILD-TYPE         21         43       16
D50V5, multiclass
             clus
vv            5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  I OR II NOS               4                 8
  STAGE 0                   3                 4
  STAGE I                   9                19
  STAGE IA                  4                13
  STAGE IB                  5                22
  STAGE II                  7                15
  STAGE IIA                 3                11
  STAGE IIB                 4                15
  STAGE IIC                 4                 8
  STAGE III                10                25
  STAGE IIIA                5                10
  STAGE IIIB               11                21
  STAGE IIIC               15                43
  STAGE IV                  3                16
[1] 14  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                T0+T1 T2 T3 T4
  5Q LOSS MUTATED      17 20 18 21
  5Q LOSS WILD-TYPE    46 51 56 46
D50V6, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              17                46
  T2                 20                51
  T3                 18                56
  T4                 21                46
[1] 4 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                 N0  N1  N2  N3
  5Q LOSS MUTATED    43  22  10  11
  5Q LOSS WILD-TYPE 125  39  28  36
D50V7, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              43               125
  N1              22                39
  N2              10                28
  N3              11                36
[1] 4 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                 M0  M1 M1A M1B M1C
  5Q LOSS MUTATED    85   0   1   1   1
  5Q LOSS WILD-TYPE 221   4   2   3   8
D50V8, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               85               221
  M1                0                 4
  M1A               1                 2
  M1B               1                 3
  M1C               1                 8
[1] 5 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
  5Q LOSS MUTATED   32 25
  5Q LOSS WILD-TYPE 97 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     32   25
  5Q LOSS WILD-TYPE   97   62
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               32                97
  YES              25                62
[1] 2 2
[1] FALSE
D50V10, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     8  87
  5Q LOSS WILD-TYPE  35 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8   87
  5Q LOSS WILD-TYPE   35  217
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                8                35
  YES              87               217
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    38  57
  5Q LOSS WILD-TYPE  93 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     38   57
  5Q LOSS WILD-TYPE   93  160
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              38                93
  MALE                57               160
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       2                         1    86
  5Q LOSS WILD-TYPE     3                         0   240
D50V13, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  86               240
[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"
D50V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0  90
  5Q LOSS WILD-TYPE   7 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   90
  5Q LOSS WILD-TYPE    7  244
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              90               244
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    26  36
  6P LOSS WILD-TYPE 142 129
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               62               271 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               36               129 
$`6P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD 
      111.09        22.55        10.29        85.32        86.76        11.41 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3ML TCGA-D3-A3MV TCGA-D3-A51N 
       36.16        92.42        56.19         6.31        29.23        21.44 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN 
       13.68        22.06        10.22         4.18        75.65       124.47 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
       11.31        13.22        14.60        51.12        39.19         9.99 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29A 
       25.15         6.64        17.56        10.55         8.12         7.99 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       11.15         8.55         8.09        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2GL TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
       49.22        35.54         8.84        98.27         2.70        47.51 
TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19J TCGA-ER-A19T TCGA-ER-A2NE 
       22.92        25.18         3.52         4.21         6.58         1.51 
TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZQ 
       15.72         2.20         3.45         3.39         7.17         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FW-A3TU TCGA-QB-A6FS TCGA-WE-A8JZ 
        8.81        49.15        40.64         0.13         5.79        11.84 
TCGA-WE-A8ZM TCGA-YG-AA3P 
       18.67         4.70 

$`6P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
        3.02         6.97         6.97        16.47         8.52        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
       70.16       110.79        28.08        45.83        81.24         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK 
       21.14        88.50        68.22        44.19         7.50         6.31 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        59.57       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        61.38        13.32        24.00         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       26.37        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       32.61        25.78       110.24        52.01        47.87        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.11        29.72        15.19       142.45       108.79        38.93 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 
        5.72         9.90        48.79        35.80        10.03        13.68 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       44.52        36.69         4.93        22.36        19.36         7.00 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       14.83        13.15         0.20         0.13        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       13.35        13.22         0.20        11.57         6.31         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.35        12.20         5.13         4.31        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       15.85         9.21         1.18         9.90        37.97        62.79 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       36.85         1.08        39.62         9.50        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        9.99        30.44         2.43        36.30         9.67        36.33 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        28.31        33.83        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MD 
        1.15        13.02        34.98        36.33         6.18         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       29.46         2.73        44.25         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       60.49        53.16        52.67         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
        3.22        21.60        21.60        16.14        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19E 
       12.95        38.40         5.72        76.41         3.78        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.11       114.15        34.88        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.87        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
       22.49         1.71         5.62        18.41        85.74         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        3.58         5.36        13.28         4.70         3.29        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       20.38         8.22        19.53        11.08        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       12.89        47.38        52.08         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        5.23        53.85         3.22         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       10.78         5.98         6.41         2.27         0.20         0.99 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 
       14.50        15.81         0.43        11.05        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       164.19         8.98        60.03         2.99        10.98 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
      185.16        71.01         5.49         6.48         7.10        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       13.12         3.72         3.42        21.83         5.36         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       19.96         1.94        12.07         6.18         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.13              0.13 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           124.47            185.16 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           11.625            15.420 
[1] "0.1 - 124.5 (11.6)" "0.1 - 185.2 (15.4)"
[1] "hr=" "1.3"
D51V2, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    26  36
  6P LOSS WILD-TYPE 147 130
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               62               277 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               36               130 
$`6P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD 
      112.04        31.59        43.43       103.10        86.76        11.87 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3ML TCGA-D3-A3MV TCGA-D3-A51N 
       42.08       171.58        56.19        13.87        45.30        22.62 
TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN 
      178.32        79.59        11.61        58.52        95.24       161.00 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
       25.18        66.25        22.95       117.21       194.83        35.93 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29A 
       53.92        68.09       215.44        27.22        94.98        63.35 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       13.97        72.07        37.35       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2GL TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
      102.90        79.66        21.67       129.27        28.83        61.51 
TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19J TCGA-ER-A19T TCGA-ER-A2NE 
      127.20        98.40        12.59         6.44         8.88        20.15 
TCGA-FR-A69P TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZQ 
       15.72        34.82        48.59        48.85         9.70       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FW-A3TU TCGA-QB-A6FS TCGA-WE-A8JZ 
       11.41       148.80        53.16        47.54         6.67        24.03 
TCGA-WE-A8ZM TCGA-YG-AA3P 
       90.28        14.43 

$`6P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.57        16.67       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
       71.80       133.25        28.08        90.90        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK 
       23.77       115.53       168.00        62.07       113.52        12.10 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        86.93        60.23        24.53         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       39.75       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       63.81        26.89       125.79       135.75       137.92        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      125.19        30.84        15.19       228.99       170.20        89.13 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      137.79        29.06       129.63       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         6.41        18.12        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 
        9.90        48.89        36.03        20.38       176.55       107.34 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       61.18        65.92        23.44        28.60        10.49        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       13.87        10.16        17.85        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       52.01         6.35        12.20        29.82         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       91.56       168.26        13.55        80.61        47.84        63.78 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       64.64         2.60        56.84        18.61        56.42        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       55.92       369.93        25.87        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       59.28        67.43       314.56       161.03       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       89.33        54.74        75.48        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MD 
       14.30        55.59        44.88        94.82        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      158.63       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      172.18        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19E 
       13.94        50.76         9.17        77.75        48.89        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93       152.35       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
       46.98        33.21         6.77        92.98       174.21       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
       15.16         7.00        38.27        29.46        94.39       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        40.27        15.45        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       23.93       101.26        74.73        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       32.48        39.58        46.36        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A693 
       59.41        65.88       357.04       294.77        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       212.22        63.02       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
      219.16       105.04        38.56        54.38         8.61        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       59.41        52.34         3.75        22.68        43.73         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       30.18        10.36        15.16        36.03        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             6.44              0.16 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           215.44            369.93 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            48.72             50.76 
[1] "6.4 - 215.4 (48.7)" "0.2 - 369.9 (50.8)"
[1] "hr=" "1.4"
D51V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P LOSS MUTATED                   11             3
  6P LOSS WILD-TYPE                 50             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6P LOSS MUTATED                                          16
  6P LOSS WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  6P LOSS MUTATED                    35
  6P LOSS WILD-TYPE                 174
D51V4, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  DISTANT METASTASIS                                     11                50
  PRIMARY TUMOR                                           3                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              16                56
  REGIONAL LYMPH NODE                                    35               174
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6P LOSS MUTATED             5       2       5        1        4        4
  6P LOSS WILD-TYPE           7       5      23       16       23       18
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6P LOSS MUTATED           2         5         0         5          5
  6P LOSS WILD-TYPE        12        14        12        30         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED            6         15        3
  6P LOSS WILD-TYPE         26         43       16
D51V5, multiclass
             clus
vv            6P LOSS MUTATED 6P LOSS WILD-TYPE
  I OR II NOS               5                 7
  STAGE 0                   2                 5
  STAGE I                   5                23
  STAGE IA                  1                16
  STAGE IB                  4                23
  STAGE II                  4                18
  STAGE IIA                 2                12
  STAGE IIB                 5                14
  STAGE IIC                 0                12
  STAGE III                 5                30
  STAGE IIIA                5                10
  STAGE IIIB                6                26
  STAGE IIIC               15                43
  STAGE IV                  3                16
[1] 14  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                T0+T1 T2 T3 T4
  6P LOSS MUTATED      10 12 17 12
  6P LOSS WILD-TYPE    53 59 57 55
D51V6, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1              10                53
  T2                 12                59
  T3                 17                57
  T4                 12                55
[1] 4 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                 N0  N1  N2  N3
  6P LOSS MUTATED    30  13   8  12
  6P LOSS WILD-TYPE 138  48  30  35
D51V7, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              30               138
  N1              13                48
  N2               8                30
  N3              12                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"
                   vv
clus                 M0  M1 M1A M1B M1C
  6P LOSS MUTATED    59   1   1   0   1
  6P LOSS WILD-TYPE 247   3   2   4   8
D51V8, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               59               247
  M1                1                 3
  M1A               1                 2
  M1B               0                 4
  M1C               1                 8
[1] 5 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
  6P LOSS MUTATED    21  19
  6P LOSS WILD-TYPE 108  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21   19
  6P LOSS WILD-TYPE  108   68
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               21               108
  YES              19                68
[1] 2 2
[1] FALSE
D51V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     9  56
  6P LOSS WILD-TYPE  34 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9   56
  6P LOSS WILD-TYPE   34  248
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                9                34
  YES              56               248
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    23  42
  6P LOSS WILD-TYPE 108 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     23   42
  6P LOSS WILD-TYPE  108  175
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              23               108
  MALE                42               175
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         0    60
  6P LOSS WILD-TYPE     4                         1   266
D51V13, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  60               266
[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"
D51V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  60
  6P LOSS WILD-TYPE   6 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   60
  6P LOSS WILD-TYPE    6  274
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              60               274
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   76 78
  6Q LOSS WILD-TYPE 92 87
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              154               179 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               78                87 
$`6Q LOSS MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 
        3.02         6.97        16.47       111.09        32.42        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       10.29        85.32        68.22        86.76        11.41        44.19 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3ML 
       36.16        92.42        56.19        64.44        15.25         6.31 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T 
      103.59        26.37        29.23        54.31        21.44        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI 
      110.24        52.01        13.68        22.06        10.22         4.18 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A6EA 
       38.93        75.65       124.47        87.62        21.93        11.31 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
       13.22        14.60        48.79        51.12        39.19         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A5UL 
       36.69        25.15         4.93         6.64        17.56        13.35 
TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       13.22        10.55         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C 
        5.13         4.31        60.23         1.18         7.99        37.97 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S 
       11.15         8.55        36.85        39.62         8.09         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       30.44         2.43        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       36.30         9.67        36.33        51.12        17.98        60.00 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 
       35.54        33.83        55.69         5.42        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A2MT 
       98.27         2.70        47.51         2.73        26.99        52.67 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J7 
       51.62         3.68        13.81        15.95        22.92        21.60 
TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
        0.95        21.73        18.61         5.72        25.18         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2NE 
       11.11         4.21        42.84        34.68         6.58         1.51 
TCGA-ER-A2NF TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC 
       13.08         1.71         5.62        15.72         3.58         2.20 
TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZF 
        4.70         3.45        23.80         3.39        20.38        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        7.17        30.87        12.92        47.38         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F5 
       49.15        40.64         8.68        27.39         5.23        28.73 
TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 
        5.98         0.99         0.13         7.23        31.33        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-LH-A9QB 
       15.42        12.16        11.84        10.65        14.50         0.43 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       11.05         5.79         0.33        11.84        18.67         3.72 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        1.94        12.07         6.18         4.70 

$`6Q LOSS WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        6.97         8.52        70.16       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK 
       81.24         8.38        21.14        88.50         7.50         6.31 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       59.57       114.67        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.32        24.00         9.34        93.21        54.74        31.30 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       32.28        32.61        47.87        17.72        23.11        29.72 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       15.19       142.45       108.79        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 
        4.01         5.72         9.90        35.80        10.03        13.68 
TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       44.52        22.36        19.36         7.00        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17X 
        0.20         0.13        23.15        19.00         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E 
        6.31         4.34        15.85         9.21         9.90        62.79 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2GC TCGA-EE-A2GH 
        1.08         9.50        12.03         8.84        34.29        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS 
       30.08        19.43        16.01        28.31         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       34.98         6.18         9.53        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       125.65       111.91        56.02        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        60.49        53.16         5.56       124.31       122.73 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
       30.15        12.72         3.22        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 
       27.35        18.41        33.60        31.40        12.95        38.40 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L 
       76.41         3.78        11.90       114.15        34.88        13.45 
TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       28.60         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        1.87        12.62        11.74         9.04         6.58        22.49 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE 
       18.41        85.74         6.71         5.36        13.28         3.29 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       64.47        11.01        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZY TCGA-FS-A4F0 
        8.22        19.53        12.89        52.08         0.82        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
        3.22         7.36        14.20        10.78         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.20         0.16        17.33         9.90         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A9SD 
       44.28        84.72        10.13        14.70        14.50        14.50 
TCGA-HR-A2OH TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       15.81        18.05         0.69       164.19         8.98        60.03 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
        2.99        10.98       185.16        71.01         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
        7.10        21.07        13.12         3.42        21.83         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.08        19.96         8.22         6.67         5.98 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.13              0.13 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           124.47            185.16 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           14.155            15.190 
[1] "0.1 - 124.5 (14.2)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1.1"
D52V2, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   78 79
  6Q LOSS WILD-TYPE 95 87
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              157               182 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               79                87 
$`6Q LOSS MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 
       17.03        61.02        16.57       112.04       112.57        31.59 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       43.43       103.10       168.00        86.76        11.87        62.07 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3ML 
       42.08       171.58        56.19        66.08        58.06        13.87 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T 
      103.59        39.75        45.30       145.12        22.62        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI 
      125.79       135.75       178.32        79.59        11.61        58.52 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A148 TCGA-D9-A1JW 
       89.13        95.24       161.00       137.79       151.53         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        6.41        22.29        25.18        66.25        22.95        48.89 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      117.21       194.83        35.93        61.18        53.92        65.92 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 
       68.09       215.44        17.29        52.01        27.22        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
       13.55        63.35        47.84        13.97        72.07        64.64 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       56.84        37.35        55.92       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       59.28       314.56       161.03        79.66        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
       13.91        94.82        21.67       129.27        28.83        61.51 
TCGA-EE-A2MF TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
      268.73       248.65        71.21        51.62         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A195 
       23.47       127.20        64.08       201.80       109.58        35.44 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N 
        9.17        98.40        12.59        26.37         6.44        44.05 
TCGA-ER-A19P TCGA-ER-A19T TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3PL TCGA-ER-A42K 
      162.08         8.88        20.15        16.37        33.21         6.77 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YX TCGA-FS-A1Z0 
       15.72        15.16        34.82        29.46        48.59       202.65 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85       357.37        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26       133.55        11.41       148.80        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-FW-A3TU 
       49.48        27.02        28.73        26.73        22.92        47.54 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
        7.23       117.93        64.44        62.79        32.48        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       12.62        21.37       357.04       294.77         6.67         0.33 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       24.03        90.28        52.34        10.36        15.16        36.03 
TCGA-YG-AA3P 
       14.43 

$`6Q LOSS WILD-TYPE`
TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       12.99        16.67        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK 
       95.74        65.49        23.77       115.53       113.52        12.10 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       59.57       130.72        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       60.23        24.53         9.34       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       32.94        63.81       137.92        18.18       125.19        30.84 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       15.19       228.99       170.20        29.06       129.63       117.17 
TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1HW 
       54.67        18.12        11.34        11.11         9.90        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       20.38       176.55       107.34        23.44        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.16        17.85        68.25        54.02 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F 
        6.35        12.20        29.82         8.65       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
      168.26        80.61        63.78         2.60        18.61        56.42 
TCGA-EE-A29R TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       14.47        67.43       208.04        48.72        89.33        54.74 
TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD 
       75.48        14.30        55.59        44.88        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      203.05       167.90        47.54        43.23       134.40       162.48 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 
       53.26       124.31       122.73        54.51       138.81       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       36.95        34.32        53.19        27.35        51.35       148.08 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19E 
       31.40        13.94        50.76        77.75        48.89        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S 
      268.93       152.35       131.51        61.05        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
      148.18        79.99        43.82        23.34        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
      247.04        80.32        46.98        92.98       174.21       210.08 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        7.00        38.27        94.39       216.92       228.59        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZK 
       28.08         7.79        27.72        53.52        40.27        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
       74.73        27.09        77.82        50.14        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-FW-A5DY 
       12.43        49.45        77.88         0.20         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         2.04        11.74       139.89        84.72        10.13 
TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-AA9O TCGA-RP-A694 
       39.58        50.10        59.41        65.88        18.05         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
      212.22        63.02       121.08         4.01        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      105.04        38.56        54.38         8.61        56.98        59.41 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-A8RT 
        3.75        22.68        43.73         2.20        30.18        23.64 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.33              0.16 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           369.93            268.93 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            48.85             51.12 
[1] "0.3 - 369.9 (48.9)" "0.2 - 268.9 (51.1)"
[1] "hr=" "1"  
D52V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q LOSS MUTATED                   31             4
  6Q LOSS WILD-TYPE                 30             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6Q LOSS MUTATED                                          36
  6Q LOSS WILD-TYPE                                        36
                   vv
clus                REGIONAL LYMPH NODE
  6Q LOSS MUTATED                    91
  6Q LOSS WILD-TYPE                 118
D52V4, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     31                30
  PRIMARY TUMOR                                           4                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              36                36
  REGIONAL LYMPH NODE                                    91               118
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  6Q LOSS MUTATED             7       4      11        7       13        7
  6Q LOSS WILD-TYPE           5       3      17       10       14       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6Q LOSS MUTATED           6         8         5        16          8
  6Q LOSS WILD-TYPE         8        11         7        19          7
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           15         31        7
  6Q LOSS WILD-TYPE         17         27       12
D52V5, multiclass
             clus
vv            6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  I OR II NOS               7                 5
  STAGE 0                   4                 3
  STAGE I                  11                17
  STAGE IA                  7                10
  STAGE IB                 13                14
  STAGE II                  7                15
  STAGE IIA                 6                 8
  STAGE IIB                 8                11
  STAGE IIC                 5                 7
  STAGE III                16                19
  STAGE IIIA                8                 7
  STAGE IIIB               15                17
  STAGE IIIC               31                27
  STAGE IV                  7                12
[1] 14  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                T0+T1 T2 T3 T4
  6Q LOSS MUTATED      28 36 31 29
  6Q LOSS WILD-TYPE    35 35 43 38
D52V6, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1              28                35
  T2                 36                35
  T3                 31                43
  T4                 29                38
[1] 4 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                N0 N1 N2 N3
  6Q LOSS MUTATED   71 32 19 24
  6Q LOSS WILD-TYPE 97 29 19 23
D52V7, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              71                97
  N1              32                29
  N2              19                19
  N3              24                23
[1] 4 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                 M0  M1 M1A M1B M1C
  6Q LOSS MUTATED   145   1   2   1   4
  6Q LOSS WILD-TYPE 161   3   1   3   5
D52V8, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              145               161
  M1                1                 3
  M1A               2                 1
  M1B               1                 3
  M1C               4                 5
[1] 5 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
  6Q LOSS MUTATED   53 46
  6Q LOSS WILD-TYPE 76 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     53   46
  6Q LOSS WILD-TYPE   76   41
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               53                76
  YES              46                41
[1] 2 2
[1] FALSE
D52V10, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    21 140
  6Q LOSS WILD-TYPE  22 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21  140
  6Q LOSS WILD-TYPE   22  164
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               21                22
  YES             140               164
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    67  95
  6Q LOSS WILD-TYPE  64 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     67   95
  6Q LOSS WILD-TYPE   64  122
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              67                64
  MALE                95               122
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       1                         1   152
  6Q LOSS WILD-TYPE     4                         0   174
D52V13, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                 152               174
[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"
D52V14, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3 155
  6Q LOSS WILD-TYPE   4 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  155
  6Q LOSS WILD-TYPE    4  179
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             155               179
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     7  11
  7P LOSS WILD-TYPE 161 154
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               315 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               154 
$`7P LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D3-A8GI TCGA-DA-A3F8 TCGA-EB-A44R 
       45.83        13.32        29.23         4.18        14.83         0.20 
TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A198 
        4.34        39.62         9.67        22.22        33.60        38.40 
TCGA-FR-A7U8 TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GN-A8LL TCGA-W3-A828 
        3.58        49.15        40.64         8.68        14.50        60.03 

$`7P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB 
       32.42        70.16       110.79        28.08        22.55        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       10.29        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.41        44.19         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       92.42        56.19        64.44        59.57       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32        82.29        61.38        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        26.37        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.31        32.28        21.44        32.61        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       52.01        47.87        13.68        17.72        23.11        29.72 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       22.06        10.22        15.19       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       75.65       124.47        87.62        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        4.01        21.93         5.72         9.90        11.31        13.22 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       14.60        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        17.56        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
        0.13        23.15        19.00        13.35        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       11.57        10.55         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       12.20         5.13         4.31        60.23        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        62.79 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55        36.85         1.08         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.84         9.99        30.44         2.43        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        49.22        36.30        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        55.69         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14         0.95        27.35        18.41        21.73 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        18.61        12.95         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
        3.78         3.52        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        6.71         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       52.08         8.65         8.81        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       53.85         3.22         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       15.81         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
        0.69       164.19         8.98         2.99        10.98       185.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       71.01        11.84         5.49         6.48         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       21.07        13.12         3.72         3.42        21.83         5.36 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        1.08        19.96         1.94        12.07         6.18         4.70 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        8.22         6.67         5.98 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.20              0.13 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            60.03            185.16 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           18.525            14.600 
[1] "0.2 - 60.0 (18.5)"  "0.1 - 185.2 (14.6)"
[1] "hr=" "1.2"
D53V2, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     7  11
  7P LOSS WILD-TYPE 166 155
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               321 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               155 
$`7P LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D3-A8GI TCGA-DA-A3F8 TCGA-EB-A44R 
       90.90        60.23        45.30        58.52        15.68        10.16 
TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A198 
      151.27        56.84        39.29        53.19       148.08        50.76 
TCGA-FR-A7U8 TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GN-A8LL TCGA-W3-A828 
       15.16       148.80        53.16        26.56        21.37       121.08 

$`7P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        31.59        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.87        62.07       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        56.19        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32       166.52        86.93        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        39.75       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
      135.75       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        11.61        15.19       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       95.24       161.00       137.79        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       22.29        11.11         9.90        25.18        66.25        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.89        36.03       117.21        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH 
       68.09        28.60        10.49       215.44        13.87        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.82        27.22         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       26.89        68.15         4.96       133.81        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        63.78 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64         2.60        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        55.92       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       126.81        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32       201.80        27.35        51.35       109.58 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        35.44        13.94         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       48.89        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      210.08         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.79        27.72        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       15.45         9.70        32.75        47.38        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       74.73       133.55        11.41        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       32.48        39.58        46.36        12.62        50.10        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       357.04       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
        0.69       212.22        63.02         4.01        42.08       219.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      105.04        24.03        38.56        54.38         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       56.98        59.41        52.34         3.75        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        2.20        30.18        10.36        15.16        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            10.16              0.16 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           151.27            369.93 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           53.175            49.480 
[1] "10.2 - 151.3 (53.2)" "0.2 - 369.9 (49.5)" 
[1] "hr=" "1.4"
D53V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P LOSS MUTATED                    5             0
  7P LOSS WILD-TYPE                 56             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7P LOSS MUTATED                                           3
  7P LOSS WILD-TYPE                                        69
                   vv
clus                REGIONAL LYMPH NODE
  7P LOSS MUTATED                    10
  7P LOSS WILD-TYPE                 199
D53V4, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  DISTANT METASTASIS                                      5                56
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               3                69
  REGIONAL LYMPH NODE                                    10               199
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7P LOSS MUTATED             0       1       2        1        4        1
  7P LOSS WILD-TYPE          12       6      26       16       23       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7P LOSS MUTATED           0         0         2         2          0
  7P LOSS WILD-TYPE        14        19        10        33         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED            3          1        0
  7P LOSS WILD-TYPE         29         57       19
D53V5, multiclass
             clus
vv            7P LOSS MUTATED 7P LOSS WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   1                 6
  STAGE I                   2                26
  STAGE IA                  1                16
  STAGE IB                  4                23
  STAGE II                  1                21
  STAGE IIA                 0                14
  STAGE IIB                 0                19
  STAGE IIC                 2                10
  STAGE III                 2                33
  STAGE IIIA                0                15
  STAGE IIIB                3                29
  STAGE IIIC                1                57
  STAGE IV                  0                19
[1] 14  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                T0+T1 T2 T3 T4
  7P LOSS MUTATED       2  9  1  2
  7P LOSS WILD-TYPE    61 62 73 65
D53V6, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               2                61
  T2                  9                62
  T3                  1                73
  T4                  2                65
[1] 4 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                 N0  N1  N2  N3
  7P LOSS MUTATED    10   2   3   1
  7P LOSS WILD-TYPE 158  59  35  46
D53V7, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              10               158
  N1               2                59
  N2               3                35
  N3               1                46
[1] 4 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                 M0  M1 M1A M1B M1C
  7P LOSS MUTATED    18   0   0   0   0
  7P LOSS WILD-TYPE 288   4   3   4   9
D53V8, multiclass
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               18               288
  M1                0                 4
  M1A               0                 3
  M1B               0                 4
  M1C               0                 9
[1] 5 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
  7P LOSS MUTATED     7   4
  7P LOSS WILD-TYPE 122  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    4
  7P LOSS WILD-TYPE  122   83
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                7               122
  YES               4                83
[1] 2 2
[1] FALSE
D53V10, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2  16
  7P LOSS WILD-TYPE  41 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   16
  7P LOSS WILD-TYPE   41  288
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                2                41
  YES              16               288
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     5  13
  7P LOSS WILD-TYPE 126 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5   13
  7P LOSS WILD-TYPE  126  204
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               5               126
  MALE                13               204
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         0    17
  7P LOSS WILD-TYPE     4                         1   309
D53V13, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  17               309
[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"
D53V14, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  18
  7P LOSS WILD-TYPE   7 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   18
  7P LOSS WILD-TYPE    7  316
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              18               316
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     6  11
  7Q LOSS WILD-TYPE 162 154
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               316 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               154 
$`7Q LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-EB-A44R TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A2A5 
       45.83        13.32         0.20        11.15        39.62         9.67 
TCGA-EE-A2GN TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19W TCGA-FS-A1ZE TCGA-FS-A1ZT 
       33.83        22.22        33.60        17.72        19.53        40.64 
TCGA-FS-A1ZU TCGA-FS-A4F0 TCGA-GN-A8LL TCGA-W3-A828 TCGA-WE-A8ZM 
        8.68        53.85        14.50        60.03        18.67 

$`7Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB 
       32.42        70.16       110.79        28.08        22.55        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       10.29        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.41        44.19         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       92.42        56.19        64.44        59.57       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32        82.29        61.38        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        26.37        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      110.24        52.01        47.87        13.68        17.72        23.11 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       29.72        22.06        10.22        15.19         4.18       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      108.79        38.93        75.65       124.47        87.62        11.44 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        5.56        24.07         4.01        21.93         5.72         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       11.31        13.22        14.60        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       17.56        14.83        13.15         0.13        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       60.23         4.34        15.85         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        9.90        37.97        62.79         8.55        36.85         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        9.50        12.03         8.09         8.84         9.99        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43        32.15         8.09        11.31        49.22        36.30 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.33        51.12        34.29        17.98        60.00        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       30.08        19.43        16.01        35.54        28.31        55.69 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
        5.42         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
        2.73        44.25         7.96        14.56        63.42       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.91        56.02        25.08        26.99        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       53.16        52.67         5.56       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
       22.92        21.60        21.60        16.14         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       18.41        21.73        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        5.72        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07         6.58        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        9.04         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       85.74        15.72         6.71         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        2.20         4.70         3.29        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       23.80        14.24        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       20.38         8.22        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82         5.23         3.22         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.85        11.61        44.28        31.33        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       16.24        15.42        12.16        14.70        11.84        10.65 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       14.50        14.50        15.81         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O 
       18.05         0.33         0.69       164.19         8.98         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       10.98       185.16        71.01        11.84         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
        7.10        21.07        13.12         3.72         3.42        21.83 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        5.36         1.08        19.96         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.20              0.13 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            60.03            185.16 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            19.53             14.53 
[1] "0.2 - 60.0 (19.5)"  "0.1 - 185.2 (14.5)"
[1] "hr=" "1.2"
D54V2, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     6  11
  7Q LOSS WILD-TYPE 167 155
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               322 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               155 
$`7Q LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-EB-A44R TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A2A5 
       90.90        60.23        10.16        13.97        56.84        39.29 
TCGA-EE-A2GN TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19W TCGA-FS-A1ZE TCGA-FS-A1ZT 
       90.97        53.19       148.08       148.18        40.27        53.16 
TCGA-FS-A1ZU TCGA-FS-A4F0 TCGA-GN-A8LL TCGA-W3-A828 TCGA-WE-A8ZM 
       26.56        77.82        21.37       121.08        90.28 

$`7Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        31.59        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.87        62.07       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
      171.58        56.19        66.08        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       46.98        46.32       166.52        86.93        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       135.75       137.92       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       30.84        79.59        11.61        15.19        58.52       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      170.20        89.13        95.24       161.00       137.79        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      129.63       117.17       151.53        54.67         3.65         6.41 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
       18.12        11.34        22.29        11.11         9.90        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       66.25        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      194.83       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        17.85        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       52.01         6.35        12.20        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      133.81       151.27        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        63.78        72.07        64.64         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        37.35        14.47        55.92       369.93 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       195.02        17.92        46.82       102.90        36.82 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
       48.72        89.33        54.74        79.66        75.48       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      268.73       103.20        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
      203.05       167.90        47.54       248.65        43.23       134.40 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      162.48        71.21        53.26       124.31       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       51.35       109.58        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
        9.17        77.75        98.40        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25         8.88        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      174.21        15.72       210.08        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        29.46        94.39       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.48        27.09        27.02        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       64.44        62.79        32.48        39.58        46.36        12.62 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       50.10        59.41        65.88       357.04       294.77         6.67 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-AA1O 
       18.05         0.33         0.69       212.22        63.02         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       42.08       219.16       105.04        24.03        38.56        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
        8.61        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       43.73         2.20        30.18        10.36        15.16        36.03 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        23.64        93.07        11.74 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            10.16              0.16 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           148.18            369.93 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           56.840            49.465 
[1] "10.2 - 148.2 (56.8)" "0.2 - 369.9 (49.5)" 
[1] "hr=" "1.4"
D54V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q LOSS MUTATED                    4             0
  7Q LOSS WILD-TYPE                 57             5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7Q LOSS MUTATED                                           5
  7Q LOSS WILD-TYPE                                        67
                   vv
clus                REGIONAL LYMPH NODE
  7Q LOSS MUTATED                     8
  7Q LOSS WILD-TYPE                 201
D54V4, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      4                57
  PRIMARY TUMOR                                           0                 5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               5                67
  REGIONAL LYMPH NODE                                     8               201
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  7Q LOSS MUTATED             0       0       1        0        4        1
  7Q LOSS WILD-TYPE          12       7      27       17       23       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7Q LOSS MUTATED           1         1         3         2          0
  7Q LOSS WILD-TYPE        13        18         9        33         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED            2          1        0
  7Q LOSS WILD-TYPE         30         57       19
D54V5, multiclass
             clus
vv            7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  I OR II NOS               0                12
  STAGE 0                   0                 7
  STAGE I                   1                27
  STAGE IA                  0                17
  STAGE IB                  4                23
  STAGE II                  1                21
  STAGE IIA                 1                13
  STAGE IIB                 1                18
  STAGE IIC                 3                 9
  STAGE III                 2                33
  STAGE IIIA                0                15
  STAGE IIIB                2                30
  STAGE IIIC                1                57
  STAGE IV                  0                19
[1] 14  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                T0+T1 T2 T3 T4
  7Q LOSS MUTATED       1  7  2  4
  7Q LOSS WILD-TYPE    62 64 72 63
D54V6, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               1                62
  T2                  7                64
  T3                  2                72
  T4                  4                63
[1] 4 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                 N0  N1  N2  N3
  7Q LOSS MUTATED    10   4   1   0
  7Q LOSS WILD-TYPE 158  57  37  47
D54V7, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              10               158
  N1               4                57
  N2               1                37
  N3               0                47
[1] 4 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                 M0  M1 M1A M1B M1C
  7Q LOSS MUTATED    16   0   0   0   0
  7Q LOSS WILD-TYPE 290   4   3   4   9
D54V8, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               16               290
  M1                0                 4
  M1A               0                 3
  M1B               0                 4
  M1C               0                 9
[1] 5 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
  7Q LOSS MUTATED     7   5
  7Q LOSS WILD-TYPE 122  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      7    5
  7Q LOSS WILD-TYPE  122   82
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                7               122
  YES               5                82
[1] 2 2
[1] FALSE
D54V10, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  16
  7Q LOSS WILD-TYPE  42 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   16
  7Q LOSS WILD-TYPE   42  288
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                42
  YES              16               288
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     6  11
  7Q LOSS WILD-TYPE 125 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      6   11
  7Q LOSS WILD-TYPE  125  206
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               6               125
  MALE                11               206
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       1                         0    15
  7Q LOSS WILD-TYPE     4                         1   311
D54V13, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  15               311
[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"
D54V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  17
  7Q LOSS WILD-TYPE   7 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   17
  7Q LOSS WILD-TYPE    7  317
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              17               317
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    28  34
  8P LOSS WILD-TYPE 140 131
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               62               271 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               34               131 
$`8P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
       16.47        10.29        88.50        11.41         7.50        92.42 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GM 
       15.25         9.34        21.44        52.01        22.06        75.65 
TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20C 
       11.31         4.93         0.20         8.12        12.20         4.34 
TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GI 
       37.97        36.85        39.62         2.43         9.67        30.08 
TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MN 
       13.02         2.73        44.25        14.56        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J3 
       26.99        53.16         5.56       124.31        51.62         3.22 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND 
       33.60        12.95         5.72        36.07         6.58         1.87 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA 
        1.51         1.71         2.20        11.01        23.80         7.30 
TCGA-FS-A1ZC TCGA-FS-A1ZT TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-OD-A75X 
       20.38        40.64         0.99        31.33        84.72        11.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-WE-A8JZ TCGA-WE-A8ZY TCGA-WE-AAA0 TCGA-WE-AAA3 
        5.79        18.05        11.84         5.36        19.96         1.94 
TCGA-YG-AA3P TCGA-Z2-AA3S 
        4.70         6.67 

$`8P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       70.16       110.79        28.08        22.55        45.83        81.24 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
       85.32         8.38        21.14        68.22        86.76        44.19 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       36.16         6.31        56.19        64.44        59.57       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        6.31       103.59        26.37        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       31.30        54.31        32.28        32.61        25.78       110.24 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD 
       47.87        13.68        17.72        23.11        29.72        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       15.19         4.18       142.45       108.79        38.93       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        5.72         9.90        13.22        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       17.56        14.83        13.15         0.20         0.13        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       19.00        13.35        13.22        11.57        10.55         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35         5.13         4.31        60.23        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
        9.21         1.18         7.99         9.90        11.15        62.79 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        8.55         1.08         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99        30.44        32.15         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       36.30        36.33        51.12        34.29        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       47.21        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       55.69         5.42         1.15        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       98.27         2.70         6.18        47.51         9.53        29.46 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ TCGA-EE-A2MR 
        7.96        63.42       125.65       111.91        21.60        60.49 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       52.67       122.73         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       12.72        22.92        21.60        21.60        16.14        22.22 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
        0.95        27.35        18.41        21.73        31.40        18.61 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       38.40        76.41        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84        34.68         9.57        17.72        78.44        11.80 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        5.62        18.41        85.74        15.72         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
        5.36        13.28         4.70         3.29        64.47         3.45 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       14.24        15.52         7.33         3.39         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       11.08         7.17        30.87        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW 
       52.08         8.65         8.81        49.15         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
        0.82         5.23        53.85         3.22         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       11.61        44.28        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       14.70        11.84        10.65        14.50        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       15.81         0.43         0.33         0.69       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
       60.03         2.99        10.98       185.16        71.01         5.49 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        6.48         7.10        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT 
        3.42        21.83         1.08        12.07         6.18         8.22 
TCGA-Z2-AA3V 
        5.98 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.20              0.13 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           124.31            185.16 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           12.575            15.420 
[1] "0.2 - 124.3 (12.6)" "0.1 - 185.2 (15.4)"
[1] "hr=" "1.3"
D55V2, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    30  34
  8P LOSS WILD-TYPE 143 132
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               64               275 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               34               132 
$`8P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
       16.57        43.43       115.53        11.87       113.52       171.58 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A8GC TCGA-D3-A8GM 
       58.06         9.34        22.62       135.75        79.59        95.24 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EB-A6L9 TCGA-EE-A180 
      151.53         3.65        25.18        65.92        12.20        94.98 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29V 
       26.89       151.27        47.84        64.64        56.84        25.87 
TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MI 
       39.29        48.72        55.59       268.73       103.20       204.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      167.90        47.54       248.65       162.48        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19S 
       51.62       172.18       148.08        13.94         9.17        37.25 
TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FR-A8YC TCGA-FS-A1YY 
        8.88        23.34        20.15        33.21        34.82       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZT TCGA-FW-A3R5 TCGA-GN-A264 
      202.65        27.72       357.37        53.16        22.92       117.93 
TCGA-GN-A265 TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-WE-A8JZ TCGA-WE-A8ZY 
       84.72       294.77         6.67        18.05        24.03        43.73 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3P TCGA-Z2-AA3S 
       30.18        10.36        14.43        93.07 

$`8P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
      103.10        65.49        23.77       168.00        86.76        62.07 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10        56.19        66.08        59.57       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       56.35       145.12        32.94        63.81        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD 
      137.92       178.32        18.18       125.19        30.84        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN 
       15.19        58.52       228.99       170.20        89.13       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JX 
      137.79        29.06       129.63       117.17        54.67         6.41 
TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC 
       18.12        11.34        22.29        11.11         9.90        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
      176.55        35.93       107.34        61.18        53.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.16        17.85        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        6.35        29.82        27.22         8.65        33.73        14.70 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       68.15         4.96       133.81        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
       63.35        80.61        13.97        63.78        72.07         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        37.35        14.47        55.92       369.93 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      195.02        17.92        46.82       102.90        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       59.28        67.43       314.56       161.03       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       14.30        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MJ 
       19.76        61.51        47.28       103.27        16.96        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB 
      158.63       203.05        43.23       134.40        71.21       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
        3.68        54.51        13.81        23.47       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       51.35       109.58        31.40        35.44        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       98.40        48.89        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      152.35         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG 
       50.89       148.18        79.99        43.82        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
      174.21        15.72       210.08        15.16         7.00        38.27 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       29.46        94.39       216.92        48.59        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.79        48.85        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       32.75        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       10.13        64.44        62.79        32.48        39.58        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       12.62        50.10        21.37        59.41        65.88       357.04 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
       42.08       219.16       105.04        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       90.28        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-AA9Y TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3V 
        2.20        15.16        36.03        23.64        11.74 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             3.65              0.16 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           357.37            369.93 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            52.39             50.10 
[1] "3.6 - 357.4 (52.4)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.1"
D55V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P LOSS MUTATED                   14             2
  8P LOSS WILD-TYPE                 47             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8P LOSS MUTATED                                           8
  8P LOSS WILD-TYPE                                        64
                   vv
clus                REGIONAL LYMPH NODE
  8P LOSS MUTATED                    39
  8P LOSS WILD-TYPE                 170
D55V4, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  DISTANT METASTASIS                                     14                47
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               8                64
  REGIONAL LYMPH NODE                                    39               170
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8P LOSS MUTATED             2       3       7        6        6        1
  8P LOSS WILD-TYPE          10       4      21       11       21       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8P LOSS MUTATED           2         5         0         6          2
  8P LOSS WILD-TYPE        12        14        12        29         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED            4         11        3
  8P LOSS WILD-TYPE         28         47       16
D55V5, multiclass
             clus
vv            8P LOSS MUTATED 8P LOSS WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   3                 4
  STAGE I                   7                21
  STAGE IA                  6                11
  STAGE IB                  6                21
  STAGE II                  1                21
  STAGE IIA                 2                12
  STAGE IIB                 5                14
  STAGE IIC                 0                12
  STAGE III                 6                29
  STAGE IIIA                2                13
  STAGE IIIB                4                28
  STAGE IIIC               11                47
  STAGE IV                  3                16
[1] 14  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                T0+T1 T2 T3 T4
  8P LOSS MUTATED      14 15  9 11
  8P LOSS WILD-TYPE    49 56 65 56
D55V6, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              14                49
  T2                 15                56
  T3                  9                65
  T4                 11                56
[1] 4 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                 N0  N1  N2  N3
  8P LOSS MUTATED    33   8   7  11
  8P LOSS WILD-TYPE 135  53  31  36
D55V7, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              33               135
  N1               8                53
  N2               7                31
  N3              11                36
[1] 4 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                 M0  M1 M1A M1B M1C
  8P LOSS MUTATED    57   0   2   1   1
  8P LOSS WILD-TYPE 249   4   1   3   8
D55V8, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               57               249
  M1                0                 4
  M1A               2                 1
  M1B               1                 3
  M1C               1                 8
[1] 5 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
  8P LOSS MUTATED    28  12
  8P LOSS WILD-TYPE 101  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     28   12
  8P LOSS WILD-TYPE  101   75
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               28               101
  YES              12                75
[1] 2 2
[1] FALSE
D55V10, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     8  56
  8P LOSS WILD-TYPE  35 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8   56
  8P LOSS WILD-TYPE   35  248
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                8                35
  YES              56               248
[1] 2 2
[1] FALSE
D55V11, continuous
D55V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    22  42
  8P LOSS WILD-TYPE 109 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     22   42
  8P LOSS WILD-TYPE  109  175
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              22               109
  MALE                42               175
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       1                         0    58
  8P LOSS WILD-TYPE     4                         1   268
D55V13, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  58               268
[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"
D55V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1  62
  8P LOSS WILD-TYPE   6 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   62
  8P LOSS WILD-TYPE    6  272
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              62               272
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    11  15
  8Q LOSS WILD-TYPE 157 150
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               26               307 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               150 
$`8Q LOSS MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A6EA TCGA-DA-A1IA 
       11.41        92.42        22.06        75.65        11.31         4.93 
TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MM 
        8.12         4.34        39.62         2.73        14.56        56.02 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E 
       26.99        53.16         5.56        33.60         5.72        11.90 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FW-A3R5 TCGA-WE-A8JZ 
        1.51         1.71         7.30        20.38         0.99        11.84 
TCGA-WE-A8ZY TCGA-YG-AA3P 
        5.36         4.70 

$`8Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        86.76        44.19         7.50        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        64.44        59.57       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32        82.29        61.38        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        26.37        29.23        93.21        54.74 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       31.30        54.31        32.28        21.44        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      110.24        52.01        47.87        13.68        17.72        23.11 
TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       29.72        10.22        15.19         4.18       142.45       108.79 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       38.93       124.47        87.62        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01        21.93         5.72         9.90        13.22        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        36.69        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 
        0.13        23.15        19.00        13.35        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       11.57        10.55         6.31         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31        60.23        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
        7.99         9.90        37.97        11.15        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       36.85         1.08         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        55.69         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46        44.25         7.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
       63.42       125.65       111.91        25.08        21.60        60.49 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67       124.31       122.73        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       21.73        31.40        18.61        12.95        38.40        76.41 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       25.18         3.78         3.52        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       36.07         6.58        17.72        78.44        11.80         1.87 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        5.62        18.41        85.74        15.72         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        3.39         8.22        19.53        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       53.85         3.22         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
        5.98         6.41         2.27         0.20         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       14.70        11.84        10.65        14.50        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       15.81         0.43        11.05         5.79        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       164.19         8.98        60.03         2.99        10.98 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      185.16        71.01         5.49         6.48         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
       21.07        13.12         3.72         3.42        21.83         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       19.96         1.94        12.07         6.18         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.99              0.13 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            92.42            185.16 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            11.36             15.42 
[1] "1.0 - 92.4 (11.4)"  "0.1 - 185.2 (15.4)"
[1] "hr=" "1.5"
D56V2, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    11  15
  8Q LOSS WILD-TYPE 162 151
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               26               313 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               151 
$`8Q LOSS MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A8GC TCGA-D3-A8GM TCGA-D9-A6EA TCGA-DA-A1IA 
       11.87       171.58        79.59        95.24        25.18        65.92 
TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29M TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MM 
       94.98       151.27        56.84       268.73       204.66       167.90 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E 
      248.65       162.48        53.26       148.08         9.17        13.02 
TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FW-A3R5 TCGA-WE-A8JZ 
       20.15        33.21        27.72       357.37        22.92        24.03 
TCGA-WE-A8ZY TCGA-YG-AA3P 
       43.73        14.43 

$`8Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        86.76        62.07       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
       46.32       166.52        86.93        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        9.34       103.59        39.75        45.30       174.84        55.73 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       56.35       145.12        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       135.75       137.92       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK 
       30.84        11.61        15.19        58.52       228.99       170.20 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
       89.13       161.00       137.79        29.06       129.63       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      151.53        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       22.29        11.11         9.90        66.25        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       36.03       117.21        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        61.18        53.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       10.49       215.44        15.68        13.87        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       68.25        54.02        17.29        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       68.15         4.96       133.81        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        80.61        47.84        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64         2.60        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       55.92       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       126.81        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       103.20        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       158.63       203.05        47.54        43.23       134.40 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       71.21       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
      109.58        31.40        35.44        13.94        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        12.59        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       16.37        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       210.08        15.16 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        7.00        38.27        34.82        29.46        94.39       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88         0.20        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       39.58        46.36        12.62        50.10        21.37        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       65.88       357.04       294.77         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       212.22        63.02       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      219.16       105.04        38.56        54.38         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
       56.98        59.41        52.34         3.75        22.68         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       30.18        10.36        15.16        36.03        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             9.17              0.16 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           357.37            369.93 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            61.38             49.48 
[1] "9.2 - 357.4 (61.4)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.2"
D56V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q LOSS MUTATED                    7             1
  8Q LOSS WILD-TYPE                 54             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8Q LOSS MUTATED                                           3
  8Q LOSS WILD-TYPE                                        69
                   vv
clus                REGIONAL LYMPH NODE
  8Q LOSS MUTATED                    15
  8Q LOSS WILD-TYPE                 194
D56V4, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      7                54
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               3                69
  REGIONAL LYMPH NODE                                    15               194
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  8Q LOSS MUTATED             2       2       4        1        2        1
  8Q LOSS WILD-TYPE          10       5      24       16       25       21
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8Q LOSS MUTATED           1         3         0         2          0
  8Q LOSS WILD-TYPE        13        16        12        33         15
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED            3          4        1
  8Q LOSS WILD-TYPE         29         54       18
D56V5, multiclass
             clus
vv            8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  I OR II NOS               2                10
  STAGE 0                   2                 5
  STAGE I                   4                24
  STAGE IA                  1                16
  STAGE IB                  2                25
  STAGE II                  1                21
  STAGE IIA                 1                13
  STAGE IIB                 3                16
  STAGE IIC                 0                12
  STAGE III                 2                33
  STAGE IIIA                0                15
  STAGE IIIB                3                29
  STAGE IIIC                4                54
  STAGE IV                  1                18
[1] 14  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                T0+T1 T2 T3 T4
  8Q LOSS MUTATED       1  7  4  8
  8Q LOSS WILD-TYPE    62 64 70 59
D56V6, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               1                62
  T2                  7                64
  T3                  4                70
  T4                  8                59
[1] 4 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                 N0  N1  N2  N3
  8Q LOSS MUTATED    17   3   2   3
  8Q LOSS WILD-TYPE 151  58  36  44
D56V7, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              17               151
  N1               3                58
  N2               2                36
  N3               3                44
[1] 4 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                 M0  M1 M1A M1B M1C
  8Q LOSS MUTATED    25   0   1   0   0
  8Q LOSS WILD-TYPE 281   4   2   4   9
D56V8, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               25               281
  M1                0                 4
  M1A               1                 2
  M1B               0                 4
  M1C               0                 9
[1] 5 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
  8Q LOSS MUTATED    10   6
  8Q LOSS WILD-TYPE 119  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10    6
  8Q LOSS WILD-TYPE  119   81
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               10               119
  YES               6                81
[1] 2 2
[1] FALSE
D56V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  25
  8Q LOSS WILD-TYPE  42 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   25
  8Q LOSS WILD-TYPE   42  279
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                1                42
  YES              25               279
[1] 2 2
[1] FALSE
D56V11, continuous
D56V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    10  16
  8Q LOSS WILD-TYPE 121 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10   16
  8Q LOSS WILD-TYPE  121  201
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              10               121
  MALE                16               201
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         0    23
  8Q LOSS WILD-TYPE     5                         1   303
D56V13, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  23               303
[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"
D56V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  24
  8Q LOSS WILD-TYPE   6 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   24
  8Q LOSS WILD-TYPE    6  310
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              24               310
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   101 115
  9P LOSS WILD-TYPE  67  50
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              216               117 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              115                50 
$`9P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.47       111.09        32.42        70.16        28.08        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JL 
       85.32        68.22        86.76        44.19         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF 
       56.19        59.57        15.25        46.98        61.38        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
        6.31         9.34       103.59        26.37        29.23        93.21 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
       54.31        21.44        25.78       110.24        47.87        13.68 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GP 
       23.11        29.72        10.22         4.18        38.93        87.62 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        5.56        24.07         4.01        21.93         5.72         9.90 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       14.60        48.79        35.80        51.12        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
        9.99        44.52        25.15         4.93         6.64        17.56 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       13.15         0.20        23.15        13.35        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B 
       10.55         8.12         1.12         1.35         4.31        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
        4.34        15.85         9.21         1.18        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       62.79         8.55         1.08         9.50        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 
        9.99         2.43        32.15         8.09        11.31         9.67 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       51.12        34.29        17.98        60.00        47.21        30.08 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        55.69         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF 
       13.02        36.33        98.27         6.18         9.53         2.73 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
        7.96       125.65       111.91        56.02        25.08        26.99 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       60.49        53.16       124.31       122.73         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        15.95        12.72         3.22        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.95        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       12.95         5.72        25.18         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
       11.11        34.88        13.45        28.60        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
       36.07         6.58        17.72         1.87        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        9.04        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       15.72         6.71         2.20        64.47         3.45        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       14.24         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       11.08        30.87        47.38         8.65         8.81        49.15 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.39         0.82        53.85         3.22         7.36        28.73 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       10.78         5.98         6.41         0.20         0.99         0.13 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 
        7.23         0.85        11.61        44.28        84.72        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       12.16        14.70        10.65        14.50        14.50        14.50 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 
       15.81        11.05         5.79         0.33         0.69         8.98 
TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 
       60.03        10.98        71.01        11.84         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY 
       18.67        21.07        13.12         3.72        21.83         5.36 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94        12.07         6.18         8.22         6.67         5.98 

$`9P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
        3.02         6.97         6.97         8.52       110.79        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD 
       45.83        81.24         8.38        21.14        88.50        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
        7.50        36.16        64.44       114.67        46.32        82.29 
TCGA-D3-A3CE TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
       13.32        54.74        31.30        32.28        32.61        52.01 
TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
       17.72        22.06        15.19       142.45       108.79        75.65 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I7 
      124.47        11.44        11.31        13.22        10.03        36.69 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5SH 
       22.36        19.36         7.00        14.83         0.13        19.00 
TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29B 
        0.20         6.31        12.20         5.13         7.99         9.90 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 
       36.85        39.62         8.84        30.44        49.22        36.30 
TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 
       36.33        19.43        16.01        34.98         8.84         2.70 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MQ 
       47.51        29.46        44.25        14.56        63.42        21.60 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD 
       52.67         5.56        51.62        22.92        21.60        27.35 
TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N 
       18.41        38.40        76.41       114.15         4.21        42.84 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7U8 
       78.44        11.80         1.51        13.08         6.58         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1Z0 TCGA-FS-A1Z4 
        5.36        13.28         4.70         3.29        23.80        15.52 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT 
       19.53         7.17        12.92        12.89        52.08        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
        8.68         5.23        14.20         2.27         0.16        17.33 
TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 TCGA-LH-A9QB 
        9.90        31.33        10.13        16.24        11.84         0.43 
TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT 
       18.05       164.19         2.99       185.16         5.49         3.42 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YG-AA3P 
        1.08        19.96         4.70 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              0.13 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           125.65            185.16 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           13.745            17.720 
[1] "0.1 - 125.7 (13.7)" "0.1 - 185.2 (17.7)"
[1] "hr=" "1.4"
D57V2, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   104 115
  9P LOSS WILD-TYPE  69  51
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              219               120 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              115                51 
$`9P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.57       112.04       112.57        71.80        28.08        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JL 
      103.10       168.00        86.76        62.07        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF 
       56.19        59.57        58.06        46.98        86.93        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
      145.12        22.62        26.89       125.79       137.92       178.32 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GP 
      125.19        30.84        11.61        58.52        89.13       137.79 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z1 
      129.63       117.17       151.53        54.67        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       22.29        11.11         9.90        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
      117.21       194.83       176.55        35.93       107.34        53.92 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       65.92        68.09       215.44        13.87        10.16        68.25 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       17.29        52.01        29.82        27.22        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       14.70         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
       13.55        47.84        13.97        63.78        72.07         2.60 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       18.61        56.42        37.35        55.92        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       17.92        46.82        39.29        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      161.03       208.04        48.72        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
      126.81        13.91        14.30        55.59        94.82       129.27 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML 
       19.76        47.28       268.73        16.96       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
      167.90        47.54       248.65       134.40       162.48       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JH 
      172.18        64.08        34.32        53.19       201.80       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
      148.08        31.40        35.44        13.94         9.17        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19L 
       48.89        12.59        13.02        26.37       152.35       131.51 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       61.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL 
       23.34        31.27        32.05       247.04        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC 
        6.77        92.98       174.21        15.72       210.08        34.82 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      216.92        48.59       228.59        20.91         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
       48.85       357.37        53.52        15.45        32.75       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 
      133.55        11.41       148.80        49.48        27.09        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        12.43        26.73        49.45 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.20        22.92        47.54         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
      139.89        84.72        62.79        32.48        39.58        12.62 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-QB-A6FS 
       50.10        21.37        59.41        65.88       294.77         6.67 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA21 
        0.33         0.69        63.02       121.08        42.08       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        54.38         8.61        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       52.34        22.68        43.73        10.36        15.16        36.03 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

$`9P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 
       17.03        61.02        12.99        16.67       133.25        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD 
       90.90        95.74        65.49        23.77       115.53        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
      113.52        42.08        66.08       130.72        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
       60.23        55.73        56.35        32.94        63.81       135.75 
TCGA-D3-A5GS TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM 
       18.18        79.59        15.19       228.99       170.20        95.24 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A6EA TCGA-D9-A6EC 
      161.00        29.06         3.65         6.41        25.18        66.25 
TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       20.38        61.18        23.44        28.60        10.49        15.68 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A183 
       17.85        54.02         6.35        12.20         8.65        26.89 
TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R 
       68.15        63.35        80.61        64.64        56.84        14.47 
TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK 
      369.93       102.90        36.82        86.14        89.33        54.74 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       44.88        21.67        28.83        61.51       103.27       103.20 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC 
      204.66        96.23        43.23        71.21        53.26        51.62 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19A 
      127.20        36.95        27.35        51.35        50.76        77.75 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
      268.93         6.44        44.05        79.99        43.82        20.15 
TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD 
       16.37        80.32        15.16         7.00        38.27        29.46 
TCGA-FR-A8YE TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       94.39       202.65        28.08        40.27         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F8 
       23.93        74.73        53.16        26.56        27.02       174.84 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 
       77.88         0.16        19.30         9.90       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-AA1O 
       64.44        46.36       357.04        18.05       212.22         4.01 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-YG-AA3P 
      219.16        38.56         3.75         2.20        30.18        14.43 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.20              0.16 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           357.37            369.93 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            50.89             46.87 
[1] "0.2 - 357.4 (50.9)" "0.2 - 369.9 (46.9)"
[1] "hr=" "1.1"
D57V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P LOSS MUTATED                   39             2
  9P LOSS WILD-TYPE                 22             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9P LOSS MUTATED                                          54
  9P LOSS WILD-TYPE                                        18
                   vv
clus                REGIONAL LYMPH NODE
  9P LOSS MUTATED                   131
  9P LOSS WILD-TYPE                  78
D57V4, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  DISTANT METASTASIS                                     39                22
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              54                18
  REGIONAL LYMPH NODE                                   131                78
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  9P LOSS MUTATED            10       4      18        9       17       15
  9P LOSS WILD-TYPE           2       3      10        8       10        7
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9P LOSS MUTATED          10        12         8        23          7
  9P LOSS WILD-TYPE         4         7         4        12          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           24         36       13
  9P LOSS WILD-TYPE          8         22        6
D57V5, multiclass
             clus
vv            9P LOSS MUTATED 9P LOSS WILD-TYPE
  I OR II NOS              10                 2
  STAGE 0                   4                 3
  STAGE I                  18                10
  STAGE IA                  9                 8
  STAGE IB                 17                10
  STAGE II                 15                 7
  STAGE IIA                10                 4
  STAGE IIB                12                 7
  STAGE IIC                 8                 4
  STAGE III                23                12
  STAGE IIIA                7                 8
  STAGE IIIB               24                 8
  STAGE IIIC               36                22
  STAGE IV                 13                 6
[1] 14  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                T0+T1 T2 T3 T4
  9P LOSS MUTATED      39 48 49 44
  9P LOSS WILD-TYPE    24 23 25 23
D57V6, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              39                24
  T2                 48                23
  T3                 49                25
  T4                 44                23
[1] 4 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                 N0  N1  N2  N3
  9P LOSS MUTATED   110  41  23  29
  9P LOSS WILD-TYPE  58  20  15  18
D57V7, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             110                58
  N1              41                20
  N2              23                15
  N3              29                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"
                   vv
clus                 M0  M1 M1A M1B M1C
  9P LOSS MUTATED   197   2   2   2   8
  9P LOSS WILD-TYPE 109   2   1   2   1
D57V8, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              197               109
  M1                2                 2
  M1A               2                 1
  M1B               2                 2
  M1C               8                 1
[1] 5 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
  9P LOSS MUTATED   81 58
  9P LOSS WILD-TYPE 48 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     81   58
  9P LOSS WILD-TYPE   48   29
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               81                48
  YES              58                29
[1] 2 2
[1] FALSE
D57V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    26 200
  9P LOSS WILD-TYPE  17 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     26  200
  9P LOSS WILD-TYPE   17  104
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               26                17
  YES             200               104
[1] 2 2
[1] FALSE
D57V11, continuous
D57V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    96 131
  9P LOSS WILD-TYPE  35  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     96  131
  9P LOSS WILD-TYPE   35   86
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              96                35
  MALE               131                86
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       3                         1   211
  9P LOSS WILD-TYPE     2                         0   115
D57V13, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                 211               115
[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"
D57V14, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2 219
  9P LOSS WILD-TYPE   5 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  219
  9P LOSS WILD-TYPE    5  115
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             219               115
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   77 92
  9Q LOSS WILD-TYPE 91 73
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              169               164 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               92                73 
$`9Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J7 
       16.47        32.42        70.16        28.08        45.83        85.32 
TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       86.76        92.42        59.57        15.25        46.98        61.38 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T 
      103.59        26.37        29.23        54.31        21.44        25.78 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI 
      110.24        47.87        23.11        29.72        10.22         4.18 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A6E9 TCGA-DA-A1HV 
       38.93        87.62         5.56        24.07         9.90        48.79 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       35.80        39.19        13.68         9.99        44.52        25.15 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UN 
        4.93         6.64        17.56         0.20        23.15        13.22 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       10.55         8.12         1.12        60.23         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N 
        9.21         1.18        11.15         8.55         1.08         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.09         9.99        32.15         8.09        11.31 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       36.30        51.12        34.29        17.98        60.00        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       30.08        19.43        35.54        28.31        33.83         5.42 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK 
       13.02        98.27         6.18         2.73         7.96       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      111.91        56.02        26.99        21.60        60.49        53.16 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73         3.68        30.15        13.81        15.95 
TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22         0.95        18.41        21.73 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
       33.60        31.40        18.61        12.95         5.72        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19P 
        3.78         3.52        11.11        34.88        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV 
        9.57         6.58        17.72        12.62        11.74        22.49 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY 
        1.71        15.72         6.71         2.20        64.47        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       14.24         7.30         3.39        20.38         8.22        11.08 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW 
       30.87        47.38         8.65         8.81        49.15        27.39 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FB 
        0.82         5.23        53.85         3.22        28.73         5.98 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 
        6.41         0.20         0.99         0.16         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       11.61        44.28        84.72        15.42        12.16        14.70 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 
       10.65        14.50        14.50        15.81        11.05         0.33 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZM 
        8.98        60.03        10.98        71.01        11.84        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-YG-AA3O 
       21.07        13.12        21.83         5.36        12.07         6.18 
TCGA-Z2-AA3S 
        6.67 

$`9Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 
        3.02         6.97         6.97         8.52       111.09       110.79 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       22.55        81.24        10.29         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        11.41        44.19         7.50        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       56.19        64.44       114.67        46.32        82.29        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       24.00         6.31         9.34        93.21        54.74        31.30 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC 
       32.28        32.61        52.01        13.68        17.72        22.06 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ 
       15.19       142.45       108.79        75.65       124.47        11.44 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01        21.93         5.72        11.31        13.22        14.60 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       51.12        10.03        36.69        22.36        19.36         7.00 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 
       14.83        13.15         0.13        19.00        13.35         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       11.57         6.31         1.35        12.20         5.13         4.31 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
        7.99         9.90        37.97        62.79        36.85        39.62 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.84        30.44         2.43        49.22         9.67        36.33 
TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       16.01        55.69         1.15        34.98        36.33         8.84 
TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
        2.70        47.51         9.53        29.46        44.25        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AH 
       63.42        25.08        52.67         5.56        51.62        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19A 
        3.22        22.92        21.60        27.35        38.40        76.41 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19S 
       11.90       114.15         4.21        13.45        42.84        36.07 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
       78.44        11.80         1.87         1.51        13.08         9.04 
TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 
        6.58         5.62        18.41        85.74         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       13.28         4.70         3.29         3.45        23.80        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
        7.33        19.53         7.17        12.92        12.89        52.08 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD 
       40.64         8.68         7.36        14.20        10.78         2.27 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        0.13        17.33         9.90        31.33        10.13        16.24 
TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 
       11.84        14.50         0.43         5.79        18.05         0.69 
TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      164.19         2.99       185.16         5.49         6.48         7.10 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3P 
        3.72         3.42         1.08        19.96         1.94         4.70 
TCGA-Z2-A8RT TCGA-Z2-AA3V 
        8.22         5.98 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.16              0.13 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           125.65            185.16 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            15.95             13.40 
[1] "0.2 - 125.7 (15.9)" "0.1 - 185.2 (13.4)"
[1] "hr=" "1.2"
D58V2, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   80 92
  9Q LOSS WILD-TYPE 93 74
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              172               167 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               92                74 
$`9Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J7 
       16.57       112.57        71.80        28.08        90.90       103.10 
TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       86.76       171.58        59.57        58.06        46.98        86.93 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T 
      103.59        39.75        45.30       145.12        22.62        26.89 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI 
      125.79       137.92       125.19        30.84        11.61        58.52 
TCGA-D3-A8GL TCGA-D3-A8GP TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
       89.13       137.79       129.63       117.17       151.53        54.67 
TCGA-D9-A1X3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 
       18.12         9.90        48.89        36.03       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
       35.93       107.34        53.92        65.92        68.09       215.44 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       10.16        68.25        52.01        27.22        94.98        33.73 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D 
      133.81       151.27        91.56       168.26        13.55        13.97 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       72.07         2.60        18.61        56.42        37.35        55.92 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC 
      195.02        17.92        46.82        36.82        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL 
      314.56       161.03       208.04        48.72        89.33        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M8 
       75.48        90.97        13.91        55.59       129.27        19.76 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
      268.73        16.96       158.63       203.05       167.90       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       43.23       134.40       162.48       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
       54.51        13.81        23.47        36.95        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
      201.80        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       13.94         9.17        98.40        48.89        12.59        26.37 
TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
      152.35        61.05       162.08        50.89         8.88       148.18 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 
       31.27        32.05        46.98        33.21        15.72       210.08 
TCGA-FR-A8YC TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       34.82       216.92       228.59        20.91        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      357.37        53.52        15.45        32.75       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       11.41       148.80        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       50.14        28.73        26.73        49.45         0.20        22.92 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 
        0.16         7.23         2.04        11.74       139.89        84.72 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       62.79        32.48        39.58        12.62        50.10        59.41 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V 
       65.88       294.77         0.33        63.02       121.08        42.08 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZX 
      105.04        24.03        90.28        56.98        59.41        22.68 
TCGA-WE-A8ZY TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3S 
       43.73        15.16        36.03        93.07 

$`9Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 
       17.03        61.02        12.99        16.67       112.04       133.25 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       31.59        95.74        43.43        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        11.87        62.07       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       56.19        66.08       130.72        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       24.53        13.87         9.34       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A8GC 
       32.94        63.81       135.75       178.32        18.18        79.59 
TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GQ 
       15.19       228.99       170.20        95.24       161.00        29.06 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA 
        3.65         6.41        11.34        22.29        11.11        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB 
       66.25        22.95       117.21        20.38        61.18        23.44 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH 
       28.60        10.49        15.68        13.87        17.85        54.02 
TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       17.29         6.35        12.20        29.82         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       26.89        68.15         4.96        63.35        80.61        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       63.78        64.64        56.84        14.47       369.93        25.87 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GR 
      102.90        39.29        86.14        54.74       126.81        14.30 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        21.67        28.83        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MT 
      103.27       103.20       204.66        96.23        47.54        71.21 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       53.26        51.62       138.81       172.18       127.20        64.08 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19J 
       27.35        50.76        77.75        13.02       268.93         6.44 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      131.51        44.05        37.25        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A42K TCGA-FR-A3YN 
       20.15        16.37       247.04        80.32         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
      174.21        15.16         7.00        38.27        29.46        94.39 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZG 
       48.59       202.65        28.08         7.79        40.27         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F4 
       47.38        23.93        74.73        53.16        26.56        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
      174.84        12.43        77.88        47.54        19.30         9.90 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-LH-A9QB 
      117.93        10.13        64.44        46.36        21.37       357.04 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-AA1O TCGA-W3-AA1W 
        6.67        18.05         0.69       212.22         4.01       219.16 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
       38.56        54.38         8.61        52.34         3.75         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3V 
       30.18        10.36        14.43        23.64        11.74 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.16              0.69 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           357.37            369.93 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            54.59             46.32 
[1] "0.2 - 357.4 (54.6)" "0.7 - 369.9 (46.3)"
[1] "hr=" "1"  
D58V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q LOSS MUTATED                   33             2
  9Q LOSS WILD-TYPE                 28             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9Q LOSS MUTATED                                          44
  9Q LOSS WILD-TYPE                                        28
                   vv
clus                REGIONAL LYMPH NODE
  9Q LOSS MUTATED                    98
  9Q LOSS WILD-TYPE                 111
D58V4, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     33                28
  PRIMARY TUMOR                                           2                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              44                28
  REGIONAL LYMPH NODE                                    98               111
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  9Q LOSS MUTATED             8       3      15        6       13       10
  9Q LOSS WILD-TYPE           4       4      13       11       14       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9Q LOSS MUTATED           8        11         7        21          6
  9Q LOSS WILD-TYPE         6         8         5        14          9
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           21         21       11
  9Q LOSS WILD-TYPE         11         37        8
D58V5, multiclass
             clus
vv            9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  I OR II NOS               8                 4
  STAGE 0                   3                 4
  STAGE I                  15                13
  STAGE IA                  6                11
  STAGE IB                 13                14
  STAGE II                 10                12
  STAGE IIA                 8                 6
  STAGE IIB                11                 8
  STAGE IIC                 7                 5
  STAGE III                21                14
  STAGE IIIA                6                 9
  STAGE IIIB               21                11
  STAGE IIIC               21                37
  STAGE IV                 11                 8
[1] 14  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                T0+T1 T2 T3 T4
  9Q LOSS MUTATED      33 35 39 35
  9Q LOSS WILD-TYPE    30 36 35 32
D58V6, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              33                30
  T2                 35                36
  T3                 39                35
  T4                 35                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"
                   vv
clus                N0 N1 N2 N3
  9Q LOSS MUTATED   89 31 21 19
  9Q LOSS WILD-TYPE 79 30 17 28
D58V7, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              89                79
  N1              31                30
  N2              21                17
  N3              19                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"
                   vv
clus                 M0  M1 M1A M1B M1C
  9Q LOSS MUTATED   154   2   2   2   6
  9Q LOSS WILD-TYPE 152   2   1   2   3
D58V8, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              154               152
  M1                2                 2
  M1A               2                 1
  M1B               2                 2
  M1C               6                 3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   66 42
  9Q LOSS WILD-TYPE 63 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     66   42
  9Q LOSS WILD-TYPE   63   45
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               66                63
  YES              42                45
[1] 2 2
[1] FALSE
D58V10, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    22 156
  9Q LOSS WILD-TYPE  21 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     22  156
  9Q LOSS WILD-TYPE   21  148
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               22                21
  YES             156               148
[1] 2 2
[1] FALSE
D58V11, continuous
D58V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    76 102
  9Q LOSS WILD-TYPE  55 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     76  102
  9Q LOSS WILD-TYPE   55  115
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              76                55
  MALE               102               115
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       2                         0   166
  9Q LOSS WILD-TYPE     3                         1   160
D58V13, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 166               160
[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"
D58V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     3 171
  9Q LOSS WILD-TYPE   4 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3  171
  9Q LOSS WILD-TYPE    4  163
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             171               163
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   92 94
  10P LOSS WILD-TYPE 76 71
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               186                147 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                94                 71 
$`10P LOSS MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        6.97         6.97        16.47       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      110.79        28.08        22.55        88.50        86.76        11.41 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
        7.50         6.31        56.19        64.44        59.57        46.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       13.32        24.00         9.34        26.37        29.23        54.74 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       54.31        32.28        25.78        52.01        47.87        13.68 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP 
       23.11        22.06        10.22         4.18       142.45        87.62 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA 
        5.56        24.07        21.93         5.72         9.90        11.31 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       14.60        35.80        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH 
       36.69        25.15         4.93        17.56         0.20        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 
       13.35        13.22         6.31         8.12         1.12         4.31 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H 
       60.23        15.85         9.21         1.18         8.55        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
        1.08        39.62        12.03         8.09        30.44        32.15 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE 
        8.09        36.30         9.67        51.12        34.29        60.00 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       47.21        30.08        19.43        28.31        33.83        55.69 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
        5.42         1.15        13.02        36.33        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
        6.18        44.25         7.96       125.65        56.02        26.99 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       53.16         5.56       124.31       122.73         3.68        30.15 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 
       22.22         0.95        18.41        21.73        33.60         5.72 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S 
        3.52        11.90        34.88        13.45        34.68        36.07 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
        6.58        17.72        11.80         1.87         1.51        12.62 
TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       11.74         6.58        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX 
       85.74        15.72         6.71         3.58         3.29         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
       23.80        14.24         7.33         7.30        20.38         8.22 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       11.08         7.17        30.87        12.92        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.81         8.68        27.39         0.82         7.36        28.73 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        2.27         0.16         7.23        31.33        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       15.42        12.16        10.65        14.50        14.50        14.50 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 
       15.81        11.05         0.33         0.69         8.98        71.01 
TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       11.84        18.67         3.72        21.83         5.36         1.08 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94        12.07         6.18         4.70         6.67         5.98 

$`10P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
        3.02         8.52        45.83        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
        8.38        21.14        68.22        44.19        36.16        92.42 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML 
      114.67        15.25        46.32        82.29        61.38         6.31 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL 
      103.59        93.21        31.30        21.44        32.61       110.24 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       17.72        29.72        15.19       108.79        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
      124.47        11.44         4.01        13.22        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       10.03        22.36         6.64        19.36         7.00        14.83 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       13.15         0.13        23.15         0.20        11.57        10.55 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B 
        1.35        12.20         5.13         4.34         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       37.97        11.15        62.79         9.50         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GK 
        2.43        11.31        49.22        36.33        17.98        16.01 
TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       35.54        34.98         8.84        47.51         9.53        29.46 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ 
        2.73        14.56        63.42       111.91        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JD 
       60.49        52.67        51.62        13.81        15.95        27.35 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        18.61        12.95        38.40        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
        3.78        11.11       114.15         4.21        28.60        42.84 
TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A7U9 TCGA-FR-A7UA 
        9.57        78.44        13.08         9.04         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB 
        2.20         4.70        64.47        11.01        15.52         3.39 
TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ 
       19.53        12.89        52.08        49.15        40.64         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       53.85         3.22        14.20        10.78         5.98         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
        0.20         0.99         0.13        17.33         9.90         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-LH-A9QB 
       11.61        44.28        84.72        14.70        11.84         0.43 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        5.79        18.05       164.19        60.03         2.99        10.98 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO 
      185.16         5.49         6.48         7.10        21.07        13.12 
TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-Z2-A8RT 
        3.42        19.96         8.22 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.16               0.13 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            142.45             185.16 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             14.50              15.25 
[1] "0.2 - 142.4 (14.5)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1.2"
D59V2, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   94 94
  10P LOSS WILD-TYPE 79 72
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               188                151 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                94                 72 
$`10P LOSS MUTATED`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       61.02        12.99        16.57       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      133.25        28.08        31.59       115.53        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
      113.52        12.10        56.19        66.08        59.57        46.98 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       60.23        24.53         9.34        39.75        45.30        55.73 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
      145.12        32.94        26.89       135.75       137.92       178.32 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GP 
      125.19        79.59        11.61        58.52       228.99       137.79 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      129.63       117.17        54.67        18.12        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.90        25.18        22.95        36.03       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 
       35.93       107.34        61.18        53.92        65.92       215.44 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 
       10.16        54.02        17.29        52.01         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       33.73         4.96       133.81        91.56       168.26        13.55 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        64.64         2.60        56.84        56.42        37.35 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
      369.93       195.02        17.92        36.82        39.29        59.28 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
       67.43       161.03       208.04        48.72        89.33        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       90.97       126.81        13.91        14.30        55.59        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
      129.27        28.83        19.76       103.20        16.96       158.63 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      167.90       248.65       162.48        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        54.51       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19       201.80        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L 
      148.08         9.17        12.59        13.02       152.35       131.51 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND 
      162.08        37.25         8.88       148.18        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       20.15        31.27        32.05        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       210.08        15.16 
TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       94.39        48.59       202.65        20.91         7.79        27.72 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
      357.37        53.52        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
      101.26       133.55        11.41        26.56        49.48        27.09 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A264 
       66.67        28.73        77.88         0.16         7.23       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LK 
       10.13        64.44        62.79        32.48        12.62        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 
       21.37        59.41        65.88       294.77         0.33         0.69 
TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZX 
       63.02       105.04        24.03        90.28        52.34        22.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
       43.73         2.20        10.36        15.16        36.03        14.43 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

$`10P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       17.03        16.67        90.90        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
       65.49        23.77       168.00        62.07        42.08       171.58 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML 
      130.72        58.06        46.32       166.52        86.93        13.87 
TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL 
      103.59       174.84        56.35        22.62        63.81       125.79 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       18.18        30.84        15.19       170.20        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      161.00        29.06       151.53         3.65         6.41        11.34 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC 
       66.25        48.89       117.21        20.38        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       28.60        10.49        15.68        13.87        17.85        68.25 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
        6.35        12.20        29.82        27.22        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       68.15       151.27        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 
       63.78        18.61        14.47        55.92        25.87        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT 
      102.90        86.14       314.56        54.74        79.66        44.88 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI 
       21.67        61.51        47.28       103.27       268.73       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
       96.23       203.05        47.54        43.23       134.40        71.21 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A195 
       51.62        13.81        23.47        27.35        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F 
       13.94        50.76        77.75        98.40        48.89        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 
      268.93         6.44        61.05        44.05        50.89        79.99 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
       16.37       247.04         7.00        38.27        34.82        29.46 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZK 
      216.92       228.59        28.08        48.85        40.27        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       74.73       148.80        53.16        27.02        77.82        50.14 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
      174.84        12.43        26.73        49.45         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       47.54        19.30         9.90         2.04        11.74       139.89 
TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       84.72        39.58        46.36       357.04         6.67        18.05 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 
      212.22       121.08         4.01        42.08       219.16        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-AAA0 
       54.38         8.61        56.98        59.41         3.75        30.18 
TCGA-Z2-A8RT 
       23.64 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.16               0.20 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            369.93             357.04 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             53.72              47.54 
[1] "0.2 - 369.9 (53.7)" "0.2 - 357.0 (47.5)"
[1] "hr=" "1"  
D59V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10P LOSS MUTATED                   34             3
  10P LOSS WILD-TYPE                 27             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10P LOSS MUTATED                                          48
  10P LOSS WILD-TYPE                                        24
                    vv
clus                 REGIONAL LYMPH NODE
  10P LOSS MUTATED                   110
  10P LOSS WILD-TYPE                  99
D59V4, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  DISTANT METASTASIS                                      34                 27
  PRIMARY TUMOR                                            3                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               48                 24
  REGIONAL LYMPH NODE                                    110                 99
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  10P LOSS MUTATED             7       4      16       12       15       13
  10P LOSS WILD-TYPE           5       3      12        5       12        9
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10P LOSS MUTATED           6         6         6        23         11
  10P LOSS WILD-TYPE         8        13         6        12          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           17         36        9
  10P LOSS WILD-TYPE         15         22       10
D59V5, multiclass
             clus
vv            10P LOSS MUTATED 10P LOSS WILD-TYPE
  I OR II NOS                7                  5
  STAGE 0                    4                  3
  STAGE I                   16                 12
  STAGE IA                  12                  5
  STAGE IB                  15                 12
  STAGE II                  13                  9
  STAGE IIA                  6                  8
  STAGE IIB                  6                 13
  STAGE IIC                  6                  6
  STAGE III                 23                 12
  STAGE IIIA                11                  4
  STAGE IIIB                17                 15
  STAGE IIIC                36                 22
  STAGE IV                   9                 10
[1] 14  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                 T0+T1 T2 T3 T4
  10P LOSS MUTATED      40 42 30 46
  10P LOSS WILD-TYPE    23 29 44 21
D59V6, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1               40                 23
  T2                  42                 29
  T3                  30                 44
  T4                  46                 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"
                    vv
clus                 N0 N1 N2 N3
  10P LOSS MUTATED   90 38 23 26
  10P LOSS WILD-TYPE 78 23 15 21
D59V7, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               90                 78
  N1               38                 23
  N2               23                 15
  N3               26                 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"
                    vv
clus                  M0  M1 M1A M1B M1C
  10P LOSS MUTATED   175   1   2   1   5
  10P LOSS WILD-TYPE 131   3   1   3   4
D59V8, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               175                131
  M1                 1                  3
  M1A                2                  1
  M1B                1                  3
  M1C                5                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   69 51
  10P LOSS WILD-TYPE 60 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     69   51
  10P LOSS WILD-TYPE   60   36
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                69                 60
  YES               51                 36
[1] 2 2
[1] FALSE
D59V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    22 172
  10P LOSS WILD-TYPE  21 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     22  172
  10P LOSS WILD-TYPE   21  132
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                22                 21
  YES              172                132
[1] 2 2
[1] FALSE
D59V11, continuous
D59V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    83 112
  10P LOSS WILD-TYPE  48 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     83  112
  10P LOSS WILD-TYPE   48  105
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               83                 48
  MALE                112                105
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       1                         0   182
  10P LOSS WILD-TYPE     4                         1   144
D59V13, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  182                144
[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"
D59V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4 187
  10P LOSS WILD-TYPE   3 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  187
  10P LOSS WILD-TYPE    3  147
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              187                147
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   102 102
  10Q LOSS WILD-TYPE  66  63
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               204                129 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               102                 63 
$`10Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        6.97        16.47       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       28.08        22.55        88.50        86.76        11.41         7.50 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
        6.31        92.42        56.19        64.44        59.57        15.25 
TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       46.98        13.32         9.34       103.59        26.37        29.23 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN 
       54.74        54.31        32.28        21.44        25.78        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       47.87        13.68        17.72        23.11        29.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS 
       10.22         4.18        75.65       124.47        87.62        24.07 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       21.93         5.72         9.90        11.31        13.22        14.60 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       35.80        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SH 
       25.15         4.93        17.56        14.83         0.20        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 
       13.35        13.22         6.31         8.12         1.12         4.31 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G 
       60.23        15.85         9.21         1.18        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
       36.85         1.08        39.62        12.03         8.09        30.44 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       32.15         8.09        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       28.31        33.83        55.69         5.42         1.15        13.02 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF 
       36.33        98.27         2.70         6.18         9.53         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
       44.25         7.96        14.56       125.65        56.02        26.99 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       124.31       122.73         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       15.95        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22         0.95        18.41        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
       31.40         5.72         3.78         3.52        11.90        34.88 
TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC 
       13.45        34.68        36.07         6.58        17.72        11.80 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
        1.51        12.62        11.74        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE 
       18.41        85.74        15.72         6.71         3.58         3.29 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.45        11.01        23.80        14.24         7.33         7.30 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
       20.38         8.22        11.08        30.87        12.92        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 
        8.65         8.81         8.68        27.39         0.82         7.36 
TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 
       28.73         5.98         2.27         0.16         7.23         0.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 
       44.28        31.33        10.13        16.24        12.16        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 
       10.65        14.50        14.50        15.81        11.05         0.33 
TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 
        0.69         8.98        71.01        11.84         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       18.67         3.72         3.42        21.83         5.36         1.08 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94        12.07         6.18         4.70         6.67         5.98 

$`10Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
        3.02         6.97         8.52        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH 
       85.32         8.38        21.14        68.22        44.19        36.16 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
      114.67        46.32        82.29        61.38        24.00         6.31 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GE TCGA-D3-A8GJ 
       93.21        31.30        32.61       110.24        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-DA-A1HV 
      108.79        38.93        11.44         5.56         4.01        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       51.12        10.03        22.36         6.64        19.36         7.00 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       13.15         0.13        23.15         0.20        11.57        10.55 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B 
        1.35        12.20         5.13         4.34         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       37.97        62.79         9.50         8.84         9.99         2.43 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 
       11.31        49.22        16.01        35.54        34.98         8.84 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ 
       47.51        29.46        63.42       111.91        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3JD TCGA-ER-A195 
       60.49        53.16        52.67        51.62        27.35        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G 
       12.95        38.40        76.41        25.18        11.11       114.15 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND 
        4.21        28.60        42.84         9.57        78.44         1.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       13.08         9.04         6.58         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG 
        4.70        64.47        15.52         3.39        19.53         7.17 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 
       12.89        52.08        49.15        40.64         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
        3.22        14.20        10.78         6.41         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A268 
        0.13        17.33         9.90        11.61        84.72        15.42 
TCGA-GN-A26D TCGA-GN-A8LL TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 
       14.70        14.50         0.43         5.79        18.05       164.19 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN 
       60.03         2.99        10.98       185.16         5.49        21.07 
TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-Z2-A8RT 
       13.12        19.96         8.22 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.16               0.13 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            125.65             185.16 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             14.53              15.42 
[1] "0.2 - 125.7 (14.5)" "0.1 - 185.2 (15.4)"
[1] "hr=" "1.1"
D60V2, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   105 102
  10Q LOSS WILD-TYPE  68  64
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               207                132 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               102                 64 
$`10Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       12.99        16.57       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       28.08        31.59       115.53        86.76        11.87       113.52 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 
       12.10       171.58        56.19        66.08        59.57        58.06 
TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       46.98        60.23         9.34       103.59        39.75        45.30 
TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN 
       55.73       145.12        32.94        22.62        26.89       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      137.92       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GS 
       11.61        58.52        95.24       161.00       137.79       117.17 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
      151.53        54.67        18.12        22.29        11.11         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 
       25.18        66.25        22.95        36.03       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 
       35.93       107.34        61.18        53.92        65.92       215.44 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17Z 
       15.68        10.16        54.02        17.29        52.01         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       94.98        33.73         4.96       133.81        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       13.55        13.97        72.07        64.64         2.60        56.84 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 
       56.42        37.35       369.93       195.02        17.92        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
      208.04        48.72        89.33        75.48        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        14.30        55.59        94.82       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        47.28       268.73       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      158.63       167.90       248.65        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB 
      127.20        36.95        64.08        34.32        53.19       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19C 
       51.35       109.58       148.08        31.40         9.17        48.89 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S 
       12.59        13.02       152.35       131.51       162.08        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
        8.88       148.18        43.82        20.15        31.27        32.05 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      210.08        15.16        94.39        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       20.91         7.79        27.72       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU 
       32.75        47.38       101.26       133.55        11.41        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FD 
       49.48        27.09        66.67        28.73        26.73        77.88 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        0.16         7.23         2.04       139.89       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       64.44        32.48        46.36        12.62        50.10        59.41 
TCGA-HR-A2OH TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A825 TCGA-W3-AA21 
       65.88       294.77         0.33         0.69        63.02       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZT 
       24.03        54.38         8.61        90.28        52.34         3.75 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       22.68        43.73         2.20        10.36        15.16        36.03 
TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       14.43        93.07        11.74 

$`10Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       17.03        61.02        16.67        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH 
      103.10        65.49        23.77       168.00        62.07        42.08 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
      130.72        46.32       166.52        86.93        24.53        13.87 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A8GE TCGA-D3-A8GJ 
      174.84        56.35        63.81       125.79        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW TCGA-D9-A1JX 
      170.20        89.13        29.06       129.63         3.65         6.41 
TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC 
       11.34        48.89       117.21        20.38        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV 
       28.60        10.49        13.87        17.85        68.25         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       12.20        29.82        27.22        14.70        26.89        68.15 
TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N 
      151.27        63.35        80.61        47.84        63.78        18.61 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GK 
       14.47        55.92        25.87        46.82       102.90        54.74 
TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MJ 
       79.66        44.88        21.67        61.51       103.27        96.23 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      203.05        47.54        43.23       134.40       162.48        71.21 
TCGA-EE-A3AC TCGA-EE-A3JD TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       51.62        27.35        35.44        13.94        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       98.40        26.37       268.93         6.44        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
       50.89        79.99        23.34        16.37       247.04        80.32 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z4 
        7.00        38.27        34.82        29.46       216.92        28.08 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS 
       48.85        40.27         9.70        23.93        74.73       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 
       53.16        27.02        77.82        50.14       174.84        12.43 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45         0.20        22.92        47.54        19.30         9.90 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A8LL TCGA-LH-A9QB 
       11.74        84.72        62.79        39.58        21.37       357.04 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        6.67        18.05       212.22       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-WE-A8K1 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA0 TCGA-Z2-A8RT 
      219.16        38.56        56.98        59.41        30.18        23.64 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.16               0.20 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            369.93             357.04 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             53.26              47.69 
[1] "0.2 - 369.9 (53.3)" "0.2 - 357.0 (47.7)"
[1] "hr=" "1.1"
D60V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10Q LOSS MUTATED                   32             4
  10Q LOSS WILD-TYPE                 29             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10Q LOSS MUTATED                                          52
  10Q LOSS WILD-TYPE                                        20
                    vv
clus                 REGIONAL LYMPH NODE
  10Q LOSS MUTATED                   126
  10Q LOSS WILD-TYPE                  83
D60V4, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      32                 29
  PRIMARY TUMOR                                            4                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               52                 20
  REGIONAL LYMPH NODE                                    126                 83
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  10Q LOSS MUTATED             9       3      18       13       16       12
  10Q LOSS WILD-TYPE           3       4      10        4       11       10
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10Q LOSS MUTATED           6        10         5        26         11
  10Q LOSS WILD-TYPE         8         9         7         9          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           20         35       13
  10Q LOSS WILD-TYPE         12         23        6
D60V5, multiclass
             clus
vv            10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  I OR II NOS                9                  3
  STAGE 0                    3                  4
  STAGE I                   18                 10
  STAGE IA                  13                  4
  STAGE IB                  16                 11
  STAGE II                  12                 10
  STAGE IIA                  6                  8
  STAGE IIB                 10                  9
  STAGE IIC                  5                  7
  STAGE III                 26                  9
  STAGE IIIA                11                  4
  STAGE IIIB                20                 12
  STAGE IIIC                35                 23
  STAGE IV                  13                  6
[1] 14  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                 T0+T1 T2 T3 T4
  10Q LOSS MUTATED      45 47 36 44
  10Q LOSS WILD-TYPE    18 24 38 23
D60V6, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1               45                 18
  T2                  47                 24
  T3                  36                 38
  T4                  44                 23
[1] 4 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                 N0 N1 N2 N3
  10Q LOSS MUTATED   97 45 24 28
  10Q LOSS WILD-TYPE 71 16 14 19
D60V7, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               97                 71
  N1               45                 16
  N2               24                 14
  N3               28                 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"
                    vv
clus                  M0  M1 M1A M1B M1C
  10Q LOSS MUTATED   187   1   2   3   8
  10Q LOSS WILD-TYPE 119   3   1   1   1
D60V8, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               187                119
  M1                 1                  3
  M1A                2                  1
  M1B                3                  1
  M1C                8                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   77 53
  10Q LOSS WILD-TYPE 52 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     77   53
  10Q LOSS WILD-TYPE   52   34
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                77                 52
  YES               53                 34
[1] 2 2
[1] FALSE
D60V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    27 186
  10Q LOSS WILD-TYPE  16 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     27  186
  10Q LOSS WILD-TYPE   16  118
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                27                 16
  YES              186                118
[1] 2 2
[1] FALSE
D60V11, continuous
D60V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    89 125
  10Q LOSS WILD-TYPE  42  92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     89  125
  10Q LOSS WILD-TYPE   42   92
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               89                 42
  MALE                125                 92
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       1                         0   200
  10Q LOSS WILD-TYPE     4                         1   126
D60V13, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  200                126
[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"
D60V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4 206
  10Q LOSS WILD-TYPE   3 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  206
  10Q LOSS WILD-TYPE    3  128
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              206                128
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    60  57
  11P LOSS WILD-TYPE 108 108
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               117                216 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                57                108 
$`11P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB 
       16.47        32.42        22.55        10.29        85.32        68.22 
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       11.41        92.42        56.19        15.25        46.98        61.38 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
        9.34        29.23        93.21        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM 
       23.11        29.72        22.06        10.22         4.18        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EG 
      124.47        87.62        21.93         5.72        11.31        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
       48.79        35.80        39.19        44.52        25.15        17.56 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A182 TCGA-EE-A20B 
        0.20        23.15        19.00        13.35         1.35        60.23 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
        4.34         1.18        37.97        11.15         1.08        39.62 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X 
        9.50        12.03         8.09         8.84         2.43         8.09 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 
       36.30         9.67        34.29        60.00        28.31        98.27 
TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
       63.42        25.08        26.99        53.16         5.56       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.68        30.15        21.60        21.60        16.14        22.22 
TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L 
       21.73        12.95         5.72         3.78         3.52        13.45 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A3EV 
       36.07         6.58         1.87         1.51         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1ZA 
        1.71        18.41        15.72        13.28        14.24         7.30 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FS-A4F5 
       11.08        30.87        47.38        27.39         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
       14.20        10.78         0.20        44.28        31.33        16.24 
TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-AA9O TCGA-WE-A8JZ 
       12.16        10.65        14.50        15.81        18.05        11.84 
TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-AAA3 TCGA-WE-AAA4 
        6.48        18.67        21.07        13.12         1.94        12.07 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
        6.18         4.70         8.22 

$`11P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
        3.02         6.97         6.97         8.52       111.09        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
      110.79        28.08        45.83        81.24         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       88.50        86.76        44.19         7.50        36.16         6.31 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       64.44        59.57       114.67        46.32        82.29        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H 
       24.00         6.31       103.59        26.37        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.31        32.28        21.44        32.61        25.78       110.24 
TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ 
       47.87        15.19       142.45       108.79        38.93        11.44 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HY 
        5.56        24.07         4.01         9.90        13.22        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       10.03        13.68         9.99        36.69         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
        6.64        19.36         7.00        14.83        13.15         0.13 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.22         0.20        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H 
        1.12        12.20         5.13         4.31        15.85         9.21 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S 
        7.99         9.90        62.79         8.55        36.85         9.99 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB 
       30.44        32.15        11.31        49.22        36.33        51.12 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       33.83        55.69         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       36.33         8.84         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       29.46         2.73        44.25         7.96        14.56       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA 
      111.91        56.02        21.60        60.49        52.67       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
        0.95        27.35        18.41        33.60        31.40        18.61 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       38.40        76.41        25.18        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
       34.88         4.21        28.60        42.84        34.68         9.57 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       17.72        78.44        11.80        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
        9.04         5.62        85.74         6.71         3.58         5.36 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        2.20         4.70         3.29        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       23.80        15.52         7.33         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       19.53         7.17        12.92        12.89        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15        40.64         8.68         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       53.85         3.22         5.98         6.41         2.27         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 
       11.61        84.72        10.13        15.42        14.70        11.84 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       14.50        14.50         0.43        11.05         5.79         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       164.19         8.98        60.03         2.99        10.98 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZT 
      185.16        71.01         5.49         7.10         3.72         3.42 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-AA3S TCGA-Z2-AA3V 
       21.83         5.36         1.08        19.96         6.67         5.98 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.20               0.13 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            124.47             185.16 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            16.240             13.745 
[1] "0.2 - 124.5 (16.2)" "0.1 - 185.2 (13.7)"
[1] "hr=" "1"  
D61V2, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    61  58
  11P LOSS WILD-TYPE 112 108
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               119                220 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                58                108 
$`11P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB 
       16.57       112.57        31.59        43.43       103.10       168.00 
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       11.87       171.58        56.19        58.06        46.98        86.93 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
        9.34        45.30       174.84       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM 
      125.19        30.84        79.59        11.61        58.52        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A4Z6 
      161.00       137.79        54.67         6.41        22.29        11.11 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 
       25.18        22.95        48.89        36.03       194.83       107.34 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       53.92       215.44        10.16        68.25        54.02        17.29 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
       14.70       133.81       151.27        13.55        47.84        13.97 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        18.61        56.42        37.35        14.47 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GE 
       25.87        17.92        36.82        39.29        67.43       161.03 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
       75.48       129.27        96.23        47.54       248.65       162.48 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 
       53.26       122.73         3.68        54.51        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C 
       34.32        53.19       109.58        13.94         9.17        48.89 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2ND TCGA-ER-A2NE 
       12.59       131.51        37.25         8.88        23.34        20.15 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7UA 
       80.32        46.98        33.21        92.98        15.72        38.27 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZW 
       20.91        27.72        15.45        32.75       101.26        49.48 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-GN-A262 
       66.67        28.73       174.84        12.43         0.20       139.89 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH 
      117.93        64.44        32.48        12.62        59.41        65.88 
TCGA-QB-AA9O TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       18.05        24.03        54.38        90.28        56.98        59.41 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       10.36        15.16        36.03        14.43        23.64 

$`11P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.67       112.04        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
      133.25        28.08        90.90        95.74        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      115.53        86.76        62.07       113.52        42.08        12.10 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       66.08        59.57       130.72        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H 
       24.53        13.87       103.59        39.75        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GQ 
      137.92        15.19       228.99       170.20        89.13        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 
      129.63       117.17       151.53         3.65        18.12        11.34 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        9.90        66.25       117.21        20.38       176.55        35.93 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       15.68        13.87        17.85        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       29.82        27.22         8.65        94.98        33.73        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
       68.15         4.96        91.56       168.26        63.35        80.61 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
       63.78        72.07        64.64        55.92       369.93       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH 
       46.82       102.90        86.14        59.28       314.56       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       48.72        89.33        54.74        79.66        90.97       126.81 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       13.91        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       158.63       203.05       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
       43.23       134.40        71.21       124.31        51.62        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JD 
       23.47       138.81       172.18       127.20       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       51.35       148.08        31.40        35.44        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       98.40        13.02        26.37       268.93       152.35         6.44 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05       162.08        50.89       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K 
       43.82        16.37        31.27        32.05       247.04         6.77 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD 
      174.21       210.08        15.16         7.00        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       94.39       216.92        48.59       228.59       202.65        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
        7.79        48.85       357.37        53.52        40.27         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       53.16        26.56        27.09        27.02        77.82        50.14 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       26.73        49.45        77.88        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 
       19.30         9.90         7.23         2.04        11.74        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
       10.13        62.79        39.58        46.36        50.10        21.37 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      357.04       294.77         6.67         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
       63.02       121.08         4.01        42.08       219.16       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       38.56         8.61        52.34         3.75        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-Z2-AA3S TCGA-Z2-AA3V 
        2.20        30.18        93.07        11.74 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.20               0.16 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            248.65             369.93 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            47.540             51.815 
[1] "0.2 - 248.7 (47.5)" "0.2 - 369.9 (51.8)"
[1] "hr=" "1.2"
D61V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P LOSS MUTATED                   17             2
  11P LOSS WILD-TYPE                 44             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11P LOSS MUTATED                                          30
  11P LOSS WILD-TYPE                                        42
                    vv
clus                 REGIONAL LYMPH NODE
  11P LOSS MUTATED                    71
  11P LOSS WILD-TYPE                 138
D61V4, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  DISTANT METASTASIS                                      17                 44
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               30                 42
  REGIONAL LYMPH NODE                                     71                138
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11P LOSS MUTATED             6       3       8        4       12        2
  11P LOSS WILD-TYPE           6       4      20       13       15       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11P LOSS MUTATED           1         7         4        13          5
  11P LOSS WILD-TYPE        13        12         8        22         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           14         24       10
  11P LOSS WILD-TYPE         18         34        9
D61V5, multiclass
             clus
vv            11P LOSS MUTATED 11P LOSS WILD-TYPE
  I OR II NOS                6                  6
  STAGE 0                    3                  4
  STAGE I                    8                 20
  STAGE IA                   4                 13
  STAGE IB                  12                 15
  STAGE II                   2                 20
  STAGE IIA                  1                 13
  STAGE IIB                  7                 12
  STAGE IIC                  4                  8
  STAGE III                 13                 22
  STAGE IIIA                 5                 10
  STAGE IIIB                14                 18
  STAGE IIIC                24                 34
  STAGE IV                  10                  9
[1] 14  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                 T0+T1 T2 T3 T4
  11P LOSS MUTATED      21 25 20 29
  11P LOSS WILD-TYPE    42 46 54 38
D61V6, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               21                 42
  T2                  25                 46
  T3                  20                 54
  T4                  29                 38
[1] 4 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                  N0  N1  N2  N3
  11P LOSS MUTATED    52  29  12  17
  11P LOSS WILD-TYPE 116  32  26  30
D61V7, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               52                116
  N1               29                 32
  N2               12                 26
  N3               17                 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"
                    vv
clus                  M0  M1 M1A M1B M1C
  11P LOSS MUTATED   104   2   2   0   6
  11P LOSS WILD-TYPE 202   2   1   4   3
D61V8, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               104                202
  M1                 2                  2
  M1A                2                  1
  M1B                0                  4
  M1C                6                  3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   42 37
  11P LOSS WILD-TYPE 87 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     42   37
  11P LOSS WILD-TYPE   87   50
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                42                 87
  YES               37                 50
[1] 2 2
[1] FALSE
D61V10, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    13 108
  11P LOSS WILD-TYPE  30 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13  108
  11P LOSS WILD-TYPE   30  196
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                13                 30
  YES              108                196
[1] 2 2
[1] FALSE
D61V11, continuous
D61V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    56  65
  11P LOSS WILD-TYPE  75 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     56   65
  11P LOSS WILD-TYPE   75  152
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               56                 75
  MALE                 65                152
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                         1   110
  11P LOSS WILD-TYPE     4                         0   216
D61V13, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  110                216
[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"
D61V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2 116
  11P LOSS WILD-TYPE   5 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2  116
  11P LOSS WILD-TYPE    5  218
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              116                218
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    74  63
  11Q LOSS WILD-TYPE  94 102
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               137                196 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                63                102 
$`11Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.47        32.42       110.79        22.55        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       85.32        68.22        11.41        92.42        56.19        64.44 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       15.25        46.98        61.38         9.34        29.23        93.21 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       52.01        13.68        17.72        23.11        29.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
       10.22         4.18       142.45        75.65       124.47        87.62 
TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        5.56        21.93        11.31        14.60        48.79        35.80 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       39.19        44.52        25.15        17.56        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20B 
       23.15        19.00        13.35         8.12         1.35        60.23 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       37.97        11.15         1.08        39.62         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.09         8.84        30.44         2.43        36.30         9.67 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MD 
       51.12        34.29        60.00        28.31        98.27         9.53 
TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       63.42        25.08        26.99        52.67         5.56       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.68        30.15        21.60        21.60        16.14        22.22 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       21.73        31.40        12.95         5.72         3.78         3.52 
TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE 
       13.45        36.07         6.58        17.72         1.87         1.51 
TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P 
       12.62         6.58        22.49         1.71        18.41        15.72 
TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZF 
       13.28        14.24         7.33         7.30        19.53        11.08 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F4 
       30.87        12.92        47.38        27.39         5.23         7.36 
TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
       28.73         2.27         0.20        31.33        10.13        16.24 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB 
       12.16        14.70        10.65        14.50        15.81         0.43 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
        5.79        18.05        10.98        11.84         5.49         6.48 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       18.67        21.07        13.12         5.36         1.08        19.96 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
        1.94        12.07         6.18         4.70         8.22 

$`11Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
        3.02         6.97         6.97         8.52       111.09        70.16 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       28.08        45.83         8.38        21.14        88.50        86.76 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ 
       44.19         7.50        36.16         6.31        59.57       114.67 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR 
       46.32        82.29        13.32        24.00         6.31       103.59 
TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       26.37        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GK 
       32.61        25.78       110.24        47.87        15.19       108.79 
TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 
       38.93        11.44        24.07         4.01         5.72         9.90 
TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       13.22        51.12        10.03        13.68         9.99        36.69 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
        4.93        22.36         6.64        19.36         7.00        14.83 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.13        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        1.12        12.20         5.13         4.31         4.34        15.85 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
        9.21         1.18         7.99         9.90        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       36.85         9.99        32.15         8.09        11.31        49.22 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       36.33        17.98        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        33.83        55.69         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       34.98        36.33         8.84         2.70         6.18        47.51 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       29.46         2.73        44.25         7.96        14.56       125.65 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
      111.91        56.02        21.60        60.49        53.16       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
        0.95        27.35        18.41        33.60        18.61        38.40 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       76.41        25.18        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 
        4.21        28.60        42.84        34.68         9.57        78.44 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A44A 
       11.80        13.08        11.74         9.04         5.62        85.74 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        6.71         3.58         5.36         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZB 
       64.47         3.45        11.01        23.80        15.52         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       20.38         8.22         7.17        12.89        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 
        8.81        49.15        40.64         8.68         0.82        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 
        3.22        14.20        10.78         5.98         6.41         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A8LK 
       11.61        44.28        84.72        15.42        11.84        14.50 
TCGA-GN-A8LL TCGA-OD-A75X TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       14.50        11.05         0.33         0.69       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZQ 
       60.03         2.99       185.16        71.01         7.10         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-Z2-AA3S TCGA-Z2-AA3V 
        3.42        21.83         6.67         5.98 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.20               0.13 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            142.45             185.16 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            16.140             14.005 
[1] "0.2 - 142.4 (16.1)" "0.1 - 185.2 (14.0)"
[1] "hr=" "1.2"
D62V2, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    75  64
  11Q LOSS WILD-TYPE  98 102
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               139                200 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                64                102 
$`11Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.57       112.57       133.25        31.59        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
      103.10       168.00        11.87       171.58        56.19        66.08 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       58.06        46.98        86.93         9.34        45.30       174.84 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      135.75       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
       11.61        58.52       228.99        95.24       161.00       137.79 
TCGA-D3-A8GR TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG 
      129.63        54.67         6.41        22.29        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
       48.89        36.03       194.83       107.34        53.92       215.44 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 
       13.87        10.16        68.25        54.02        17.29        94.98 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
       14.70       133.81        47.84        13.97         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       18.61        56.42        37.35        14.47       369.93        25.87 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GM 
       36.82        39.29        59.28        67.43       161.03        75.48 
TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT 
      129.27        47.28        96.23        47.54       248.65        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 
       53.26       122.73         3.68        54.51        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 
       34.32        53.19       109.58        31.40        13.94         9.17 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       48.89        12.59       131.51        37.25         8.88       148.18 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       23.34        20.15        31.27        80.32        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A7UA TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       92.98        15.72        38.27        20.91         7.79        27.72 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZW 
       40.27        15.45        32.75        47.38       101.26        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A264 
       27.02        66.67        28.73        77.88         0.20       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-GN-A9SD 
       10.13        64.44        32.48        39.58        12.62        59.41 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O TCGA-W3-AA1V TCGA-WE-A8JZ 
       65.88       357.04         6.67        18.05        42.08        24.03 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZY 
       38.56        54.38        90.28        56.98        59.41        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        2.20        30.18        10.36        15.16        36.03        14.43 
TCGA-Z2-A8RT 
       23.64 

$`11Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.67       112.04        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC 
       28.08        90.90        65.49        23.77       115.53        86.76 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ 
       62.07       113.52        42.08        12.10        59.57       130.72 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR 
       46.32       166.52        60.23        24.53        13.87       103.59 
TCGA-D3-A3MU TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       39.75        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A8GE TCGA-D3-A8GK 
       63.81        26.89       125.79       137.92        15.19       170.20 
TCGA-D3-A8GL TCGA-D3-A8GQ TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1X3 
       89.13        29.06       117.17       151.53         3.65        18.12 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I0 
       11.34        11.11         9.90        66.25       117.21        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      176.55        35.93        61.18        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV 
       28.60        10.49        15.68        17.85        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       12.20        29.82        27.22         8.65        33.73        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       68.15         4.96       151.27        91.56       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S 
       63.35        80.61        63.78        72.07        64.64        55.92 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD 
      195.02        17.92        46.82       102.90        86.14       314.56 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      208.04        48.72        89.33        54.74        79.66        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
      126.81        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF 
       21.67        28.83        19.76        61.51       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66       158.63       203.05       167.90 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
       43.23       134.40       162.48       124.31        51.62        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JB TCGA-EE-A3JD 
       23.47       138.81       172.18       127.20       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       51.35       148.08        35.44        50.76        77.75        98.40 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       13.02        26.37       268.93       152.35         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF 
       44.05       162.08        50.89        79.99        43.82        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       32.05       247.04         6.77       174.21       210.08        15.16 
TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
        7.00        34.82        29.46        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59       202.65        28.08        48.85       357.37        53.52 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        23.93        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
       53.16        26.56        27.09        77.82        50.14       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       12.43        26.73        49.45        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-OD-A75X 
       84.72        62.79        46.36        50.10        21.37       294.77 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K6 TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
      219.16       105.04         8.61        52.34         3.75        22.68 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.20               0.16 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            369.93             357.37 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             47.28              52.75 
[1] "0.2 - 369.9 (47.3)" "0.2 - 357.4 (52.8)"
[1] "hr=" "1"  
D62V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q LOSS MUTATED                   23             2
  11Q LOSS WILD-TYPE                 38             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11Q LOSS MUTATED                                          33
  11Q LOSS WILD-TYPE                                        39
                    vv
clus                 REGIONAL LYMPH NODE
  11Q LOSS MUTATED                    83
  11Q LOSS WILD-TYPE                 126
D62V4, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      23                 38
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               33                 39
  REGIONAL LYMPH NODE                                     83                126
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  11Q LOSS MUTATED             6       3       8        5       13        4
  11Q LOSS WILD-TYPE           6       4      20       12       14       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11Q LOSS MUTATED           2         9         6        15          5
  11Q LOSS WILD-TYPE        12        10         6        20         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           15         30        9
  11Q LOSS WILD-TYPE         17         28       10
D62V5, multiclass
             clus
vv            11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  I OR II NOS                6                  6
  STAGE 0                    3                  4
  STAGE I                    8                 20
  STAGE IA                   5                 12
  STAGE IB                  13                 14
  STAGE II                   4                 18
  STAGE IIA                  2                 12
  STAGE IIB                  9                 10
  STAGE IIC                  6                  6
  STAGE III                 15                 20
  STAGE IIIA                 5                 10
  STAGE IIIB                15                 17
  STAGE IIIC                30                 28
  STAGE IV                   9                 10
[1] 14  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                 T0+T1 T2 T3 T4
  11Q LOSS MUTATED      24 29 26 32
  11Q LOSS WILD-TYPE    39 42 48 35
D62V6, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               24                 39
  T2                  29                 42
  T3                  26                 48
  T4                  32                 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"
                    vv
clus                  N0  N1  N2  N3
  11Q LOSS MUTATED    60  30  13  23
  11Q LOSS WILD-TYPE 108  31  25  24
D62V7, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               60                108
  N1               30                 31
  N2               13                 25
  N3               23                 24
[1] 4 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                  M0  M1 M1A M1B M1C
  11Q LOSS MUTATED   122   2   2   0   5
  11Q LOSS WILD-TYPE 184   2   1   4   4
D62V8, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               122                184
  M1                 2                  2
  M1A                2                  1
  M1B                0                  4
  M1C                5                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V9, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   51 45
  11Q LOSS WILD-TYPE 78 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     51   45
  11Q LOSS WILD-TYPE   78   42
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                51                 78
  YES               45                 42
[1] 2 2
[1] FALSE
D62V10, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    16 126
  11Q LOSS WILD-TYPE  27 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     16  126
  11Q LOSS WILD-TYPE   27  178
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                16                 27
  YES              126                178
[1] 2 2
[1] FALSE
D62V11, continuous
D62V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    67  75
  11Q LOSS WILD-TYPE  64 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     67   75
  11Q LOSS WILD-TYPE   64  142
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               67                 64
  MALE                 75                142
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                         1   127
  11Q LOSS WILD-TYPE     3                         0   199
D62V13, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  127                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"
D62V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3 136
  11Q LOSS WILD-TYPE   4 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3  136
  11Q LOSS WILD-TYPE    4  198
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              136                198
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    29  22
  12P LOSS WILD-TYPE 139 143
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                51                282 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                22                143 
$`12P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR 
       10.29        92.42        64.44        21.44        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D9-A6EA 
       17.72        29.72        10.22         4.18       124.47        11.31 
TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29Q 
       39.19        19.00        60.23         4.34         8.55         8.09 
TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP 
        9.99        36.30         5.42        44.25       125.65        26.99 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
       53.16         5.56        30.15         3.22        21.60        22.22 
TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2NG TCGA-ER-A42K TCGA-FS-A1YX 
       11.90        36.07         6.58        12.62         5.62         3.45 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F5 
       15.52         7.30        30.87         8.65        40.64        28.73 
TCGA-FW-A3R5 TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 
        0.99        14.50        15.81         0.43        11.05         0.33 
TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZY 
       10.98        11.84         5.36 

$`12P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       81.24        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.41        44.19         7.50        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        59.57       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       54.31        32.28        32.61        25.78       110.24        52.01 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       23.11        22.06        15.19       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
       75.65        87.62        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       21.93         5.72         9.90        13.22        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        10.03        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       23.15        13.35        13.22         0.20        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.31        15.85         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15        62.79        36.85         1.08        39.62 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        9.50        12.03         8.84        30.44         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83        55.69         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46         2.73         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       14.56        63.42       111.91        56.02        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       60.49        52.67       124.31       122.73        51.62         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81        15.95        12.72        22.92        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.78         3.52        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       13.45        28.60        42.84        34.68         9.57        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       78.44        11.80         1.87         1.51        13.08        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        9.04         6.58        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72         6.71         3.58         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.70         3.29        64.47        11.01        23.80        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.33         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
        7.17        12.92        12.89        47.38        52.08         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       49.15         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        3.22         7.36        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.13         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       10.13        16.24        15.42        12.16        14.70        11.84 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 
       10.65        14.50        14.50         5.79        18.05         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 
      164.19         8.98        60.03         2.99       185.16        71.01 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
        5.49         6.48         7.10        18.67        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        3.72         3.42        21.83         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         4.70         8.22         6.67         5.98 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.33               0.13 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            125.65             185.16 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             13.68              15.01 
[1] "0.3 - 125.7 (13.7)" "0.1 - 185.2 (15.0)"
[1] "hr=" "1.1"
D63V2, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    30  22
  12P LOSS WILD-TYPE 143 144
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                52                287 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                22                144 
$`12P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR 
       43.43       171.58        66.08        22.62       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D9-A1X3 
       18.18        30.84        11.61        58.52       161.00        18.12 
TCGA-D9-A6EA TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29G 
       25.18       194.83        54.02       133.81       151.27        72.07 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MK 
       37.35        55.92        36.82        13.91       103.20       158.63 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 
      248.65       162.48        53.26        54.51       172.18        64.08 
TCGA-EE-A3JA TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A2NG TCGA-ER-A42K 
       53.19        13.02        37.25         8.88        31.27         6.77 
TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       48.59        28.08        27.72        32.75       133.55        53.16 
TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       28.73        22.92        21.37        65.88       357.04       294.77 
TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZY 
        0.33        42.08        24.03        43.73 

$`12P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.87        62.07       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        63.81        26.89       125.79       135.75 
TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
      125.19        79.59        15.19       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       95.24       137.79        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         3.65         6.41        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        66.25        22.95        48.89        36.03       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       65.92        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL 
       15.68        13.87        10.16        17.85        68.25        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       52.01         6.35        12.20        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        64.64         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        14.47       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48        90.97       126.81        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       268.73        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       203.05       167.90        47.54        43.23       134.40 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       71.21       124.31       122.73        51.62         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB 
       23.47       138.81       127.20        36.95        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05       162.08        50.89       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
      210.08        15.16         7.00        38.27        34.82        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       94.39       216.92       228.59       202.65        20.91         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26        74.73        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67       174.84        12.43        26.73        49.45        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.04        11.74       139.89       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       64.44        62.79        32.48        39.58        46.36        12.62 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 
       50.10        59.41         6.67        18.05         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
       63.02       121.08         4.01       219.16       105.04        38.56 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       54.38         8.61        90.28        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
        3.75        22.68         2.20        30.18        10.36        15.16 
TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       36.03        14.43        23.64        93.07        11.74 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.33               0.16 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            357.04             369.93 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            50.875             50.140 
[1] "0.3 - 357.0 (50.9)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.3"
D63V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P LOSS MUTATED                   12             2
  12P LOSS WILD-TYPE                 49             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12P LOSS MUTATED                                          13
  12P LOSS WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  12P LOSS MUTATED                    28
  12P LOSS WILD-TYPE                 181
D63V4, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  DISTANT METASTASIS                                      12                 49
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 59
  REGIONAL LYMPH NODE                                     28                181
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12P LOSS MUTATED             4       1       5        3        4        4
  12P LOSS WILD-TYPE           8       6      23       14       23       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12P LOSS MUTATED           2         2         1         5          1
  12P LOSS WILD-TYPE        12        17        11        30         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED            5          7        6
  12P LOSS WILD-TYPE         27         51       13
D63V5, multiclass
             clus
vv            12P LOSS MUTATED 12P LOSS WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    1                  6
  STAGE I                    5                 23
  STAGE IA                   3                 14
  STAGE IB                   4                 23
  STAGE II                   4                 18
  STAGE IIA                  2                 12
  STAGE IIB                  2                 17
  STAGE IIC                  1                 11
  STAGE III                  5                 30
  STAGE IIIA                 1                 14
  STAGE IIIB                 5                 27
  STAGE IIIC                 7                 51
  STAGE IV                   6                 13
[1] 14  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                 T0+T1 T2 T3 T4
  12P LOSS MUTATED       8  9 11 14
  12P LOSS WILD-TYPE    55 62 63 53
D63V6, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                8                 55
  T2                   9                 62
  T3                  11                 63
  T4                  14                 53
[1] 4 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                  N0  N1  N2  N3
  12P LOSS MUTATED    26   7   6   8
  12P LOSS WILD-TYPE 142  54  32  39
D63V7, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               26                142
  N1                7                 54
  N2                6                 32
  N3                8                 39
[1] 4 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                  M0  M1 M1A M1B M1C
  12P LOSS MUTATED    45   0   1   0   5
  12P LOSS WILD-TYPE 261   4   2   4   4
D63V8, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                45                261
  M1                 0                  4
  M1A                1                  2
  M1B                0                  4
  M1C                5                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    19  16
  12P LOSS WILD-TYPE 110  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     19   16
  12P LOSS WILD-TYPE  110   71
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                19                110
  YES               16                 71
[1] 2 2
[1] FALSE
D63V10, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     5  49
  12P LOSS WILD-TYPE  38 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5   49
  12P LOSS WILD-TYPE   38  255
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 5                 38
  YES               49                255
[1] 2 2
[1] FALSE
D63V11, continuous
D63V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    24  31
  12P LOSS WILD-TYPE 107 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     24   31
  12P LOSS WILD-TYPE  107  186
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               24                107
  MALE                 31                186
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0    52
  12P LOSS WILD-TYPE     5                         1   274
D63V13, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   52                274
[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"
D63V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  53
  12P LOSS WILD-TYPE   7 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   53
  12P LOSS WILD-TYPE    7  281
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               53                281
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    31  28
  12Q LOSS WILD-TYPE 137 137
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                59                274 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                28                137 
$`12Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A51N 
        6.97        16.47        10.29        92.42        61.38        21.44 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D9-A6EA 
       47.87        13.68        22.06         4.18       124.47        11.31 
TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29G 
       13.22        39.19        19.00        60.23         4.34         8.55 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GP 
        8.09         9.99         8.09        36.30         9.67         5.42 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS 
        1.15        36.33        44.25       125.65        26.99        53.16 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3J7 
        5.56       124.31         3.68        30.15         3.22        21.60 
TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A3PL TCGA-ER-A42K 
       22.22         5.72        11.90        36.07         1.71         5.62 
TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT 
        3.45        15.52         7.30        30.87         8.65        40.64 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB 
        3.22        28.73         0.99        14.50        15.81         0.43 
TCGA-OD-A75X TCGA-RP-A693 TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZY 
       11.05         0.33        11.84        18.67         5.36 

$`12Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        3.02         6.97         8.52       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
      110.79        28.08        22.55        45.83        81.24        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
        8.38        21.14        88.50        68.22        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       44.19         7.50        36.16         6.31        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       59.57       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU 
       32.61        25.78       110.24        52.01        17.72        23.11 
TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       29.72        10.22        15.19       142.45       108.79        38.93 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
       75.65        87.62        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       21.93         5.72         9.90        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        10.03        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       17.56        14.83        13.15         0.20         0.13        23.15 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.12         1.12         1.35        12.20         5.13         4.31 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       15.85         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15        62.79        36.85         1.08        39.62         9.50 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 
       12.03         8.84        30.44         2.43        32.15        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       49.22        36.33        51.12        34.29        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.21        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       33.83        55.69        13.02        34.98         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
        7.96        14.56        63.42       111.91        56.02        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF 
       21.60        60.49        52.67       122.73        51.62        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB 
       15.95        12.72        22.92        21.60        16.14         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        18.41        21.73        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       12.95        38.40        76.41        25.18         3.78         3.52 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57         6.58        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       11.80         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        9.04         6.58        22.49        18.41        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
        6.71         3.58         5.36        13.28         2.20         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
        3.29        64.47        11.01        23.80        14.24         7.33 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        12.89        47.38        52.08         8.81        49.15 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.68        27.39         0.82         5.23        53.85         7.36 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16        17.33         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.61        44.28        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       15.42        12.16        14.70        11.84        10.65        14.50 
TCGA-GN-A9SD TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 
       14.50         5.79        18.05         0.69       164.19         8.98 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 
       60.03         2.99        10.98       185.16        71.01         5.49 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        6.48         7.10        21.07        13.12         3.72         3.42 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       21.83         1.08        19.96         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.33               0.13 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            125.65             185.16 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             13.22              15.22 
[1] "0.3 - 125.7 (13.2)" "0.1 - 185.2 (15.2)"
[1] "hr=" "1.1"
D64V2, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    32  28
  12Q LOSS WILD-TYPE 141 138
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                60                279 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                28                138 
$`12Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A3CC TCGA-D3-A51N 
       12.99        16.57        43.43       171.58        86.93        22.62 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GC TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D9-A1X3 
      137.92       178.32        79.59        58.52       161.00        18.12 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C 
       25.18        66.25       194.83        54.02       133.81       151.27 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
       72.07        37.35        55.92        17.92        36.82        39.29 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP 
       13.91        14.30        94.82       103.20       158.63       248.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
      162.48        53.26       124.31         3.68        54.51       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A3PL 
       64.08        53.19         9.17        13.02        37.25        33.21 
TCGA-ER-A42K TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ 
        6.77        48.59        28.08        27.72        32.75       133.55 
TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-GN-A8LL TCGA-HR-A2OH 
       53.16        50.14        28.73        22.92        21.37        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-RP-A693 TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZY 
      357.04       294.77         0.33        24.03        90.28        43.73 

$`12Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       17.03        61.02        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
      133.25        28.08        31.59        90.90        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
       65.49        23.77       115.53       168.00        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07       113.52        42.08        12.10        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       59.57       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU 
       63.81        26.89       125.79       135.75        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       30.84        11.61        15.19       228.99       170.20        89.13 
TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
       95.24       137.79        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         3.65         6.41        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
      176.55        35.93       107.34        61.18        53.92        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       23.44        68.09        28.60        10.49       215.44        15.68 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        17.85        68.25        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
        6.35        12.20        29.82        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F 
       33.73        14.70        26.89        68.15         4.96        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
      168.26        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       63.78        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
       14.47       369.93        25.87       195.02        46.82       102.90 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       86.14        59.28        67.43       314.56       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      126.81        55.59        44.88        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       268.73        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
      204.66        96.23       203.05       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
      134.40        71.21       122.73        51.62        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      138.81       127.20        36.95        34.32       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       50.76        77.75        98.40        48.89        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       80.32        46.98        92.98       174.21        15.72       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       15.16         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      216.92       228.59       202.65        20.91         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      357.37        53.52        40.27        15.45         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       23.93       101.26        74.73        11.41       148.80        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 
       49.48        27.09        27.02        77.82        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       12.43        26.73        49.45        77.88         0.20        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A9SD 
       32.48        39.58        46.36        12.62        50.10        59.41 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        6.67        18.05         0.69       212.22        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
        4.01        42.08       219.16       105.04        38.56        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
        8.61        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        2.20        30.18        10.36        15.16        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.33               0.16 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            357.04             369.93 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            53.175             49.480 
[1] "0.3 - 357.0 (53.2)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.2"
D64V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q LOSS MUTATED                   11             2
  12Q LOSS WILD-TYPE                 50             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12Q LOSS MUTATED                                          18
  12Q LOSS WILD-TYPE                                        54
                    vv
clus                 REGIONAL LYMPH NODE
  12Q LOSS MUTATED                    31
  12Q LOSS WILD-TYPE                 178
D64V4, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      11                 50
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               18                 54
  REGIONAL LYMPH NODE                                     31                178
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  12Q LOSS MUTATED             4       1       5        4        6        4
  12Q LOSS WILD-TYPE           8       6      23       13       21       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12Q LOSS MUTATED           2         2         3         7          3
  12Q LOSS WILD-TYPE        12        17         9        28         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED            5          7        4
  12Q LOSS WILD-TYPE         27         51       15
D64V5, multiclass
             clus
vv            12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    1                  6
  STAGE I                    5                 23
  STAGE IA                   4                 13
  STAGE IB                   6                 21
  STAGE II                   4                 18
  STAGE IIA                  2                 12
  STAGE IIB                  2                 17
  STAGE IIC                  3                  9
  STAGE III                  7                 28
  STAGE IIIA                 3                 12
  STAGE IIIB                 5                 27
  STAGE IIIC                 7                 51
  STAGE IV                   4                 15
[1] 14  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                 T0+T1 T2 T3 T4
  12Q LOSS MUTATED      11 12 10 16
  12Q LOSS WILD-TYPE    52 59 64 51
D64V6, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               11                 52
  T2                  12                 59
  T3                  10                 64
  T4                  16                 51
[1] 4 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                  N0  N1  N2  N3
  12Q LOSS MUTATED    32   9   7   7
  12Q LOSS WILD-TYPE 136  52  31  40
D64V7, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               32                136
  N1                9                 52
  N2                7                 31
  N3                7                 40
[1] 4 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                  M0  M1 M1A M1B M1C
  12Q LOSS MUTATED    54   0   1   0   3
  12Q LOSS WILD-TYPE 252   4   2   4   6
D64V8, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                54                252
  M1                 0                  4
  M1A                1                  2
  M1B                0                  4
  M1C                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    21  17
  12Q LOSS WILD-TYPE 108  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     21   17
  12Q LOSS WILD-TYPE  108   70
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                21                108
  YES               17                 70
[1] 2 2
[1] FALSE
D64V10, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     8  53
  12Q LOSS WILD-TYPE  35 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8   53
  12Q LOSS WILD-TYPE   35  251
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 8                 35
  YES               53                251
[1] 2 2
[1] FALSE
D64V11, continuous
D64V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    28  34
  12Q LOSS WILD-TYPE 103 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     28   34
  12Q LOSS WILD-TYPE  103  183
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               28                103
  MALE                 34                183
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0    58
  12Q LOSS WILD-TYPE     5                         1   268
D64V13, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   58                268
[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"
D64V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  60
  12Q LOSS WILD-TYPE   7 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   60
  12Q LOSS WILD-TYPE    7  274
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               60                274
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    39  34
  13Q LOSS WILD-TYPE 129 131
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                73                260 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                34                131 
$`13Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A3MR 
       28.08        85.32        88.50        86.76        92.42       103.59 
TCGA-D3-A3MU TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GD 
       26.37       110.24        52.01        13.68        29.72        10.22 
TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV 
      108.79         5.56        24.07        21.93        11.31        48.79 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IC 
       35.80        13.68         9.99        44.52        25.15         6.64 
TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
       13.22         1.12         5.13         1.18        37.97        11.15 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 
       39.62         9.50         8.09        30.44        32.15        36.33 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MH 
       60.00        30.08        19.43         8.84        44.25         7.96 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       60.49        53.16         5.56       122.73         3.68        30.15 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19B 
       12.72        21.60         0.95        21.73        31.40        25.18 
TCGA-ER-A19H TCGA-ER-A19T TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FS-A1ZA 
       34.88         6.58        12.62        18.41         5.36         7.30 
TCGA-FS-A1ZH TCGA-FS-A4F4 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A8LK TCGA-GN-A9SD 
       30.87         7.36        10.13        14.70        14.50        14.50 
TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YG-AA3O 
        0.33        10.98        18.67         3.72         5.36         6.18 
TCGA-YG-AA3P 
        4.70 

$`13Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       32.42        70.16       110.79        22.55        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF 
       10.29         8.38        21.14        68.22        11.41        44.19 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        7.50        36.16         6.31        56.19        64.44        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00         6.31         9.34        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       54.74        31.30        54.31        32.28        21.44        32.61 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GE 
       25.78        47.87        17.72        23.11        22.06        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
        4.18       142.45        38.93        75.65       124.47        87.62 
TCGA-D3-A8GQ TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
       11.44         4.01         5.72         9.90        13.22        14.60 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       51.12        10.03        39.19        36.69         4.93        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       19.36         7.00        17.56        14.83        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13        23.15        19.00        13.35         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       10.55         6.31         8.12         1.35        12.20         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
       60.23         4.34        15.85         9.21         7.99         9.90 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
       62.79         8.55        36.85         1.08        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         2.43         8.09        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GK 
        9.67        51.12        34.29        17.98        47.21        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        55.69         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51         9.53        29.46         2.73        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      125.65       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       52.67       124.31        51.62        13.81        15.95         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       22.92        21.60        16.14        22.22        27.35        18.41 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
       33.60        18.61        12.95        38.40         5.72        76.41 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J 
        3.78         3.52        11.90        11.11       114.15         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       17.72        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC 
       85.74        15.72         6.71         3.58        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.70         3.29        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       14.24        15.52         7.33         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       19.53        11.08         7.17        12.92        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       52.08         8.65         8.81        49.15        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 
       27.39         0.82         5.23        53.85         3.22        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16        17.33         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.85        11.61        44.28        31.33        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OH 
       15.42        12.16        11.84        10.65        14.50        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 
        0.43        11.05         5.79        18.05         0.69       164.19 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
        8.98        60.03         2.99       185.16        71.01        11.84 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT 
        5.49         6.48         7.10        21.07        13.12         3.42 
TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT 
       21.83         1.08        19.96         1.94        12.07         8.22 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.33               0.13 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            122.73             185.16 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             18.67              14.53 
[1] "0.3 - 122.7 (18.7)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.2"
D65V2, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    41  34
  13Q LOSS WILD-TYPE 132 132
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                75                264 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                34                132 
$`13Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JL TCGA-D3-A3MR 
       28.08       103.10       115.53        86.76       171.58       103.59 
TCGA-D3-A3MU TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A8GB TCGA-D3-A8GD 
       39.75       125.79       135.75       178.32        30.84        11.61 
TCGA-D3-A8GK TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 
      170.20       129.63       117.17       151.53        54.67        22.29 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       25.18        48.89        36.03       176.55        35.93       107.34 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20I 
       53.92        68.09        52.01        33.73        68.15        13.55 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T 
       47.84        13.97        56.84        18.61        37.35       369.93 
TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2M5 
      195.02        86.14       161.03        48.72        89.33        21.67 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB 
      103.20        16.96       134.40       162.48        53.26       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JB TCGA-EE-A3JH 
        3.68        54.51       138.81        36.95       201.80       109.58 
TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A19T TCGA-ER-A2NG TCGA-FR-A3YN 
       31.40        98.40       152.35         8.88        31.27        92.98 
TCGA-FR-A7U9 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A4F4 TCGA-GN-A266 TCGA-GN-A26D 
        7.00        27.72        32.75        66.67        10.13        39.58 
TCGA-GN-A8LK TCGA-GN-A9SD TCGA-RP-A693 TCGA-W3-AA1V TCGA-WE-A8ZM TCGA-WE-A8ZQ 
       50.10        59.41         0.33        42.08        90.28        52.34 
TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-YG-AA3P 
       43.73        36.03        14.43 

$`13Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF 
       43.43        65.49        23.77       168.00        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08        12.10        56.19        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53        13.87         9.34        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       55.73        56.35       145.12        32.94        22.62        63.81 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GE 
       26.89       137.92        18.18       125.19        79.59        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP 
       58.52       228.99        89.13        95.24       161.00       137.79 
TCGA-D3-A8GQ TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 
       29.06         3.65         6.41        18.12        11.34        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        66.25        22.95       117.21        20.38       194.83 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       61.18        65.92        23.44        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.16        17.85        68.25        54.02 
TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       17.29         6.35        12.20        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       94.98        14.70        26.89         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
       91.56       168.26        63.35        80.61        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       64.64         2.60        56.42        14.47        55.92        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
       17.92        46.82       102.90        36.82        39.29        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       67.43       314.56       208.04        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       126.81        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       268.73       204.66        96.23       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA 
      167.90        47.54       248.65        43.23        71.21       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       51.62        13.81        23.47       172.18       127.20        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 
       34.32        53.19        27.35        51.35       148.08        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       13.94        50.76         9.17        77.75        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02        26.37       268.93         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21         6.77       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      210.08        15.16        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        47.38        23.93       101.26        74.73       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       11.41       148.80        53.16        26.56        49.48        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        50.14        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      139.89       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       46.36        12.62        21.37        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
        6.67        18.05         0.69       212.22        63.02       121.08 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
        4.01       219.16       105.04        24.03        38.56        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y 
        8.61        56.98        59.41         3.75        22.68         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       30.18        10.36        15.16        23.64        93.07        11.74 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.33               0.16 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            369.93             357.37 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             53.92              48.87 
[1] "0.3 - 369.9 (53.9)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1.2"
D65V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q LOSS MUTATED                   10             2
  13Q LOSS WILD-TYPE                 51             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  13Q LOSS MUTATED                                          17
  13Q LOSS WILD-TYPE                                        55
                    vv
clus                 REGIONAL LYMPH NODE
  13Q LOSS MUTATED                    46
  13Q LOSS WILD-TYPE                 163
D65V4, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      10                 51
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               17                 55
  REGIONAL LYMPH NODE                                     46                163
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  13Q LOSS MUTATED             2       2       6        6        7        4
  13Q LOSS WILD-TYPE          10       5      22       11       20       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  13Q LOSS MUTATED           4         3         2         8          2
  13Q LOSS WILD-TYPE        10        16        10        27         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED            7          9        6
  13Q LOSS WILD-TYPE         25         49       13
D65V5, multiclass
             clus
vv            13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    2                  5
  STAGE I                    6                 22
  STAGE IA                   6                 11
  STAGE IB                   7                 20
  STAGE II                   4                 18
  STAGE IIA                  4                 10
  STAGE IIB                  3                 16
  STAGE IIC                  2                 10
  STAGE III                  8                 27
  STAGE IIIA                 2                 13
  STAGE IIIB                 7                 25
  STAGE IIIC                 9                 49
  STAGE IV                   6                 13
[1] 14  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                 T0+T1 T2 T3 T4
  13Q LOSS MUTATED      18 12 20 11
  13Q LOSS WILD-TYPE    45 59 54 56
D65V6, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               18                 45
  T2                  12                 59
  T3                  20                 54
  T4                  11                 56
[1] 4 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                  N0  N1  N2  N3
  13Q LOSS MUTATED    37  13   9   8
  13Q LOSS WILD-TYPE 131  48  29  39
D65V7, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               37                131
  N1               13                 48
  N2                9                 29
  N3                8                 39
[1] 4 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                  M0  M1 M1A M1B M1C
  13Q LOSS MUTATED    64   0   1   2   4
  13Q LOSS WILD-TYPE 242   4   2   2   5
D65V8, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                64                242
  M1                 0                  4
  M1A                1                  2
  M1B                2                  2
  M1C                4                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   36 15
  13Q LOSS WILD-TYPE 93 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     36   15
  13Q LOSS WILD-TYPE   93   72
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                36                 93
  YES               15                 72
[1] 2 2
[1] FALSE
D65V10, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8  67
  13Q LOSS WILD-TYPE  35 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8   67
  13Q LOSS WILD-TYPE   35  237
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                 35
  YES               67                237
[1] 2 2
[1] FALSE
D65V11, continuous
D65V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    25  50
  13Q LOSS WILD-TYPE 106 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     25   50
  13Q LOSS WILD-TYPE  106  167
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               25                106
  MALE                 50                167
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         0    70
  13Q LOSS WILD-TYPE     5                         1   256
D65V13, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   70                256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     2  72
  13Q LOSS WILD-TYPE   5 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   72
  13Q LOSS WILD-TYPE    5  262
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               72                262
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    55  51
  14Q LOSS WILD-TYPE 113 114
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               106                227 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                51                114 
$`14Q LOSS MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A2JN 
        6.97        16.47       111.09        10.29        44.19        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV 
       64.44        59.57        61.38        13.32       103.59        29.23 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GC 
       54.31        21.44        52.01        47.87        13.68        22.06 
TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-DA-A1HV 
        4.18       124.47        24.07         5.72        11.31        48.79 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R 
       51.12        39.19        44.52        25.15        17.56         0.20 
TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29V TCGA-EE-A29X 
       13.35         1.12        37.97         8.55         2.43         8.09 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GP TCGA-EE-A2M6 
       36.30         9.67        36.33        60.00         5.42        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
        2.70         6.18         9.53        44.25         7.96       125.65 
TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 
       25.08        53.16       124.31        12.72         3.22        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 
       21.60        22.22         0.95        18.41        33.60        12.95 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S 
        5.72        25.18        11.90       114.15        34.88        36.07 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 
        1.87         1.71         5.62        85.74         3.45        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM 
        7.33         7.30        20.38        19.53        30.87        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
        8.65         8.81        40.64         3.22        28.73        14.20 
TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 
       10.78         0.13         7.23         0.85        11.61        31.33 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-LH-A9QB 
       16.24        15.42        12.16        10.65        14.50         0.43 
TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZX 
       11.05         8.98        10.98        11.84        18.67        21.83 
TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
        5.36         6.18         4.70         8.22 

$`14Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
        3.02         6.97         8.52        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        45.83        81.24        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        86.76        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       36.16         6.31        92.42       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       46.32        82.29        24.00         6.31         9.34        26.37 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       93.21        54.74        31.30        32.28        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
      110.24        17.72        23.11        29.72        10.22        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ 
      142.45       108.79        38.93        75.65        87.62        11.44 
TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        5.56         4.01        21.93         9.90        13.22        14.60 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
       35.80        10.03        13.68         9.99        36.69         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        14.83        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13        23.15        19.00        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       10.55         6.31         8.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.31        60.23         4.34        15.85         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        7.99         9.90        11.15        62.79        36.85         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       39.62         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC 
       30.44        32.15        11.31        49.22        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83        55.69         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI 
       36.33         8.84        47.51        29.46         2.73        14.56 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       63.42       111.91        56.02        26.99        21.60        60.49 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       52.67         5.56       122.73        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH 
       13.81        15.95        22.92        16.14        27.35        21.73 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       31.40        18.61        38.40        76.41         3.78         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       11.11         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
        9.57         6.58        17.72        78.44        11.80         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
       18.41        15.72         6.71         3.58         5.36        13.28 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        2.20         4.70         3.29        64.47        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       14.24         3.39         8.22        11.08         7.17        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       12.89        52.08        49.15         8.68        27.39         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        5.23        53.85         7.36         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 
        0.20         0.99         0.16        17.33         9.90        44.28 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-GN-A9SD 
       84.72        10.13        14.70        11.84        14.50        14.50 
TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
       15.81         5.79        18.05         0.33         0.69       164.19 
TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 
       60.03         2.99       185.16        71.01         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y 
        7.10        21.07        13.12         3.72         3.42         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S TCGA-Z2-AA3V 
       19.96         1.94        12.07         6.67         5.98 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.13               0.13 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            125.65             185.16 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             15.47              14.60 
[1] "0.1 - 125.7 (15.5)" "0.1 - 185.2 (14.6)"
[1] "hr=" "1"  
D66V2, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    56  51
  14Q LOSS WILD-TYPE 117 115
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               107                232 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                51                115 
$`14Q LOSS MUTATED`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A2JN 
       61.02        16.57       112.04        43.43        62.07        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV 
       66.08        59.57        86.93        60.23       103.59        45.30 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A8GC 
      145.12        22.62       135.75       137.92       178.32        79.59 
TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A4Z6 TCGA-D9-A6EA 
       58.52       161.00       117.17        54.67        11.11        25.18 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
       48.89       117.21       194.83       107.34        53.92       215.44 
TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29V 
       10.16        17.29        33.73        47.84        72.07        25.87 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GP 
       17.92        36.82        39.29        86.14       161.03        13.91 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH 
      129.27        28.83        19.76        47.28       103.20        16.96 
TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 
      158.63        47.54       162.48       124.31       138.81       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JI 
       36.95        64.08        53.19       201.80        51.35       148.08 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       13.94         9.17        98.40        13.02       268.93       152.35 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A44A TCGA-FS-A1YX 
       37.25        23.34        33.21         6.77       174.21        48.59 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH 
       28.08         7.79        27.72       357.37        40.27        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 
      101.26       133.55        11.41        53.16        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
      174.84        12.43        47.54         7.23         2.04        11.74 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-GN-A8LK 
      117.93        64.44        62.79        32.48        12.62        50.10 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8ZM 
      357.04       294.77        63.02        42.08        24.03        90.28 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-A8RT 
       22.68        43.73        36.03        14.43        23.64 

$`14Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       17.03        12.99        16.67       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        90.90        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        86.76        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       42.08        12.10       171.58       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       46.32       166.52        24.53        13.87         9.34        39.75 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
      174.84        55.73        56.35        32.94        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE 
      125.79        18.18       125.19        30.84        11.61        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ 
      228.99       170.20        89.13        95.24       137.79        29.06 
TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      129.63       151.53         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 
       22.29         9.90        66.25        22.95        36.03        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      176.55        35.93        61.18        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       28.60        10.49        15.68        13.87        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       54.02        52.01         6.35        12.20        29.82        27.22 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      133.81       151.27        91.56       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       80.61        13.97        63.78        64.64         2.60        56.84 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       18.61        56.42        37.35        14.47        55.92       369.93 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      195.02        46.82       102.90        59.28        67.43       314.56 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97       126.81        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       21.67        61.51       103.27       268.73       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      203.05       167.90       248.65        43.23       134.40        71.21 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       53.26       122.73        51.62         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 
       23.47       127.20        34.32        27.35       109.58        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       35.44        50.76        77.75        48.89        12.59        26.37 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        8.88       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       31.27        32.05       247.04        80.32        46.98        92.98 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72       210.08        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       29.46        94.39       216.92       228.59       202.65        20.91 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       48.85        53.52        15.45         9.70        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       74.73       148.80        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       77.82        66.67        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 
       22.92         0.16        19.30         9.90       139.89        84.72 
TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       10.13        39.58        46.36        21.37        59.41        65.88 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        6.67        18.05         0.33         0.69       212.22       121.08 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
        4.01       219.16       105.04        38.56        54.38         8.61 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AA9Y TCGA-WE-AAA0 
       56.98        59.41        52.34         3.75         2.20        30.18 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-AA3S TCGA-Z2-AA3V 
       10.36        15.16        93.07        11.74 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              2.04               0.16 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            357.37             369.93 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            51.350             49.465 
[1] "2.0 - 357.4 (51.4)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1.2"
D66V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q LOSS MUTATED                   22             1
  14Q LOSS WILD-TYPE                 39             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  14Q LOSS MUTATED                                          28
  14Q LOSS WILD-TYPE                                        44
                    vv
clus                 REGIONAL LYMPH NODE
  14Q LOSS MUTATED                    58
  14Q LOSS WILD-TYPE                 151
D66V4, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      22                 39
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               28                 44
  REGIONAL LYMPH NODE                                     58                151
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  14Q LOSS MUTATED             5       0      11        3        8       10
  14Q LOSS WILD-TYPE           7       7      17       14       19       12
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  14Q LOSS MUTATED           2         5         3        14          3
  14Q LOSS WILD-TYPE        12        14         9        21         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           11         20        4
  14Q LOSS WILD-TYPE         21         38       15
D66V5, multiclass
             clus
vv            14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  I OR II NOS                5                  7
  STAGE 0                    0                  7
  STAGE I                   11                 17
  STAGE IA                   3                 14
  STAGE IB                   8                 19
  STAGE II                  10                 12
  STAGE IIA                  2                 12
  STAGE IIB                  5                 14
  STAGE IIC                  3                  9
  STAGE III                 14                 21
  STAGE IIIA                 3                 12
  STAGE IIIB                11                 21
  STAGE IIIC                20                 38
  STAGE IV                   4                 15
[1] 14  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                 T0+T1 T2 T3 T4
  14Q LOSS MUTATED      24 23 20 22
  14Q LOSS WILD-TYPE    39 48 54 45
D66V6, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1               24                 39
  T2                  23                 48
  T3                  20                 54
  T4                  22                 45
[1] 4 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                  N0  N1  N2  N3
  14Q LOSS MUTATED    50  24   8  16
  14Q LOSS WILD-TYPE 118  37  30  31
D66V7, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               50                118
  N1               24                 37
  N2                8                 30
  N3               16                 31
[1] 4 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                  M0  M1 M1A M1B M1C
  14Q LOSS MUTATED    98   0   1   0   3
  14Q LOSS WILD-TYPE 208   4   2   4   6
D66V8, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                98                208
  M1                 0                  4
  M1A                1                  2
  M1B                0                  4
  M1C                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   37 28
  14Q LOSS WILD-TYPE 92 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     37   28
  14Q LOSS WILD-TYPE   92   59
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                37                 92
  YES               28                 59
[1] 2 2
[1] FALSE
D66V10, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    15  94
  14Q LOSS WILD-TYPE  28 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     15   94
  14Q LOSS WILD-TYPE   28  210
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                15                 28
  YES               94                210
[1] 2 2
[1] FALSE
D66V11, continuous
D66V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    45  65
  14Q LOSS WILD-TYPE  86 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     45   65
  14Q LOSS WILD-TYPE   86  152
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               45                 86
  MALE                 65                152
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       1                         0   102
  14Q LOSS WILD-TYPE     4                         1   224
D66V13, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  102                224
[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"
D66V14, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     3 105
  14Q LOSS WILD-TYPE   4 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3  105
  14Q LOSS WILD-TYPE    4  229
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              105                229
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    18  29
  15Q LOSS WILD-TYPE 150 136
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                47                286 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                29                136 
$`15Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A5GN TCGA-D3-A5GO 
        6.97        15.25        61.38        26.37        52.01        47.87 
TCGA-D3-A8GC TCGA-D3-A8GN TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-DA-A1IA 
       22.06       124.47        13.22        39.19        25.15         4.93 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A29P 
        0.20         0.13        19.00         8.12         1.08        12.03 
TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MF 
        8.09         9.67        47.21         8.84        47.51         2.73 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J7 
        7.96       125.65        56.02         5.56       122.73        21.60 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A3EV 
       22.22        18.41        12.95         5.72        11.90        22.49 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-GN-A266 
        3.45        23.80        15.52        47.38        40.64        10.13 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-W3-AA1V TCGA-WE-A8JZ 
       10.65        14.50        14.50        10.98        11.84 

$`15Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97        16.47         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       70.16       110.79        28.08        22.55        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       10.29        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.41        44.19         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       92.42        56.19        64.44        59.57       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        82.29        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR 
       32.28        21.44        32.61        25.78       110.24        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       17.72        23.11        29.72        10.22        15.19         4.18 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ 
      142.45       108.79        38.93        75.65        87.62        11.44 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        5.56        24.07         4.01        21.93         5.72         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        14.60        48.79        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A1IC 
       13.68         9.99        44.52        36.69        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG 
       19.36         7.00        17.56        14.83        13.15        23.15 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         9.21         1.18         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M 
       37.97        11.15        62.79         8.55        36.85        39.62 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        9.50         8.84         9.99        30.44         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        36.30        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        55.69         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33        98.27         2.70         6.18 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
        9.53        29.46        44.25        14.56        63.42       111.91 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        60.49        53.16        52.67 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31        51.62         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB 
       12.72         3.22        22.92        21.60        16.14         0.95 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        21.73        33.60        31.40        18.61        38.40 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       76.41        25.18         3.78         3.52        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       34.88         4.21        13.45        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58         1.71         5.62        18.41        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD 
        6.71         3.58         5.36        13.28         2.20         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.29        64.47        11.01        14.24         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        12.92        12.89        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       49.15         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        3.22         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        84.72        16.24        15.42        12.16        14.70 
TCGA-GN-A4U8 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        14.50        15.81         0.43        11.05         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.33         0.69       164.19         8.98        60.03 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
        2.99       185.16        71.01         5.49         6.48         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       18.67        21.07        13.12         3.72         3.42        21.83 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        5.36         1.08        19.96         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.13               0.13 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            125.65             185.16 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            14.500             14.765 
[1] "0.1 - 125.7 (14.5)" "0.1 - 185.2 (14.8)"
[1] "hr=" "1.3"
D67V2, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    19  29
  15Q LOSS WILD-TYPE 154 137
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                48                291 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                29                137 
$`15Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A5GN TCGA-D3-A5GO 
       12.99        58.06        86.93        39.75       135.75       137.92 
TCGA-D3-A8GC TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A1I8 
       79.59       161.00       151.53        66.25       194.83        53.92 
TCGA-DA-A1IA TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A29L 
       65.92        10.16        17.85        54.02        94.98         2.60 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2MC 
       56.42        37.35        39.29       208.04        21.67        61.51 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB 
      268.73        16.96       158.63       167.90        53.26       122.73 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E 
       64.08        53.19        51.35        13.94         9.17        13.02 
TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZT 
       46.98        48.59       202.65        28.08       101.26        53.16 
TCGA-GN-A266 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-W3-AA1V TCGA-WE-A8JZ 
       10.13        12.62        50.10        21.37        42.08        24.03 

$`15Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       86.76        11.87        62.07       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
      171.58        56.19        66.08        59.57       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR 
       32.94        22.62        63.81        26.89       125.79       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       18.18       125.19        30.84        11.61        15.19        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ 
      228.99       170.20        89.13        95.24       137.79        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       117.17        54.67         3.65         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
       11.34        22.29        11.11         9.90        25.18        22.95 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03       117.21        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
      107.34        61.18        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN 
      215.44        15.68        13.87        68.25        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        6.35        12.20        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       91.56       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       13.97        63.78        72.07        64.64        56.84        18.61 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        55.92       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       126.81        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       44.88        94.82       129.27        28.83        19.76        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      103.27       103.20       204.66        96.23       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
      248.65        43.23       134.40       162.48        71.21       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD 
      172.18       127.20        36.95        34.32       201.80        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
      109.58       148.08        31.40        35.44        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       98.40        48.89        12.59        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       37.25         8.88       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       33.21         6.77        92.98       174.21        15.72       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
       15.16         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      216.92       228.59        20.91         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
      357.37        53.52        40.27        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       26.56        49.48        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       84.72        64.44        62.79        32.48        39.58        46.36 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       59.41        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
      219.16       105.04        38.56        54.38         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       56.98        59.41        52.34         3.75        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        2.20        30.18        10.36        15.16        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              2.60               0.16 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            268.73             369.93 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            53.225             48.890 
[1] "2.6 - 268.7 (53.2)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.3"
D67V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q LOSS MUTATED                    8             1
  15Q LOSS WILD-TYPE                 53             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  15Q LOSS MUTATED                                          12
  15Q LOSS WILD-TYPE                                        60
                    vv
clus                 REGIONAL LYMPH NODE
  15Q LOSS MUTATED                    27
  15Q LOSS WILD-TYPE                 182
D67V4, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       8                 53
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               12                 60
  REGIONAL LYMPH NODE                                     27                182
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  15Q LOSS MUTATED             1       1       9        2        5        2
  15Q LOSS WILD-TYPE          11       6      19       15       22       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  15Q LOSS MUTATED           0         1         3         9          3
  15Q LOSS WILD-TYPE        14        18         9        26         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED            5          6        0
  15Q LOSS WILD-TYPE         27         52       19
D67V5, multiclass
             clus
vv            15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  I OR II NOS                1                 11
  STAGE 0                    1                  6
  STAGE I                    9                 19
  STAGE IA                   2                 15
  STAGE IB                   5                 22
  STAGE II                   2                 20
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  3                  9
  STAGE III                  9                 26
  STAGE IIIA                 3                 12
  STAGE IIIB                 5                 27
  STAGE IIIC                 6                 52
  STAGE IV                   0                 19
[1] 14  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                 T0+T1 T2 T3 T4
  15Q LOSS MUTATED       8 16  5 14
  15Q LOSS WILD-TYPE    55 55 69 53
D67V6, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1                8                 55
  T2                  16                 55
  T3                   5                 69
  T4                  14                 53
[1] 4 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                  N0  N1  N2  N3
  15Q LOSS MUTATED    27   8   4   7
  15Q LOSS WILD-TYPE 141  53  34  40
D67V7, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               27                141
  N1                8                 53
  N2                4                 34
  N3                7                 40
[1] 4 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                  M0  M1 M1A M1B M1C
  15Q LOSS MUTATED    46   0   0   1   0
  15Q LOSS WILD-TYPE 260   4   3   3   9
D67V8, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                46                260
  M1                 0                  4
  M1A                0                  3
  M1B                1                  3
  M1C                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20  13
  15Q LOSS WILD-TYPE 109  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20   13
  15Q LOSS WILD-TYPE  109   74
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                20                109
  YES               13                 74
[1] 2 2
[1] FALSE
D67V10, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     5  44
  15Q LOSS WILD-TYPE  38 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5   44
  15Q LOSS WILD-TYPE   38  260
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 5                 38
  YES               44                260
[1] 2 2
[1] FALSE
D67V11, continuous
D67V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    19  30
  15Q LOSS WILD-TYPE 112 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19   30
  15Q LOSS WILD-TYPE  112  187
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               19                112
  MALE                 30                187
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       2                         0    46
  15Q LOSS WILD-TYPE     3                         1   280
D67V13, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   46                280
[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"
D67V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0  48
  15Q LOSS WILD-TYPE   7 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   48
  15Q LOSS WILD-TYPE    7  286
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               48                286
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    32  32
  16P LOSS WILD-TYPE 136 133
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                64                269 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                32                133 
$`16P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL 
      111.09        32.42        45.83        68.22        86.76        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A8GD 
       56.19        64.44       114.67        61.38        21.44        10.22 
TCGA-D3-A8GM TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EB-A44R 
       75.65        11.31        13.22        35.80        13.68         0.20 
TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29D 
       13.35         6.31         8.12         1.12         1.18        11.15 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GC 
        1.08        39.62        32.15         8.09        11.31        34.29 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU 
       55.69         8.84       125.65        56.02        21.60         5.56 
TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
      122.73        21.60        22.22        33.60        31.40        12.95 
TCGA-ER-A19E TCGA-ER-A19T TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZT 
       11.90         6.58         1.87         2.20        23.80        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 
        8.68        27.39         0.99         0.13        44.28        31.33 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-OD-A75X TCGA-WE-A8JZ TCGA-WE-A8K5 
       16.24        15.42        14.70        11.05        11.84         6.48 
TCGA-WE-A8ZQ TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
        3.72         6.18         4.70         6.67 

$`16P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
        3.02         6.97         6.97        16.47         8.52        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      110.79        28.08        22.55        81.24        10.29        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
        8.38        21.14        88.50        11.41        44.19         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       36.16         6.31        59.57        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       82.29        13.32        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       32.28        32.61        25.78       110.24        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE 
       13.68        17.72        23.11        29.72        22.06        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
        4.18       142.45       108.79        38.93       124.47        87.62 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       11.44         5.56        24.07         4.01        21.93         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        14.60        48.79        51.12        10.03        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13        23.15        19.00        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       10.55         1.35        12.20         5.13         4.31        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.34        15.85         9.21         7.99         9.90        37.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       62.79         8.55        36.85         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.84         9.99        30.44         2.43        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        36.33        51.12        17.98        60.00        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       30.08        19.43        16.01        35.54        28.31        33.83 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
        5.42         1.15        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
       44.25         7.96        14.56        63.42       111.91        25.08 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
       26.99        60.49        53.16        52.67       124.31        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        30.15        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       22.92        21.60        16.14         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       21.73        18.61        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.78         3.52        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       17.72        78.44        11.80         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74        15.72         6.71         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       13.28         4.70         3.29        64.47         3.45        11.01 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       14.24        15.52         7.33         7.30         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        8.22        19.53        11.08         7.17        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
        0.82         5.23        53.85         3.22         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       84.72        10.13        12.16        11.84        10.65        14.50 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        14.50        15.81         0.43         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       10.98       185.16        71.01         5.49         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       21.07        13.12         3.42        21.83         5.36         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3V 
       19.96         1.94        12.07         8.22         5.98 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.13               0.13 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            125.65             185.16 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             15.06              14.60 
[1] "0.1 - 125.7 (15.1)" "0.1 - 185.2 (14.6)"
[1] "hr=" "1.1"
D68V2, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    32  32
  16P LOSS WILD-TYPE 141 134
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                64                275 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                32                134 
$`16P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JL 
      112.04       112.57        90.90       168.00        86.76       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A51N TCGA-D3-A8GD 
       56.19        66.08       130.72        86.93        22.62        11.61 
TCGA-D3-A8GM TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EB-A44R 
       95.24        25.18        66.25        36.03       176.55        10.16 
TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29D 
       17.29         8.65        94.98        33.73        13.55        13.97 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GC 
        2.60        56.84       195.02        17.92        46.82        67.43 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU 
      126.81        21.67       158.63       167.90        43.23        53.26 
TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
      122.73        36.95        53.19       148.08        31.40        13.94 
TCGA-ER-A19E TCGA-ER-A19T TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZT 
       13.02         8.88        23.34        34.82       202.65        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 
       26.56        49.48        22.92        47.54       139.89       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-OD-A75X TCGA-WE-A8JZ TCGA-WE-A8K5 
       64.44        62.79        39.58       294.77        24.03        54.38 
TCGA-WE-A8ZQ TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S 
       52.34        36.03        14.43        93.07 

$`16P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
      133.25        28.08        31.59        95.74        43.43       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       65.49        23.77       115.53        11.87        62.07       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       42.08        12.10        59.57        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
      166.52        60.23        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       32.94        63.81        26.89       125.79       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE 
      178.32        18.18       125.19        30.84        79.59        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP 
       58.52       228.99       170.20        89.13       161.00       137.79 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       29.06       129.63       117.17       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        6.41        18.12        11.34        22.29        11.11         9.90 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       22.95        48.89       117.21        20.38       194.83        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      107.34        61.18        53.92        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       28.60        10.49       215.44        15.68        13.87        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       68.25        54.02        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       27.22        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        91.56       168.26        63.35        80.61        47.84 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.78        72.07        64.64        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        55.92       369.93        25.87       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        59.28       314.56       161.03       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       48.72        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       13.91        14.30        55.59        44.88        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      103.20        16.96       204.66        96.23       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      248.65       134.40       162.48        71.21       124.31        51.62 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
        3.68        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        64.08        34.32       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      109.58        35.44        50.76         9.17        77.75        98.40 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       48.89        12.59        26.37       268.93       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
      148.18        79.99        43.82        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       38.27        29.46        94.39       216.92        48.59       228.59 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       23.93       101.26        74.73       133.55        11.41       148.80 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       27.09        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK 
       84.72        10.13        32.48        46.36        12.62        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-QB-AA9O 
       21.37        59.41        65.88       357.04         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       42.08       219.16       105.04        38.56         8.61        90.28 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       56.98        59.41         3.75        22.68        43.73         2.20 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3V 
       30.18        10.36        15.16        23.64        11.74 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              2.60               0.16 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            294.77             369.93 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            53.175             49.450 
[1] "2.6 - 294.8 (53.2)" "0.2 - 369.9 (49.5)"
[1] "hr=" "1"  
D68V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P LOSS MUTATED                   11             3
  16P LOSS WILD-TYPE                 50             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16P LOSS MUTATED                                           8
  16P LOSS WILD-TYPE                                        64
                    vv
clus                 REGIONAL LYMPH NODE
  16P LOSS MUTATED                    43
  16P LOSS WILD-TYPE                 166
D68V4, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  DISTANT METASTASIS                                      11                 50
  PRIMARY TUMOR                                            3                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                8                 64
  REGIONAL LYMPH NODE                                     43                166
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16P LOSS MUTATED             3       2       3        3        5        2
  16P LOSS WILD-TYPE           9       5      25       14       22       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16P LOSS MUTATED           2         8         3         9          3
  16P LOSS WILD-TYPE        12        11         9        26         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED            5          8        5
  16P LOSS WILD-TYPE         27         50       14
D68V5, multiclass
             clus
vv            16P LOSS MUTATED 16P LOSS WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    2                  5
  STAGE I                    3                 25
  STAGE IA                   3                 14
  STAGE IB                   5                 22
  STAGE II                   2                 20
  STAGE IIA                  2                 12
  STAGE IIB                  8                 11
  STAGE IIC                  3                  9
  STAGE III                  9                 26
  STAGE IIIA                 3                 12
  STAGE IIIB                 5                 27
  STAGE IIIC                 8                 50
  STAGE IV                   5                 14
[1] 14  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                 T0+T1 T2 T3 T4
  16P LOSS MUTATED       9 13 11 18
  16P LOSS WILD-TYPE    54 58 63 49
D68V6, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1                9                 54
  T2                  13                 58
  T3                  11                 63
  T4                  18                 49
[1] 4 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                  N0  N1  N2  N3
  16P LOSS MUTATED    34  12   6   8
  16P LOSS WILD-TYPE 134  49  32  39
D68V7, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               34                134
  N1               12                 49
  N2                6                 32
  N3                8                 39
[1] 4 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                  M0  M1 M1A M1B M1C
  16P LOSS MUTATED    56   0   1   0   4
  16P LOSS WILD-TYPE 250   4   2   4   5
D68V8, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                56                250
  M1                 0                  4
  M1A                1                  2
  M1B                0                  4
  M1C                4                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   30 16
  16P LOSS WILD-TYPE 99 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     30   16
  16P LOSS WILD-TYPE   99   71
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                30                 99
  YES               16                 71
[1] 2 2
[1] FALSE
D68V10, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     4  62
  16P LOSS WILD-TYPE  39 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4   62
  16P LOSS WILD-TYPE   39  242
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 4                 39
  YES               62                242
[1] 2 2
[1] FALSE
D68V11, continuous
D68V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    30  36
  16P LOSS WILD-TYPE 101 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     30   36
  16P LOSS WILD-TYPE  101  181
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               30                101
  MALE                 36                181
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         1    60
  16P LOSS WILD-TYPE     4                         0   266
D68V13, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   60                266
[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"
D68V14, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  62
  16P LOSS WILD-TYPE   4 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   62
  16P LOSS WILD-TYPE    4  272
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               62                272
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    46  50
  16Q LOSS WILD-TYPE 122 115
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                96                237 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                50                115 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
      111.09        32.42       110.79        45.83        68.22        86.76 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC 
       44.19        92.42        56.19        64.44       114.67        61.38 
TCGA-D3-A51N TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A3Z3 
       21.44        10.22         4.18        75.65        24.07        21.93 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 
       11.31        13.22        35.80        13.68         9.99        14.83 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 
        0.20        23.15         6.31         8.12         1.12         4.31 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
        4.34         1.18         9.90        11.15         1.08        39.62 
TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC 
       12.03        32.15         8.09        11.31         9.67        34.29 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MJ 
       47.21        55.69         5.42         8.84         9.53        63.42 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE 
      125.65        56.02        21.60         5.56       122.73        30.15 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 
       13.81        22.92        21.60        22.22        33.60        31.40 
TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19N TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A2ND 
       12.95        25.18        42.84         6.58        17.72         1.87 
TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZP TCGA-FS-A1ZT 
        2.20        23.80         3.39        11.08        52.08        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        8.68        27.39         3.22         0.20         0.99         0.13 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-LH-A9QB 
       44.28        31.33        16.24        15.42        14.70         0.43 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8ZQ 
       11.05         5.79        18.05        11.84         6.48         3.72 
TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       21.83         1.94         6.18         4.70         6.67         5.98 

$`16Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
        3.02         6.97         6.97        16.47         8.52        70.16 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        22.55        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       21.14        88.50        11.41         7.50        36.16         6.31 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       59.57        15.25        46.98        46.32        82.29        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       93.21        54.74        31.30        54.31        32.28        32.61 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       25.78       110.24        52.01        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       23.11        29.72        22.06        15.19       142.45       108.79 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 
       38.93       124.47        87.62        11.44         5.56         4.01 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        5.72         9.90        14.60        48.79        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       39.19        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH 
        6.64        19.36         7.00        17.56        13.15         0.13 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       19.00        13.35        13.22         0.20        11.57        10.55 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        1.35        12.20         5.13        60.23        15.85         9.21 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
        7.99        37.97        62.79         8.55        36.85         9.50 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 
        8.09         8.84         9.99        30.44         2.43        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       36.30        36.33        51.12        17.98        60.00        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       19.43        16.01        35.54        28.31        33.83         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      111.91        25.08        26.99        60.49        53.16        52.67 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        51.62         3.68        15.95        12.72         3.22 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14         0.95        27.35        18.41        21.73 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       18.61        38.40         5.72        76.41         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC 
       28.60        34.68         9.57        36.07        78.44        11.80 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.51        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       22.49         1.71         5.62        18.41        85.74        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
        6.71         3.58         5.36        13.28         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47         3.45        11.01        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.30        20.38         8.22        19.53         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        12.89        47.38         8.65         8.81        49.15 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
        0.82         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY 
       10.78         5.98         6.41         2.27         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 
        9.90         7.23         0.85        11.61        84.72        10.13 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       12.16        11.84        10.65        14.50        14.50        14.50 
TCGA-HR-A2OH TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       15.81         0.33         0.69       164.19         8.98        60.03 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 
        2.99        10.98       185.16        71.01         5.49         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y 
       18.67        21.07        13.12         3.42         5.36         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA4 TCGA-Z2-A8RT 
       19.96        12.07         8.22 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.13               0.13 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            125.65             185.16 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            14.765             14.600 
[1] "0.1 - 125.7 (14.8)" "0.1 - 185.2 (14.6)"
[1] "hr=" "1.1"
D69V2, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    48  50
  16Q LOSS WILD-TYPE 125 116
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                98                241 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                50                116 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
      112.04       112.57       133.25        90.90       168.00        86.76 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC 
       62.07       171.58        56.19        66.08       130.72        86.93 
TCGA-D3-A51N TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GM TCGA-D3-A8GS TCGA-D9-A148 
       22.62        11.61        58.52        95.24       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 
       54.67        22.29        25.18        66.25        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EE-A17Z TCGA-EE-A180 
       35.93        15.68        10.16        68.25         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D 
       33.73         4.96       151.27        13.55        80.61        13.97 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        2.60        56.84        56.42       195.02        17.92        46.82 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 
       39.29        67.43       208.04       126.81        13.91        21.67 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU 
       47.28        96.23       158.63       167.90        43.23        53.26 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA 
      122.73        54.51        13.81       127.20        36.95        53.19 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19N TCGA-ER-A19T 
      148.08        31.40        13.94        98.40        44.05         8.88 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-FR-A8YC TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZF 
      148.18        23.34        34.82       202.65        48.85        15.45 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FW-A3I3 
       74.73        53.16        26.56        49.48        50.14         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       22.92        47.54       139.89       117.93        64.44        62.79 
TCGA-GN-A26D TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-WE-A8JZ 
       39.58       357.04       294.77         6.67        18.05        24.03 
TCGA-WE-A8K5 TCGA-WE-A8ZQ TCGA-WE-A8ZX TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-YG-AA3P 
       54.38        52.34        22.68        10.36        36.03        14.43 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
       93.07        11.74 

$`16Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       28.08        31.59        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       115.53        11.87       113.52        42.08        12.10 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       59.57        58.06        46.98        46.32       166.52        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
      174.84        55.73        56.35       145.12        32.94        63.81 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       26.89       125.79       135.75       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
      125.19        30.84        79.59        15.19       228.99       170.20 
TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A1JW 
       89.13       161.00       137.79        29.06       129.63         3.65 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG 
        6.41        18.12        11.34        11.11         9.90        22.95 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       48.89       117.21        20.38       194.83       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
      215.44        13.87        17.85        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
        6.35        12.20        29.82        27.22        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       68.15       133.81        91.56       168.26        63.35        47.84 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       63.78        72.07        64.64        18.61        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       55.92       369.93        25.87       102.90        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       59.28       314.56       161.03        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        75.48        90.97        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME 
       94.82       129.27        28.83        19.76        61.51       103.27 
TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN 
      268.73       103.20        16.96       204.66       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      248.65       134.40       162.48        71.21       124.31        51.62 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 
        3.68        23.47       138.81       172.18        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 
      201.80        27.35        51.35       109.58        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
        9.17        77.75        48.89        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
      268.93       152.35         6.44       131.51        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89        37.25        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       210.08        15.16 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
        7.00        38.27        29.46        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      228.59        20.91        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        40.27         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      101.26       133.55        11.41       148.80        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       77.82        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       49.45        77.88         0.16        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 
        2.04        11.74        84.72        10.13        32.48        46.36 
TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-RP-A693 
       12.62        50.10        21.37        59.41        65.88         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       212.22        63.02       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
      219.16       105.04        38.56         8.61        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA4 
       59.41         3.75        43.73         2.20        30.18        15.16 
TCGA-Z2-A8RT 
       23.64 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.20               0.16 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            357.04             369.93 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            53.225             48.890 
[1] "0.2 - 357.0 (53.2)" "0.2 - 369.9 (48.9)"
[1] "hr=" "1.1"
D69V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q LOSS MUTATED                   19             3
  16Q LOSS WILD-TYPE                 42             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16Q LOSS MUTATED                                          16
  16Q LOSS WILD-TYPE                                        56
                    vv
clus                 REGIONAL LYMPH NODE
  16Q LOSS MUTATED                    61
  16Q LOSS WILD-TYPE                 148
D69V4, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      19                 42
  PRIMARY TUMOR                                            3                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               16                 56
  REGIONAL LYMPH NODE                                     61                148
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  16Q LOSS MUTATED             3       3       5        7        6        6
  16Q LOSS WILD-TYPE           9       4      23       10       21       16
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16Q LOSS MUTATED           2         9         6         9          3
  16Q LOSS WILD-TYPE        12        10         6        26         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED            9         14        6
  16Q LOSS WILD-TYPE         23         44       13
D69V5, multiclass
             clus
vv            16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    3                  4
  STAGE I                    5                 23
  STAGE IA                   7                 10
  STAGE IB                   6                 21
  STAGE II                   6                 16
  STAGE IIA                  2                 12
  STAGE IIB                  9                 10
  STAGE IIC                  6                  6
  STAGE III                  9                 26
  STAGE IIIA                 3                 12
  STAGE IIIB                 9                 23
  STAGE IIIC                14                 44
  STAGE IV                   6                 13
[1] 14  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                 T0+T1 T2 T3 T4
  16Q LOSS MUTATED      17 15 18 26
  16Q LOSS WILD-TYPE    46 56 56 41
D69V6, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               17                 46
  T2                  15                 56
  T3                  18                 56
  T4                  26                 41
[1] 4 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                  N0  N1  N2  N3
  16Q LOSS MUTATED    53  15   9  13
  16Q LOSS WILD-TYPE 115  46  29  34
D69V7, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               53                115
  N1               15                 46
  N2                9                 29
  N3               13                 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"
                    vv
clus                  M0  M1 M1A M1B M1C
  16Q LOSS MUTATED    84   1   1   1   4
  16Q LOSS WILD-TYPE 222   3   2   3   5
D69V8, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                84                222
  M1                 1                  3
  M1A                1                  2
  M1B                1                  3
  M1C                4                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   43 26
  16Q LOSS WILD-TYPE 86 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     43   26
  16Q LOSS WILD-TYPE   86   61
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                43                 86
  YES               26                 61
[1] 2 2
[1] FALSE
D69V10, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    10  90
  16Q LOSS WILD-TYPE  33 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     10   90
  16Q LOSS WILD-TYPE   33  214
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                10                 33
  YES               90                214
[1] 2 2
[1] FALSE
D69V11, continuous
D69V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    44  56
  16Q LOSS WILD-TYPE  87 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     44   56
  16Q LOSS WILD-TYPE   87  161
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               44                 87
  MALE                 56                161
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         1    92
  16Q LOSS WILD-TYPE     4                         0   234
D69V13, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   92                234
[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"
D69V14, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3  96
  16Q LOSS WILD-TYPE   4 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   96
  16Q LOSS WILD-TYPE    4  238
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               96                238
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    57  60
  17P LOSS WILD-TYPE 111 105
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               117                216 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                60                105 
$`17P LOSS MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB 
        3.02         6.97         6.97        45.83        10.29        68.22 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3ML 
       11.41         7.50        92.42        56.19        64.44         6.31 
TCGA-D3-A3MO TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC 
        9.34        21.44        25.78        47.87        29.72        22.06 
TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D9-A6EA TCGA-DA-A1HV 
        4.18        38.93        75.65       124.47        11.31        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F3 
       35.80        51.12        13.68        44.52        25.15         7.00 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 
       17.56         0.20        13.35        13.22        11.57         8.12 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        5.13         4.31         4.34        37.97        62.79         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       36.85         1.08        39.62         9.99        30.44         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GI 
        8.09        49.22        36.30         9.67        34.29        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC 
       19.43         5.42        34.98         8.84        98.27        47.51 
TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
        9.53        44.25        25.08        26.99        21.60        60.49 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 
       53.16         5.56       124.31        51.62        30.15        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       21.60        16.14         0.95        21.73        31.40        18.61 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19S TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A3YN 
        5.72         3.78        36.07        12.62        22.49        18.41 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A8YC TCGA-FS-A1YX TCGA-FS-A1Z4 
       85.74         6.71         5.36         2.20         3.45        15.52 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       30.87        12.92         8.65        40.64         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A265 
        0.82         3.22        10.78         0.20         0.99        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-QB-AA9O TCGA-W3-AA21 
       10.13        16.24        15.42        10.65        18.05        71.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       11.84         5.49        21.83         5.36         1.08        19.96 
TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3V 
        1.94         6.18         5.98 

$`17P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.47         8.52       111.09        32.42        70.16       110.79 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        22.55        81.24        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP 
       88.50        86.76        44.19        36.16         6.31        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00       103.59        26.37        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
       54.74        31.30        54.31        32.28        32.61       110.24 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GE 
       52.01        13.68        17.72        23.11        10.22        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      142.45       108.79        87.62        11.44         5.56        24.07 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01        21.93         5.72         9.90        13.22        14.60 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       10.03        39.19         9.99        36.69         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
        6.64        19.36        14.83        13.15         0.13        23.15 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       19.00         0.20        10.55         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       12.20        60.23        15.85         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        9.90        11.15         9.50        12.03         8.09         8.84 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       32.15        11.31        36.33        51.12        17.98        60.00 
TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       47.21        16.01        35.54        28.31        33.83        55.69 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
        1.15        13.02        36.33         2.70         6.18        29.46 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        2.73         7.96        14.56        63.42       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
       56.02        52.67       122.73         3.68        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       12.72         3.22        22.92        22.22        27.35        18.41 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       33.60        12.95        38.40        76.41        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       28.60        42.84        34.68         9.57         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       78.44        11.80         1.87         1.51        13.08        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 
        9.04         6.58         1.71         5.62        15.72         3.58 
TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       13.28         4.70         3.29        64.47        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       14.24         7.33         7.30         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       19.53        11.08         7.17        12.89        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.81        49.15         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
       14.20         5.98         6.41         2.27         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       17.33         9.90         7.23         0.85        11.61        44.28 
TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL 
       31.33        12.16        14.70        11.84        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       14.50        15.81         0.43        11.05         5.79         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.69       164.19         8.98        60.03         2.99        10.98 
TCGA-W3-AA1W TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
      185.16         6.48         7.10        18.67        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
        3.72         3.42        12.07         4.70         8.22         6.67 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.20               0.13 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            124.47             185.16 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             16.24              14.50 
[1] "0.2 - 124.5 (16.2)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.1"
D70V2, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    59  60
  17P LOSS WILD-TYPE 114 106
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               119                220 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                60                106 
$`17P LOSS MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB 
       17.03        61.02        12.99        90.90        43.43       168.00 
TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3ML 
       11.87       113.52       171.58        56.19        66.08        13.87 
TCGA-D3-A3MO TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A8GB TCGA-D3-A8GC 
        9.34        22.62        26.89       137.92        30.84        79.59 
TCGA-D3-A8GI TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D9-A148 TCGA-D9-A1JW 
       58.52        89.13        95.24       161.00       151.53         3.65 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I5 
       25.18        48.89        36.03       117.21       176.55       107.34 
TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UL TCGA-EB-A5UN 
       53.92        10.49       215.44        10.16        17.29        52.01 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29C 
       29.82        94.98        68.15         4.96       151.27        47.84 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S 
       63.78        72.07        64.64         2.60        56.84        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      369.93        25.87        17.92       102.90        36.82        39.29 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M5 
       67.43        48.72        89.33        13.91        44.88        21.67 
TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MN TCGA-EE-A2MP 
      129.27        61.51        47.28       103.20        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       43.23       134.40       162.48        53.26       124.31        51.62 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
       54.51        36.95        64.08        34.32       201.80       109.58 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19S TCGA-ER-A2NG 
       31.40        35.44         9.17        48.89        37.25        31.27 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A8YC 
       46.98        92.98       174.21       210.08         7.00        34.82 
TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       48.59        28.08        32.75        47.38       133.55        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 
       26.56        49.48        27.09        50.14        12.43         0.20 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
       22.92        84.72        10.13        64.44        62.79        12.62 
TCGA-QB-AA9O TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZX TCGA-WE-A8ZY 
       18.05       105.04        24.03        38.56        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-YG-AA3O TCGA-Z2-AA3V 
        2.20        30.18        10.36        36.03        11.74 

$`17P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
       16.57        16.67       112.04       112.57        71.80       133.25 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        31.59        95.74       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP 
      115.53        86.76        62.07        42.08        12.10        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
       55.73        56.35       145.12        32.94        63.81       125.79 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GD TCGA-D3-A8GE 
      135.75       178.32        18.18       125.19        11.61        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS 
      228.99       170.20       137.79        29.06       129.63       117.17 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         6.41        18.12        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
        9.90        66.25        22.95        20.38       194.83        35.93 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
       61.18        65.92        23.44        68.09        28.60        15.68 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        17.85        68.25        54.02         6.35        12.20 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B 
       27.22         8.65        33.73        14.70        26.89       133.81 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       91.56       168.26        13.55        63.35        80.61        13.97 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A0 
       18.61        56.42        37.35        14.47       195.02        46.82 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
       86.14        59.28       314.56       161.03       208.04        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48        90.97       126.81        14.30        55.59 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
       94.82        28.83        19.76       103.27       268.73        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT 
      204.66        96.23       158.63       203.05       167.90        71.21 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73         3.68        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 
      127.20        53.19        27.35        51.35       148.08        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       50.76        77.75        98.40        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89         8.88       148.18        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        16.37        32.05       247.04        80.32 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD 
       33.21         6.77        15.72        15.16        38.27        29.46 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       94.39       216.92       228.59       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        23.93       101.26        74.73        11.41       148.80 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB 
       27.02        77.82        66.67        28.73       174.84        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45        77.88        47.54         0.16        19.30         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A26A 
        7.23         2.04        11.74       139.89       117.93        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       39.58        46.36        50.10        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      357.04       294.77         6.67         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8K5 
       63.02       121.08         4.01        42.08       219.16        54.38 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT 
        8.61        90.28        56.98        59.41        52.34         3.75 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       15.16        14.43        23.64        93.07 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.20               0.16 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            369.93             357.37 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            48.590             53.355 
[1] "0.2 - 369.9 (48.6)" "0.2 - 357.4 (53.4)"
[1] "hr=" "1.2"
D70V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P LOSS MUTATED                   19             1
  17P LOSS WILD-TYPE                 42             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17P LOSS MUTATED                                          18
  17P LOSS WILD-TYPE                                        54
                    vv
clus                 REGIONAL LYMPH NODE
  17P LOSS MUTATED                    85
  17P LOSS WILD-TYPE                 124
D70V4, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  DISTANT METASTASIS                                      19                 42
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               18                 54
  REGIONAL LYMPH NODE                                     85                124
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17P LOSS MUTATED             5       3      14       10        9        4
  17P LOSS WILD-TYPE           7       4      14        7       18       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17P LOSS MUTATED           4         7         3        11          7
  17P LOSS WILD-TYPE        10        12         9        24          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           11         22        4
  17P LOSS WILD-TYPE         21         36       15
D70V5, multiclass
             clus
vv            17P LOSS MUTATED 17P LOSS WILD-TYPE
  I OR II NOS                5                  7
  STAGE 0                    3                  4
  STAGE I                   14                 14
  STAGE IA                  10                  7
  STAGE IB                   9                 18
  STAGE II                   4                 18
  STAGE IIA                  4                 10
  STAGE IIB                  7                 12
  STAGE IIC                  3                  9
  STAGE III                 11                 24
  STAGE IIIA                 7                  8
  STAGE IIIB                11                 21
  STAGE IIIC                22                 36
  STAGE IV                   4                 15
[1] 14  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                 T0+T1 T2 T3 T4
  17P LOSS MUTATED      23 29 23 25
  17P LOSS WILD-TYPE    40 42 51 42
D70V6, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               23                 40
  T2                  29                 42
  T3                  23                 51
  T4                  25                 42
[1] 4 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                  N0  N1  N2  N3
  17P LOSS MUTATED    59  21  14  18
  17P LOSS WILD-TYPE 109  40  24  29
D70V7, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               59                109
  N1               21                 40
  N2               14                 24
  N3               18                 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"
                    vv
clus                  M0  M1 M1A M1B M1C
  17P LOSS MUTATED   113   1   0   1   3
  17P LOSS WILD-TYPE 193   3   3   3   6
D70V8, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               113                193
  M1                 1                  3
  M1A                0                  3
  M1B                1                  3
  M1C                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   54 32
  17P LOSS WILD-TYPE 75 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     54   32
  17P LOSS WILD-TYPE   75   55
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                54                 75
  YES               32                 55
[1] 2 2
[1] FALSE
D70V10, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    14 109
  17P LOSS WILD-TYPE  29 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     14  109
  17P LOSS WILD-TYPE   29  195
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                14                 29
  YES              109                195
[1] 2 2
[1] FALSE
D70V11, continuous
D70V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    38  85
  17P LOSS WILD-TYPE  93 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     38   85
  17P LOSS WILD-TYPE   93  132
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               38                 93
  MALE                 85                132
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       1                         1   113
  17P LOSS WILD-TYPE     4                         0   213
D70V13, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  113                213
[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"
D70V14, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1 119
  17P LOSS WILD-TYPE   6 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1  119
  17P LOSS WILD-TYPE    6  215
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              119                215
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    29  30
  17Q LOSS WILD-TYPE 139 135
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                59                274 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                30                135 
$`17Q LOSS MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JN 
        3.02         6.97        10.29        11.41         7.50        56.19 
TCGA-D3-A2JO TCGA-D3-A51N TCGA-D3-A8GI TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW 
       64.44        21.44         4.18        11.31        13.22        35.80 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A180 TCGA-EE-A29C TCGA-EE-A29E 
       13.68        44.52        25.15         8.12        37.97        62.79 
TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M5 
        8.09         9.67        30.08         5.42        34.98         8.84 
TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AA 
       98.27        47.51        44.25        26.99        21.60       124.31 
TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-ER-A193 
       30.15        21.60        16.14         0.95        21.73        31.40 
TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19S TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A8YC 
        3.78        13.45        36.07         6.71         5.36         2.20 
TCGA-FS-A1Z4 TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
       15.52        30.87         8.65        40.64        27.39         0.82 
TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A267 TCGA-QB-AA9O 
        3.22        10.78         0.20         0.99        16.24        18.05 
TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-AA3V 
       21.83         5.36         1.08         6.18         5.98 

$`17Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
        6.97        16.47         8.52       111.09        32.42        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
      110.79        28.08        22.55        45.83        81.24        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
        8.38        21.14        88.50        68.22        86.76        44.19 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       36.16         6.31        92.42        59.57       114.67        15.25 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32        82.29        61.38        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
        6.31         9.34       103.59        26.37        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       54.74        31.30        54.31        32.28        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      110.24        52.01        47.87        13.68        17.72        23.11 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       29.72        22.06        10.22        15.19       142.45       108.79 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       38.93        75.65       124.47        87.62        11.44         5.56 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG 
       24.07         4.01        21.93         5.72         9.90        14.60 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 
       48.79        51.12        10.03        39.19         9.99        36.69 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       14.83        13.15         0.20         0.13        23.15        19.00 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       13.35        13.22         0.20        11.57        10.55         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        60.23 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34        15.85         9.21         1.18         7.99         9.90 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15         8.55        36.85         1.08        39.62         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.09         8.84         9.99        30.44         2.43 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
       32.15        11.31        49.22        36.30        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        60.00        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        28.31        33.83        55.69         1.15        13.02 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       36.33         2.70         6.18         9.53        29.46         2.73 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
       25.08        60.49        53.16        52.67         5.56       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
       51.62         3.68        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       22.92        21.60        22.22        27.35        18.41        33.60 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.52        11.90        11.11       114.15        34.88         4.21 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W 
       28.60        42.84        34.68         9.57         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD 
       18.41        85.74        15.72         3.58        13.28         4.70 
TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.29        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       11.08         7.17        12.92        12.89        47.38        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.81        49.15         8.68         5.23        53.85         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU 
       28.73        14.20         5.98         6.41         2.27         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A 
       44.28        31.33        84.72        10.13        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
       14.70        11.84        10.65        14.50        14.50        14.50 
TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       15.81         0.43        11.05         5.79         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W 
      164.19         8.98        60.03         2.99        10.98       185.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       71.01        11.84         5.49         6.48         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA3 
       21.07        13.12         3.72         3.42        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       12.07         4.70         8.22         6.67 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.13 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            124.31             185.16 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            13.680             14.765 
[1] "0.2 - 124.3 (13.7)" "0.1 - 185.2 (14.8)"
[1] "hr=" "1.2"
D71V2, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    30  30
  17Q LOSS WILD-TYPE 143 136
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                60                279 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                30                136 
$`17Q LOSS MUTATED`
TCGA-3N-A9WB TCGA-3N-A9WD TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JN 
       17.03        12.99        43.43        11.87       113.52        56.19 
TCGA-D3-A2JO TCGA-D3-A51N TCGA-D3-A8GI TCGA-D9-A148 TCGA-D9-A6EA TCGA-D9-A6EC 
       66.08        22.62        58.52       151.53        25.18        66.25 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A180 TCGA-EE-A29C 
       36.03       176.55       107.34        53.92        94.98        47.84 
TCGA-EE-A29E TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GT 
       63.78        17.92        39.29        48.72        13.91        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MQ 
       21.67       129.27        61.51       103.20       248.65        43.23 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
      124.31        54.51        64.08        34.32       201.80       109.58 
TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19S TCGA-FR-A729 TCGA-FR-A7U9 
       31.40        48.89       131.51        37.25       210.08         7.00 
TCGA-FR-A8YC TCGA-FS-A1Z4 TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
       34.82        28.08        32.75       133.55        53.16        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A267 
       27.09        50.14        12.43         0.20        22.92        64.44 
TCGA-QB-AA9O TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-AA3V 
       18.05        22.68        43.73         2.20        36.03        11.74 

$`17Q LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 
       61.02        16.57        16.67       112.04       112.57        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
      133.25        28.08        31.59        90.90        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        86.76        62.07 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10       171.58        59.57       130.72        58.06 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       46.98        46.32       166.52        86.93        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T 
       55.73        56.35       145.12        32.94        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      125.79       135.75       137.92       178.32        18.18       125.19 
TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GJ TCGA-D3-A8GK 
       30.84        79.59        11.61        15.19       228.99       170.20 
TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR 
       89.13        95.24       161.00       137.79        29.06       129.63 
TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 
      117.17        54.67         3.65         6.41        18.12        11.34 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       22.29        11.11         9.90        22.95        48.89       117.21 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       20.38       194.83        35.93        61.18        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.16        17.85        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        6.35        12.20        29.82        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
       14.70        26.89        68.15         4.96       133.81       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       91.56       168.26        13.55        63.35        80.61        13.97 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        64.64         2.60        56.84        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       37.35        14.47        55.92       369.93        25.87       195.02 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       161.03       208.04        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU 
       75.48        90.97       126.81        14.30        55.59        94.82 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
       28.83        19.76        47.28       103.27       268.73        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       158.63       203.05       167.90        47.54 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      134.40       162.48        71.21        53.26       122.73        51.62 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 
       36.95        53.19        27.35        51.35       148.08        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       13.94        50.76         9.17        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       13.02        26.37       268.93       152.35         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89         8.88       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
      247.04        80.32        46.98        33.21         6.77        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7UA TCGA-FR-A8YD TCGA-FR-A8YE 
      174.21        15.72        15.16        38.27        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
      216.92        48.59       228.59       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
        9.70        47.38        23.93       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
      148.80        26.56        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV 
      174.84        26.73        49.45        77.88        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 
       19.30         9.90         7.23         2.04        11.74       139.89 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        10.13        62.79        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       46.36        12.62        50.10        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 
      357.04       294.77         6.67         0.33         0.69       212.22 
TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
       63.02       121.08         4.01        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        38.56        54.38         8.61        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 
       59.41        52.34         3.75        30.18        10.36        15.16 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       14.43        23.64        93.07 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.16 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            248.65             369.93 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             46.36              52.01 
[1] "0.2 - 248.7 (46.4)" "0.2 - 369.9 (52.0)"
[1] "hr=" "1.2"
D71V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q LOSS MUTATED                    9             2
  17Q LOSS WILD-TYPE                 52             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17Q LOSS MUTATED                                          10
  17Q LOSS WILD-TYPE                                        62
                    vv
clus                 REGIONAL LYMPH NODE
  17Q LOSS MUTATED                    42
  17Q LOSS WILD-TYPE                 167
D71V4, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       9                 52
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               10                 62
  REGIONAL LYMPH NODE                                     42                167
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  17Q LOSS MUTATED             3       1       9        5        4        0
  17Q LOSS WILD-TYPE           9       6      19       12       23       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17Q LOSS MUTATED           2         4         1         6          6
  17Q LOSS WILD-TYPE        12        15        11        29          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED            5          9        4
  17Q LOSS WILD-TYPE         27         49       15
D71V5, multiclass
             clus
vv            17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    1                  6
  STAGE I                    9                 19
  STAGE IA                   5                 12
  STAGE IB                   4                 23
  STAGE II                   0                 22
  STAGE IIA                  2                 12
  STAGE IIB                  4                 15
  STAGE IIC                  1                 11
  STAGE III                  6                 29
  STAGE IIIA                 6                  9
  STAGE IIIB                 5                 27
  STAGE IIIC                 9                 49
  STAGE IV                   4                 15
[1] 14  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                 T0+T1 T2 T3 T4
  17Q LOSS MUTATED      13 15 13 11
  17Q LOSS WILD-TYPE    50 56 61 56
D71V6, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1               13                 50
  T2                  15                 56
  T3                  13                 61
  T4                  11                 56
[1] 4 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                  N0  N1  N2  N3
  17Q LOSS MUTATED    29  14   5   9
  17Q LOSS WILD-TYPE 139  47  33  38
D71V7, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               29                139
  N1               14                 47
  N2                5                 33
  N3                9                 38
[1] 4 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                  M0  M1 M1A M1B M1C
  17Q LOSS MUTATED    55   1   0   1   3
  17Q LOSS WILD-TYPE 251   3   3   3   6
D71V8, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                55                251
  M1                 1                  3
  M1A                0                  3
  M1B                1                  3
  M1C                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   30 14
  17Q LOSS WILD-TYPE 99 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     30   14
  17Q LOSS WILD-TYPE   99   73
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                30                 99
  YES               14                 73
[1] 2 2
[1] FALSE
D71V10, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     7  56
  17Q LOSS WILD-TYPE  36 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   56
  17Q LOSS WILD-TYPE   36  248
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 7                 36
  YES               56                248
[1] 2 2
[1] FALSE
D71V11, continuous
D71V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    21  42
  17Q LOSS WILD-TYPE 110 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21   42
  17Q LOSS WILD-TYPE  110  175
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               21                110
  MALE                 42                175
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0    59
  17Q LOSS WILD-TYPE     5                         1   267
D71V13, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   59                267
[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"
D71V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  62
  17Q LOSS WILD-TYPE   6 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   62
  17Q LOSS WILD-TYPE    6  272
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               62                272
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    48  49
  18P LOSS WILD-TYPE 120 116
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                97                236 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                49                116 
$`18P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       16.47        70.16        85.32        86.76        11.41        44.19 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MR 
       92.42        64.44        59.57        15.25        46.98       103.59 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       26.37        54.31       110.24        13.68        23.11        22.06 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A6EG 
       10.22         4.18       124.47         5.56        24.07        14.60 
TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A5SG 
       48.79        13.68        36.69        25.15        17.56        23.15 
TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G 
       13.22        60.23         4.34         7.99        11.15         8.55 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GC 
       39.62        30.44         2.43        32.15         8.09        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG 
       17.98        60.00        30.08         5.42         1.15        44.25 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      125.65        56.02        21.60        53.16         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      122.73         3.68        30.15        15.95        12.72         3.22 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 
       16.14        22.22        21.73        33.60        31.40         5.72 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19Q TCGA-ER-A19S 
       25.18         3.78        11.90        34.88         9.57        36.07 
TCGA-ER-A19T TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1ZA 
        6.58         5.62        85.74        15.72         3.58         7.30 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY 
       47.38         8.65         8.81        49.15        27.39         0.82 
TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
        0.13        15.42        10.65        14.50        14.50        14.50 
TCGA-W3-A825 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
        8.98        11.84         5.49         5.36         1.08         6.18 
TCGA-Z2-A8RT 
        8.22 

$`18P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.79        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH 
        8.38        21.14        88.50        68.22         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
        6.31        56.19       114.67        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       13.32        24.00         6.31         9.34        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       54.74        31.30        32.28        21.44        32.61        25.78 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ 
       52.01        47.87        17.72        29.72        15.19       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A3Z1 
      108.79        38.93        75.65        87.62        11.44         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW 
       21.93         5.72         9.90        11.31        13.22        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA 
       51.12        10.03        39.19         9.99        44.52         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17X 
        0.20         0.13        19.00        13.35         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B 
        5.13         4.31        15.85         9.21         1.18         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        62.79        36.85         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.09         8.84         9.99        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
        9.67        36.33        51.12        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT 
       35.54        28.31        33.83        55.69        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46         2.73         7.96        14.56        63.42 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC 
      111.91        25.08        26.99        60.49        52.67        51.62 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD 
       13.81        22.92        21.60        21.60         0.95        27.35 
TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D 
       18.41        18.61        12.95        38.40        76.41         3.52 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       11.11       114.15         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       34.68        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
        1.71        18.41         6.71         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        4.70         3.29        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       14.24        15.52         7.33         3.39        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       19.53        11.08         7.17        30.87        12.92        12.89 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       52.08        40.64         8.68         5.23        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.99         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-HR-A2OH 
       10.13        16.24        12.16        14.70        11.84        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
        0.43        11.05         5.79        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      164.19        60.03         2.99        10.98       185.16        71.01 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        6.48         7.10        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P 
        3.42        21.83        19.96         1.94        12.07         4.70 
TCGA-Z2-AA3S TCGA-Z2-AA3V 
        6.67         5.98 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.13               0.13 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            125.65             185.16 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             16.47              13.40 
[1] "0.1 - 125.7 (16.5)" "0.1 - 185.2 (13.4)"
[1] "hr=" "1.1"
D72V2, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    49  50
  18P LOSS WILD-TYPE 124 116
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                99                240 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                50                116 
$`18P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       16.57        71.80       103.10        86.76        11.87        62.07 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MR 
      171.58        66.08        59.57        58.06        46.98       103.59 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC 
       39.75       145.12       125.79       178.32       125.19        79.59 
TCGA-D3-A8GD TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A1JX 
       11.61        58.52       161.00       129.63       117.17         6.41 
TCGA-D9-A1X3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 
       18.12        22.95        48.89       176.55        61.18        53.92 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A 
      215.44        68.25        52.01       133.81       151.27        63.35 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       13.97        72.07        56.84       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GP 
       17.92        67.43       314.56       161.03        48.72        13.91 
TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS 
       14.30       103.20       158.63       167.90        43.23       162.48 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
       53.26       124.31       122.73         3.68        54.51        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
      138.81       172.18        34.32        53.19       109.58       148.08 
TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H 
       31.40         9.17        98.40        48.89        13.02       152.35 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A42K TCGA-FR-A44A TCGA-FR-A69P 
       50.89        37.25         8.88         6.77       174.21        15.72 
TCGA-FR-A7U8 TCGA-FS-A1ZA TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       15.16        27.72       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK 
       49.48        27.09        47.54        62.79        12.62        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-W3-A825 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZY 
       21.37        59.41        63.02        24.03        38.56        43.73 
TCGA-WE-AA9Y TCGA-YG-AA3O TCGA-Z2-A8RT 
        2.20        36.03        23.64 

$`18P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH 
       65.49        23.77       115.53       168.00       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       12.10        56.19       130.72        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       60.23        24.53        13.87         9.34        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       55.73        56.35        32.94        22.62        63.81        26.89 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GJ 
      135.75       137.92        18.18        30.84        15.19       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D9-A148 
      170.20        89.13        95.24       137.79        29.06       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
       54.67         3.65        11.34        22.29        11.11         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        66.25        36.03       117.21        20.38       194.83 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93       107.34        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
       10.49        15.68        13.87        10.16        17.85        54.02 
TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       17.29         6.35        12.20        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       91.56       168.26        13.55        80.61        47.84        63.78 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64         2.60        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       55.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       59.28       208.04        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       90.97       126.81        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      268.73        16.96       204.66        96.23       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 
      248.65       134.40        71.21        51.62        13.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 
       36.95        64.08       201.80        27.35        51.35        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       13.94        50.76        77.75        12.59        26.37       268.93 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W 
        6.44       131.51        61.05        44.05       162.08       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       32.05       247.04        80.32        46.98        33.21        92.98 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      210.08         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      216.92        48.59       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.79        48.85       357.37        53.52        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT 
        9.70        32.75        47.38        23.93        74.73        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       22.92         0.16        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       32.48        39.58        46.36        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        6.67        18.05         0.33         0.69       212.22       121.08 
TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 
        4.01        42.08       219.16       105.04        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       90.28        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-AA3S TCGA-Z2-AA3V 
       30.18        10.36        15.16        14.43        93.07        11.74 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              2.20               0.16 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            369.93             357.37 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             58.06              47.13 
[1] "2.2 - 369.9 (58.1)" "0.2 - 357.4 (47.1)"
[1] "hr=" "1.1"
D72V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P LOSS MUTATED                   18             1
  18P LOSS WILD-TYPE                 43             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18P LOSS MUTATED                                          24
  18P LOSS WILD-TYPE                                        48
                    vv
clus                 REGIONAL LYMPH NODE
  18P LOSS MUTATED                    60
  18P LOSS WILD-TYPE                 149
D72V4, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  DISTANT METASTASIS                                      18                 43
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               24                 48
  REGIONAL LYMPH NODE                                     60                149
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18P LOSS MUTATED             5       3       7        6       10        7
  18P LOSS WILD-TYPE           7       4      21       11       17       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18P LOSS MUTATED           1         6         2        12          6
  18P LOSS WILD-TYPE        13        13        10        23          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED            6         19        2
  18P LOSS WILD-TYPE         26         39       17
D72V5, multiclass
             clus
vv            18P LOSS MUTATED 18P LOSS WILD-TYPE
  I OR II NOS                5                  7
  STAGE 0                    3                  4
  STAGE I                    7                 21
  STAGE IA                   6                 11
  STAGE IB                  10                 17
  STAGE II                   7                 15
  STAGE IIA                  1                 13
  STAGE IIB                  6                 13
  STAGE IIC                  2                 10
  STAGE III                 12                 23
  STAGE IIIA                 6                  9
  STAGE IIIB                 6                 26
  STAGE IIIC                19                 39
  STAGE IV                   2                 17
[1] 14  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                 T0+T1 T2 T3 T4
  18P LOSS MUTATED      23 21 17 21
  18P LOSS WILD-TYPE    40 50 57 46
D72V6, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               23                 40
  T2                  21                 50
  T3                  17                 57
  T4                  21                 46
[1] 4 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                  N0  N1  N2  N3
  18P LOSS MUTATED    45  16  13  15
  18P LOSS WILD-TYPE 123  45  25  32
D72V7, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               45                123
  N1               16                 45
  N2               13                 25
  N3               15                 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"
                    vv
clus                  M0  M1 M1A M1B M1C
  18P LOSS MUTATED    93   0   1   0   1
  18P LOSS WILD-TYPE 213   4   2   4   8
D72V8, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                93                213
  M1                 0                  4
  M1A                1                  2
  M1B                0                  4
  M1C                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   36 24
  18P LOSS WILD-TYPE 93 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     36   24
  18P LOSS WILD-TYPE   93   63
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                36                 93
  YES               24                 63
[1] 2 2
[1] FALSE
D72V10, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    16  86
  18P LOSS WILD-TYPE  27 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16   86
  18P LOSS WILD-TYPE   27  218
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                16                 27
  YES               86                218
[1] 2 2
[1] FALSE
D72V11, continuous
D72V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    40  63
  18P LOSS WILD-TYPE  91 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     40   63
  18P LOSS WILD-TYPE   91  154
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               40                 91
  MALE                 63                154
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         0    99
  18P LOSS WILD-TYPE     5                         1   227
D72V13, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   99                227
[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"
D72V14, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     2  99
  18P LOSS WILD-TYPE   5 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   99
  18P LOSS WILD-TYPE    5  235
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               99                235
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    42  48
  18Q LOSS WILD-TYPE 126 117
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                90                243 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                48                117 
$`18Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD 
       16.47        70.16        22.55        85.32        86.76        11.41 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MR 
       44.19        92.42        64.44        15.25        13.32       103.59 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       26.37        54.31        13.68        23.11        22.06        10.22 
TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A6EC TCGA-DA-A1HV 
        4.18       124.47         5.56        24.07        13.22        48.79 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A5SG 
       13.68        36.69        25.15         4.93        17.56        23.15 
TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G 
       13.22        60.23         4.34         7.99        11.15         8.55 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2GC 
       39.62        30.44         2.43        32.15         8.09        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG 
       17.98        60.00        30.08         5.42         1.15        44.25 
TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
      125.65        21.60         5.56       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH 
       30.15        12.72         3.22        16.14        22.22        21.73 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19H 
       33.60        31.40         5.72        25.18         3.78        34.88 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P 
       36.07         6.58        17.72        22.49        85.74        15.72 
TCGA-FR-A7U8 TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY 
        3.58        47.38         8.65        49.15        27.39         0.82 
TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD 
        0.13        15.42        10.65        14.50        14.50        14.50 
TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3O 
        8.98        10.98         5.49         5.36         1.08         6.18 

$`18Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      110.79        28.08        45.83        81.24        10.29         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       21.14        88.50        68.22         7.50        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        59.57       114.67        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       61.38        24.00         6.31         9.34        29.23        93.21 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       54.74        31.30        32.28        21.44        32.61        25.78 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE 
      110.24        52.01        47.87        17.72        29.72        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ 
      142.45       108.79        38.93        75.65        87.62        11.44 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
        4.01        21.93         5.72         9.90        11.31        14.60 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        10.03        39.19         9.99        44.52 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       22.36         6.64        19.36         7.00        14.83        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17X 
        0.20         0.13        19.00        13.35         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B 
        5.13         4.31        15.85         9.21         1.18         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        62.79        36.85         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.09         8.84         9.99        11.31        49.22        36.30 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
        9.67        36.33        51.12        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT 
       35.54        28.31        33.83        55.69        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46         2.73         7.96        14.56        63.42 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      111.91        56.02        25.08        26.99        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 
       52.67        51.62        13.81        15.95        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 
       21.60         0.95        27.35        18.41        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
       38.40        76.41         3.52        11.90        11.11       114.15 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
       11.74         9.04         6.58         1.71         5.62        18.41 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        6.71         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
        7.33         7.30         3.39        20.38         8.22        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        12.89        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
        8.81        40.64         8.68         5.23        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        7.36        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.20         0.99         0.16        17.33         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        7.23         0.85        11.61        44.28        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-HR-A2OH 
       10.13        16.24        12.16        14.70        11.84        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
        0.43        11.05         5.79        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ 
      164.19        60.03         2.99       185.16        71.01        11.84 
TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
        6.48         7.10        18.67        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P 
        3.42        21.83        19.96         1.94        12.07         4.70 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        8.22         6.67         5.98 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.13               0.13 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            125.65             185.16 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             17.64              13.45 
[1] "0.1 - 125.7 (17.6)" "0.1 - 185.2 (13.4)"
[1] "hr=" "1"  
D73V2, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    44  48
  18Q LOSS WILD-TYPE 129 118
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                92                247 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                48                118 
$`18Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JD 
       16.57        71.80        31.59       103.10        86.76        11.87 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MR 
       62.07       171.58        66.08        58.06        60.23       103.59 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       39.75       145.12       178.32       125.19        79.59        11.61 
TCGA-D3-A8GI TCGA-D3-A8GN TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1X3 
       58.52       161.00       129.63       117.17       151.53        18.12 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       66.25        48.89       176.55        61.18        53.92        65.92 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A 
      215.44        68.25        52.01       133.81       151.27        63.35 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       13.97        72.07        56.84       369.93        25.87       195.02 
TCGA-EE-A29X TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GP 
       17.92        67.43       314.56       161.03        48.72        13.91 
TCGA-EE-A2GR TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA 
       14.30       103.20       158.63        43.23        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J8 
      122.73         3.68        54.51       138.81       172.18        34.32 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B 
       53.19       109.58       148.08        31.40         9.17        98.40 
TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A3EV 
       48.89       152.35        37.25         8.88       148.18        46.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
      174.21        15.72        15.16       101.26       133.55       148.80 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A8LK 
       49.48        27.09        47.54        62.79        12.62        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8K1 TCGA-WE-A8ZY 
       21.37        59.41        63.02        42.08        38.56        43.73 
TCGA-WE-AA9Y TCGA-YG-AA3O 
        2.20        36.03 

$`18Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 
      133.25        28.08        90.90        95.74        43.43        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       115.53       168.00       113.52        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        59.57       130.72        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E 
       86.93        24.53        13.87         9.34        45.30       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       55.73        56.35        32.94        22.62        63.81        26.89 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A8GB TCGA-D3-A8GE 
      125.79       135.75       137.92        18.18        30.84        15.19 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ 
      228.99       170.20        89.13        95.24       137.79        29.06 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         3.65         6.41        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.90        25.18        22.95        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      194.83        35.93       107.34        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
       10.49        15.68        13.87        10.16        17.85        54.02 
TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
       17.29         6.35        12.20        29.82        27.22         8.65 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       94.98        33.73        14.70        26.89        68.15         4.96 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       91.56       168.26        13.55        80.61        47.84        63.78 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       64.64         2.60        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       55.92        46.82       102.90        36.82        39.29        86.14 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       59.28       208.04        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       90.97       126.81        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      268.73        16.96       204.66        96.23       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC 
       47.54       248.65       134.40       162.48        71.21        51.62 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JB 
       13.81        23.47       127.20        36.95        64.08       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       27.35        51.35        35.44        13.94        50.76        77.75 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       12.59        13.02        26.37       268.93         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC 
       61.05        44.05       162.08        50.89        79.99        43.82 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       23.34        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U9 
       80.32        33.21         6.77        92.98       210.08         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        29.46        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT 
       32.75        47.38        23.93        74.73        11.41        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        27.02        77.82        50.14        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
      174.84        12.43        26.73        49.45        77.88         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       22.92         0.16        19.30         9.90         7.23         2.04 
TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       11.74       139.89       117.93        84.72        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       32.48        39.58        46.36        65.88       357.04       294.77 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        6.67        18.05         0.33         0.69       212.22       121.08 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K5 TCGA-WE-A8K6 
        4.01       219.16       105.04        24.03        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       90.28        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       30.18        10.36        15.16        14.43        23.64        93.07 
TCGA-Z2-AA3V 
       11.74 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              2.20               0.16 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            369.93             357.37 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            61.625             46.320 
[1] "2.2 - 369.9 (61.6)" "0.2 - 357.4 (46.3)"
[1] "hr=" "1.1"
D73V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q LOSS MUTATED                   19             2
  18Q LOSS WILD-TYPE                 42             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18Q LOSS MUTATED                                          21
  18Q LOSS WILD-TYPE                                        51
                    vv
clus                 REGIONAL LYMPH NODE
  18Q LOSS MUTATED                    54
  18Q LOSS WILD-TYPE                 155
D73V4, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      19                 42
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               21                 51
  REGIONAL LYMPH NODE                                     54                155
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  18Q LOSS MUTATED             5       3       6        6        8        6
  18Q LOSS WILD-TYPE           7       4      22       11       19       16
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18Q LOSS MUTATED           1         5         2        12          6
  18Q LOSS WILD-TYPE        13        14        10        23          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED            6         17        2
  18Q LOSS WILD-TYPE         26         41       17
D73V5, multiclass
             clus
vv            18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  I OR II NOS                5                  7
  STAGE 0                    3                  4
  STAGE I                    6                 22
  STAGE IA                   6                 11
  STAGE IB                   8                 19
  STAGE II                   6                 16
  STAGE IIA                  1                 13
  STAGE IIB                  5                 14
  STAGE IIC                  2                 10
  STAGE III                 12                 23
  STAGE IIIA                 6                  9
  STAGE IIIB                 6                 26
  STAGE IIIC                17                 41
  STAGE IV                   2                 17
[1] 14  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                 T0+T1 T2 T3 T4
  18Q LOSS MUTATED      21 18 17 19
  18Q LOSS WILD-TYPE    42 53 57 48
D73V6, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               21                 42
  T2                  18                 53
  T3                  17                 57
  T4                  19                 48
[1] 4 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                  N0  N1  N2  N3
  18Q LOSS MUTATED    40  16  12  14
  18Q LOSS WILD-TYPE 128  45  26  33
D73V7, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               40                128
  N1               16                 45
  N2               12                 26
  N3               14                 33
[1] 4 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                  M0  M1 M1A M1B M1C
  18Q LOSS MUTATED    84   0   1   1   1
  18Q LOSS WILD-TYPE 222   4   2   3   8
D73V8, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                84                222
  M1                 0                  4
  M1A                1                  2
  M1B                1                  3
  M1C                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   36 20
  18Q LOSS WILD-TYPE 93 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     36   20
  18Q LOSS WILD-TYPE   93   67
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                36                 93
  YES               20                 67
[1] 2 2
[1] FALSE
D73V10, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    14  82
  18Q LOSS WILD-TYPE  29 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     14   82
  18Q LOSS WILD-TYPE   29  222
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                14                 29
  YES               82                222
[1] 2 2
[1] FALSE
D73V11, continuous
D73V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    36  60
  18Q LOSS WILD-TYPE  95 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     36   60
  18Q LOSS WILD-TYPE   95  157
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               36                 95
  MALE                 60                157
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         0    93
  18Q LOSS WILD-TYPE     5                         1   233
D73V13, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   93                233
[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"
D73V14, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     2  93
  18Q LOSS WILD-TYPE   5 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   93
  18Q LOSS WILD-TYPE    5  241
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               93                241
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    33  35
  19P LOSS WILD-TYPE 135 130
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                68                265 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                35                130 
$`19P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A3MU 
       16.47        22.55        11.41        92.42        13.32        26.37 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GN 
       25.78       110.24        52.01        10.22        75.65       124.47 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       87.62        24.07        21.93        11.31        48.79        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44R 
       10.03        44.52        36.69        25.15         4.93         0.20 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H 
       13.35        11.57         9.21         1.18        11.15        36.85 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MS 
        8.09        11.31        28.31        44.25        26.99        53.16 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
       52.67       122.73         3.68        21.60        22.22        27.35 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19Q TCGA-ER-A19T TCGA-ER-A2NH TCGA-ER-A3EV 
       25.18         3.78         9.57         6.58        11.74        22.49 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       85.74        15.72        30.87        12.92         8.65        40.64 
TCGA-FS-A1ZW TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 
       27.39         5.98         2.27         0.16         7.23        44.28 
TCGA-GN-A268 TCGA-GN-A26A TCGA-W3-A825 TCGA-W3-AA1V TCGA-WE-A8JZ TCGA-WE-A8K1 
       15.42        12.16         8.98        10.98        11.84         5.49 
TCGA-WE-A8ZM TCGA-YG-AA3P 
       18.67         4.70 

$`19P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16       110.79        28.08        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
       85.32         8.38        21.14        88.50        68.22        86.76 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       44.19         7.50        36.16         6.31        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       59.57       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
       61.38        24.00         6.31         9.34       103.59        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       32.61        47.87        13.68        17.72        23.11        29.72 
TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       22.06        15.19         4.18       142.45       108.79        38.93 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC 
       11.44         5.56         4.01         5.72         9.90        13.22 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB 
       14.60        51.12        39.19        13.68         9.99        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
        6.64        19.36         7.00        17.56        14.83        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y 
        0.13        23.15        19.00        13.22         0.20        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B 
        4.31        60.23         4.34        15.85         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97        62.79         8.55         1.08        39.62         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.09         8.84         9.99        30.44         2.43 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       32.15        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        33.83        55.69         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46         2.73         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       125.65       111.91        56.02        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
       21.60        60.49         5.56       124.31        51.62        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14         0.95        18.41        21.73        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D 
       18.61        12.95        38.40         5.72        76.41         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       11.90        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       28.60        42.84        34.68        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       11.80         1.87         1.51        13.08        12.62         9.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 
        6.58         1.71         5.62        18.41         6.71         3.58 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        5.36        13.28         2.20         4.70         3.29        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.45        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.17        12.89        47.38        52.08         8.81        49.15 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
        8.68         0.82         5.23        53.85         3.22         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       28.73        14.20        10.78         6.41         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 
        0.13        17.33         9.90         0.85        11.61        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        10.13        16.24        14.70        11.84        10.65 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       14.50        14.50        14.50        15.81         0.43        11.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 
        5.79        18.05         0.33         0.69       164.19        60.03 
TCGA-W3-AA1O TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
        2.99       185.16        71.01         6.48         7.10        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y 
       13.12         3.72         3.42        21.83         5.36         1.08 
TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S 
       19.96         1.94        12.07         6.18         8.22         6.67 
TCGA-Z2-AA3V 
        5.98 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.16               0.13 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            124.47             185.16 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             17.57              14.50 
[1] "0.2 - 124.5 (17.6)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1"  
D74V2, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    35  35
  19P LOSS WILD-TYPE 138 131
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                70                269 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                35                131 
$`19P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A3MU 
       16.57        31.59        11.87       171.58        60.23        39.75 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GM TCGA-D3-A8GN 
       26.89       125.79       135.75        11.61        95.24       161.00 
TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1X3 TCGA-D9-A3Z3 TCGA-D9-A6EA 
      137.79       117.17       151.53        18.12        22.29        25.18 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       48.89        36.03        20.38       107.34        61.18        53.92 
TCGA-DA-A1IA TCGA-EB-A44R TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A20I 
       65.92        10.16        17.29        29.82       168.26        13.55 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2MG 
       13.97        64.64        17.92        46.82        75.48       103.20 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3J5 
      248.65       162.48        71.21       122.73         3.68        36.95 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19Q TCGA-ER-A19T 
       53.19        27.35        98.40        48.89        50.89         8.88 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       32.05        46.98       174.21        15.72        32.75        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TV 
      133.55        53.16        49.48        26.73        77.88         0.16 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-W3-A825 TCGA-W3-AA1V 
        7.23       139.89        62.79        32.48        63.02        42.08 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8ZM TCGA-YG-AA3P 
       24.03        38.56        90.28        14.43 

$`19P LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        28.08        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC 
      103.10        65.49        23.77       115.53       168.00        86.76 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       62.07       113.52        42.08        12.10        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       59.57       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
       86.93        24.53        13.87         9.34       103.59        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB 
       63.81       137.92       178.32        18.18       125.19        30.84 
TCGA-D3-A8GC TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL 
       79.59        15.19        58.52       228.99       170.20        89.13 
TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
       29.06       129.63        54.67         3.65         6.41        11.34 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
       11.11         9.90        66.25        22.95       117.21       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
      176.55        35.93        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        15.68        13.87        17.85        68.25        54.02 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       52.01         6.35        12.20        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      151.27        91.56        63.35        80.61        47.84        63.78 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07         2.60        56.84        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 
       14.47        55.92       369.93        25.87       195.02       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       36.82        39.29        86.14        59.28        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      161.03       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       126.81        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       94.82        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       268.73        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      158.63       203.05       167.90        47.54        43.23       134.40 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       53.26       124.31        51.62        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
      138.81       172.18       127.20        64.08        34.32       201.80 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       50.76         9.17        77.75        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      268.93       152.35         6.44       131.51        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      162.08        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       20.15        16.37        31.27       247.04        80.32        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA 
        6.77        92.98       210.08        15.16         7.00        38.27 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       34.82        29.46        94.39       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      202.65        20.91        28.08         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZK 
      357.37        53.52        40.27        15.45         9.70        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
      101.26        74.73        11.41       148.80        26.56        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY 
       12.43        49.45         0.20        22.92        47.54        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        9.90         2.04        11.74       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       64.44        39.58        46.36        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       59.41        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1W 
        0.33         0.69       212.22       121.08         4.01       219.16 
TCGA-W3-AA21 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      105.04        54.38         8.61        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        3.75        22.68        43.73         2.20        30.18        10.36 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        36.03        23.64        93.07        11.74 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.16               0.20 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            248.65             369.93 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            48.135             51.620 
[1] "0.2 - 248.7 (48.1)" "0.2 - 369.9 (51.6)"
[1] "hr=" "1.2"
D74V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P LOSS MUTATED                   12             2
  19P LOSS WILD-TYPE                 49             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19P LOSS MUTATED                                          12
  19P LOSS WILD-TYPE                                        60
                    vv
clus                 REGIONAL LYMPH NODE
  19P LOSS MUTATED                    45
  19P LOSS WILD-TYPE                 164
D74V4, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  DISTANT METASTASIS                                      12                 49
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               12                 60
  REGIONAL LYMPH NODE                                     45                164
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19P LOSS MUTATED             4       0       7        2        4        4
  19P LOSS WILD-TYPE           8       7      21       15       23       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19P LOSS MUTATED           1         3         1        11          2
  19P LOSS WILD-TYPE        13        16        11        24         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           10         12        5
  19P LOSS WILD-TYPE         22         46       14
D74V5, multiclass
             clus
vv            19P LOSS MUTATED 19P LOSS WILD-TYPE
  I OR II NOS                4                  8
  STAGE 0                    0                  7
  STAGE I                    7                 21
  STAGE IA                   2                 15
  STAGE IB                   4                 23
  STAGE II                   4                 18
  STAGE IIA                  1                 13
  STAGE IIB                  3                 16
  STAGE IIC                  1                 11
  STAGE III                 11                 24
  STAGE IIIA                 2                 13
  STAGE IIIB                10                 22
  STAGE IIIC                12                 46
  STAGE IV                   5                 14
[1] 14  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                 T0+T1 T2 T3 T4
  19P LOSS MUTATED      14 16 12 16
  19P LOSS WILD-TYPE    49 55 62 51
D74V6, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               14                 49
  T2                  16                 55
  T3                  12                 62
  T4                  16                 51
[1] 4 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                  N0  N1  N2  N3
  19P LOSS MUTATED    30  16  11  12
  19P LOSS WILD-TYPE 138  45  27  35
D74V7, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               30                138
  N1               16                 45
  N2               11                 27
  N3               12                 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"
                    vv
clus                  M0  M1 M1A M1B M1C
  19P LOSS MUTATED    62   0   2   1   3
  19P LOSS WILD-TYPE 244   4   1   3   6
D74V8, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                62                244
  M1                 0                  4
  M1A                2                  1
  M1B                1                  3
  M1C                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    27  15
  19P LOSS WILD-TYPE 102  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     27   15
  19P LOSS WILD-TYPE  102   72
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                27                102
  YES               15                 72
[1] 2 2
[1] FALSE
D74V10, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     9  62
  19P LOSS WILD-TYPE  34 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9   62
  19P LOSS WILD-TYPE   34  242
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 9                 34
  YES               62                242
[1] 2 2
[1] FALSE
D74V11, continuous
D74V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    32  39
  19P LOSS WILD-TYPE  99 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     32   39
  19P LOSS WILD-TYPE   99  178
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               32                 99
  MALE                 39                178
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         0    67
  19P LOSS WILD-TYPE     4                         1   259
D74V13, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   67                259
[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"
D74V14, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  68
  19P LOSS WILD-TYPE   6 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   68
  19P LOSS WILD-TYPE    6  266
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               68                266
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    32  32
  19Q LOSS WILD-TYPE 136 133
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                64                269 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                32                133 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A3MU TCGA-D3-A51T TCGA-D3-A5GL 
       22.55        11.41        92.42        26.37        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A3Z3 TCGA-D9-A6EA 
       52.01        75.65        87.62        24.07        21.93        11.31 
TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       48.79        10.03        44.52        36.69        25.15         4.93 
TCGA-EB-A44R TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H 
        0.20        11.57         9.21         1.18        11.15        36.85 
TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2GO TCGA-EE-A2MG TCGA-EE-A2MM 
       39.62         9.99         8.09        55.69        44.25        56.02 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG 
       26.99        53.16        52.67       122.73         3.68        15.95 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19T TCGA-ER-A2NH 
       22.22        27.35        25.18         3.78         6.58        11.74 
TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZT 
       22.49        85.74        15.72        30.87        12.92        40.64 
TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO 
       27.39         3.22         5.98         2.27         0.16         7.23 
TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-W3-A825 TCGA-W3-AA21 
       44.28        15.42        12.16        14.70         8.98        71.01 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-YG-AA3P 
        5.49         6.48        18.67         4.70 

$`19Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       32.42        70.16       110.79        28.08        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       10.29        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       86.76        44.19         7.50        36.16         6.31        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       64.44        59.57       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        29.23        93.21        54.74        31.30        54.31 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.28        21.44        32.61        47.87        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       23.11        29.72        22.06        10.22        15.19         4.18 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      142.45       108.79        38.93       124.47        11.44         5.56 
TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
        4.01         5.72         9.90        13.22        14.60        35.80 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC 
       51.12        39.19        13.68         9.99        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH 
       19.36         7.00        17.56        14.83        13.15         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y 
       23.15        19.00        13.35        13.22         0.20        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.31         8.12         1.12         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B 
        4.31        60.23         4.34        15.85         7.99         9.90 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        62.79         8.55         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 
        8.09         8.84        30.44         2.43        32.15        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       35.54        28.31        33.83         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       34.98        36.33         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46         2.73         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
       63.42       125.65       111.91        25.08        21.60        60.49 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
        5.56       124.31        51.62        30.15        13.81        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
        3.22        22.92        21.60        21.60        16.14         0.95 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       38.40         5.72        76.41         3.52        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
      114.15        34.88         4.21        13.45        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
        1.87         1.51        13.08        12.62         9.04         6.58 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
        1.71         5.62        18.41         6.71         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       13.28         2.20         4.70         3.29        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        3.39        20.38         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.89        47.38        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.68         0.82         5.23        53.85         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       14.20        10.78         6.41         0.20         0.99         0.13 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
       17.33         9.90         0.85        11.61        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       10.13        16.24        11.84        10.65        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        15.81         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
        0.33         0.69       164.19        60.03         2.99        10.98 
TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
      185.16        11.84         7.10        21.07        13.12         3.72 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
        3.42        21.83         5.36         1.08        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       12.07         6.18         8.22         6.67         5.98 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.16               0.13 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            122.73             185.16 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            22.075             14.240 
[1] "0.2 - 122.7 (22.1)" "0.1 - 185.2 (14.2)"
[1] "hr=" "1.1"
D75V2, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    34  32
  19Q LOSS WILD-TYPE 139 134
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                66                273 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                32                134 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A3MU TCGA-D3-A51T TCGA-D3-A5GL 
       31.59        11.87       171.58        39.75        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1X3 
      135.75        95.24       137.79       117.17       151.53        18.12 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.29        25.18        48.89        20.38       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44R TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A20I 
       53.92        65.92        10.16        29.82       168.26        13.55 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2GO 
       13.97        64.64        56.84        55.92        17.92       126.81 
TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB 
      103.20       167.90       248.65       162.48        71.21       122.73 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C 
        3.68        23.47        53.19        27.35        98.40        48.89 
TCGA-ER-A19T TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH 
        8.88        32.05        46.98       174.21        15.72        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FD 
       47.38        53.16        49.48        50.14        26.73        77.88 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
        0.16         7.23       139.89        62.79        32.48        39.58 
TCGA-W3-A825 TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8ZM TCGA-YG-AA3P 
       63.02       105.04        38.56        54.38        90.28        14.43 

$`19Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
      112.57        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       86.76        62.07       113.52        42.08        12.10        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       66.08        59.57       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
      103.59        45.30       174.84        55.73        56.35       145.12 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       32.94        22.62        63.81       137.92       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
      125.19        30.84        79.59        11.61        15.19        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GN TCGA-D3-A8GQ TCGA-D3-A8GR 
      228.99       170.20        89.13       161.00        29.06       129.63 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A4Z6 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34        11.11         9.90 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       66.25        22.95        36.03       117.21       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       35.93        23.44        68.09        28.60        10.49       215.44 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       15.68        13.87        17.85        68.25        54.02        17.29 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       52.01         6.35        12.20        27.22         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       33.73        14.70        26.89        68.15         4.96       133.81 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      151.27        91.56        63.35        80.61        47.84        63.78 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       72.07         2.60        18.61        56.42        37.35        14.47 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
      369.93        25.87       195.02        46.82       102.90        36.82 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        86.14        59.28        67.43       314.56       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       90.97        13.91        14.30        55.59        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       21.67       129.27        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       268.73        16.96       204.66        96.23       158.63 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
      203.05        47.54        43.23       134.40        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       51.62        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32       201.80        51.35       109.58 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      148.08        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       77.75        12.59        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25       148.18        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-ER-A42K 
       16.37        31.27       247.04        80.32        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       92.98       210.08        15.16         7.00        38.27        34.82 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       29.46        94.39       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
       20.91        28.08         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM 
       53.52        40.27        15.45         9.70        23.93       101.26 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       74.73       133.55        11.41       148.80        26.56        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        77.82        66.67        28.73       174.84        12.43 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45         0.20        22.92        47.54        19.30         9.90 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.04        11.74       117.93        84.72        10.13        64.44 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       46.36        12.62        50.10        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      357.04       294.77         6.67        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ 
      212.22       121.08         4.01        42.08       219.16        24.03 
TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
        8.61        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       43.73         2.20        30.18        10.36        15.16        36.03 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.16               0.20 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            248.65             369.93 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             51.65              50.10 
[1] "0.2 - 248.7 (51.6)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1"  
D75V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q LOSS MUTATED                   10             2
  19Q LOSS WILD-TYPE                 51             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19Q LOSS MUTATED                                          14
  19Q LOSS WILD-TYPE                                        58
                    vv
clus                 REGIONAL LYMPH NODE
  19Q LOSS MUTATED                    41
  19Q LOSS WILD-TYPE                 168
D75V4, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      10                 51
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               14                 58
  REGIONAL LYMPH NODE                                     41                168
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  19Q LOSS MUTATED             2       0       9        2        5        4
  19Q LOSS WILD-TYPE          10       7      19       15       22       18
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19Q LOSS MUTATED           1         3         2         9          2
  19Q LOSS WILD-TYPE        13        16        10        26         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED            8         10        6
  19Q LOSS WILD-TYPE         24         48       13
D75V5, multiclass
             clus
vv            19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  I OR II NOS                2                 10
  STAGE 0                    0                  7
  STAGE I                    9                 19
  STAGE IA                   2                 15
  STAGE IB                   5                 22
  STAGE II                   4                 18
  STAGE IIA                  1                 13
  STAGE IIB                  3                 16
  STAGE IIC                  2                 10
  STAGE III                  9                 26
  STAGE IIIA                 2                 13
  STAGE IIIB                 8                 24
  STAGE IIIC                10                 48
  STAGE IV                   6                 13
[1] 14  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                 T0+T1 T2 T3 T4
  19Q LOSS MUTATED      12 20 12 14
  19Q LOSS WILD-TYPE    51 51 62 53
D75V6, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1               12                 51
  T2                  20                 51
  T3                  12                 62
  T4                  14                 53
[1] 4 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                  N0  N1  N2  N3
  19Q LOSS MUTATED    31  11  12  11
  19Q LOSS WILD-TYPE 137  50  26  36
D75V7, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               31                137
  N1               11                 50
  N2               12                 26
  N3               11                 36
[1] 4 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                  M0  M1 M1A M1B M1C
  19Q LOSS MUTATED    56   0   2   1   4
  19Q LOSS WILD-TYPE 250   4   1   3   5
D75V8, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                56                250
  M1                 0                  4
  M1A                2                  1
  M1B                1                  3
  M1C                4                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    26  14
  19Q LOSS WILD-TYPE 103  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     26   14
  19Q LOSS WILD-TYPE  103   73
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                26                103
  YES               14                 73
[1] 2 2
[1] FALSE
D75V10, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     8  59
  19Q LOSS WILD-TYPE  35 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8   59
  19Q LOSS WILD-TYPE   35  245
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 8                 35
  YES               59                245
[1] 2 2
[1] FALSE
D75V11, continuous
D75V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    29  38
  19Q LOSS WILD-TYPE 102 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     29   38
  19Q LOSS WILD-TYPE  102  179
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               29                102
  MALE                 38                179
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         0    64
  19Q LOSS WILD-TYPE     4                         1   262
D75V13, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   64                262
[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"
D75V14, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  65
  19Q LOSS WILD-TYPE   6 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   65
  19Q LOSS WILD-TYPE    6  269
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               65                269
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    13   9
  20P LOSS WILD-TYPE 155 156
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                311 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                156 
$`20P LOSS MUTATED`
TCGA-3N-A9WB TCGA-D3-A2JC TCGA-D3-A3CF TCGA-D3-A5GO TCGA-D3-A8GK TCGA-DA-A1HV 
        3.02        86.76        24.00        47.87       108.79        48.79 
TCGA-DA-A1I1 TCGA-EE-A29E TCGA-EE-A29G TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H 
       39.19        62.79         8.55         3.78        11.90        34.88 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FS-A1ZE TCGA-FS-A1ZR TCGA-FS-A4F4 
       17.72        12.62         1.71        19.53         8.81         7.36 
TCGA-W3-AA1W TCGA-WE-A8K5 TCGA-YG-AA3O TCGA-YG-AA3P 
      185.16         6.48         6.18         4.70 

$`20P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        6.97         6.97        16.47         8.52       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       70.16       110.79        28.08        22.55        45.83        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       10.29        85.32         8.38        21.14        88.50        68.22 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        44.19         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        64.44        59.57       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        82.29        61.38        13.32         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       54.31        32.28        21.44        32.61        25.78       110.24 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
       52.01        13.68        17.72        23.11        29.72        22.06 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM 
       10.22        15.19         4.18       142.45        38.93        75.65 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 
      124.47        87.62        11.44         5.56        24.07         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       21.93         5.72         9.90        11.31        13.22        14.60 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        10.03        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       23.15        19.00        13.35        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        60.23         4.34        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
        1.18         7.99         9.90        37.97        11.15        36.85 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        39.62         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        9.99        30.44         2.43        32.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        36.30         9.67        36.33        51.12        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       35.54        28.31        33.83        55.69         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
        6.18        47.51         9.53        29.46         2.73        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        7.96        14.56        63.42       125.65       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.08        26.99        21.60        60.49        53.16        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        51.62         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        15.95        12.72         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       21.60        16.14        22.22         0.95        27.35        18.41 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       21.73        33.60        31.40        18.61        12.95        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
        5.72        76.41        25.18         3.52        11.11       114.15 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        4.21        13.45        28.60        42.84        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07         6.58        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       13.08        11.74         9.04         6.58        22.49         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74        15.72         6.71         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       13.28         2.20         4.70         3.29        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        3.39        20.38         8.22        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       12.92        12.89        47.38        52.08         8.65        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       40.64         8.68        27.39         0.82         5.23        53.85 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        3.22        28.73        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16        17.33 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         0.85        11.61        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        16.24        15.42        12.16        14.70 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       11.84        10.65        14.50        14.50        14.50        15.81 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
        0.43        11.05         5.79        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA21 
      164.19         8.98        60.03         2.99        10.98        71.01 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       11.84         5.49         7.10        18.67        21.07        13.12 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
        3.72         3.42        21.83         5.36         1.08        19.96 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94        12.07         8.22         6.67         5.98 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1.71               0.13 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            185.16             164.19 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             15.17              14.70 
[1] "1.7 - 185.2 (15.2)" "0.1 - 164.2 (14.7)"
[1] "hr=" "1.3"
D76V2, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    13   9
  20P LOSS WILD-TYPE 160 157
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                317 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                157 
$`20P LOSS MUTATED`
TCGA-3N-A9WB TCGA-D3-A2JC TCGA-D3-A3CF TCGA-D3-A5GO TCGA-D3-A8GK TCGA-DA-A1HV 
       17.03        86.76        24.53       137.92       170.20        48.89 
TCGA-DA-A1I1 TCGA-EE-A29E TCGA-EE-A29G TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H 
      194.83        63.78        72.07        48.89        13.02       152.35 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FS-A1ZE TCGA-FS-A1ZR TCGA-FS-A4F4 
      148.18        31.27        33.21        40.27        11.41        66.67 
TCGA-W3-AA1W TCGA-WE-A8K5 TCGA-YG-AA3O TCGA-YG-AA3P 
      219.16        54.38        36.03        14.43 

$`20P LOSS WILD-TYPE`
TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       61.02        12.99        16.57        16.67       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB 
       71.80       133.25        28.08        31.59        90.90        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       43.43       103.10        65.49        23.77       115.53       168.00 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        62.07       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       56.19        66.08        59.57       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        86.93        60.23        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      145.12        32.94        22.62        63.81        26.89       125.79 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC 
      135.75       178.32        18.18       125.19        30.84        79.59 
TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM 
       11.61        15.19        58.52       228.99        89.13        95.24 
TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 
      161.00       137.79        29.06       129.63       117.17       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       54.67         3.65         6.41        18.12        11.34        22.29 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       11.11         9.90        25.18        66.25        22.95        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       13.55        63.35        80.61        47.84        13.97        64.64 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        56.84        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       55.92       369.93        25.87       195.02        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        36.82        39.29        86.14        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       126.81        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       55.59        44.88        94.82        21.67       129.27        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG 
       19.76        61.51        47.28       103.27       268.73       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       16.96       204.66        96.23       158.63       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       47.54       248.65        43.23       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       13.81        23.47       138.81       172.18       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       64.08        34.32        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      109.58       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        98.40        12.59        26.37       268.93 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        6.44       131.51        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       37.25         8.88        79.99        43.82        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A42K 
       16.37        32.05       247.04        80.32        46.98         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        29.46        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS 
       47.38        23.93       101.26        74.73       133.55       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       53.16        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
        9.90         7.23         2.04        11.74       139.89       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.13        64.44        62.79        32.48        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH 
       46.36        12.62        50.10        21.37        59.41        65.88 
TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 
      357.04       294.77         6.67        18.05         0.33         0.69 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V TCGA-W3-AA21 
      212.22        63.02       121.08         4.01        42.08       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO 
       24.03        38.56         8.61        90.28        56.98        59.41 
TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 
       52.34         3.75        22.68        43.73         2.20        30.18 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       10.36        15.16        23.64        93.07        11.74 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             11.41               0.16 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            219.16             369.93 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            51.635             50.140 
[1] "11.4 - 219.2 (51.6)" "0.2 - 369.9 (50.1)" 
[1] "hr=" "1.3"
D76V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P LOSS MUTATED                    7             0
  20P LOSS WILD-TYPE                 54             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20P LOSS MUTATED                                           8
  20P LOSS WILD-TYPE                                        64
                    vv
clus                 REGIONAL LYMPH NODE
  20P LOSS MUTATED                     8
  20P LOSS WILD-TYPE                 201
D76V4, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  DISTANT METASTASIS                                       7                 54
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                8                 64
  REGIONAL LYMPH NODE                                      8                201
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20P LOSS MUTATED             0       0       1        1        1        3
  20P LOSS WILD-TYPE          12       7      27       16       26       19
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20P LOSS MUTATED           2         1         1         1          1
  20P LOSS WILD-TYPE        12        18        11        34         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED            2          3        3
  20P LOSS WILD-TYPE         30         55       16
D76V5, multiclass
             clus
vv            20P LOSS MUTATED 20P LOSS WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    1                 27
  STAGE IA                   1                 16
  STAGE IB                   1                 26
  STAGE II                   3                 19
  STAGE IIA                  2                 12
  STAGE IIB                  1                 18
  STAGE IIC                  1                 11
  STAGE III                  1                 34
  STAGE IIIA                 1                 14
  STAGE IIIB                 2                 30
  STAGE IIIC                 3                 55
  STAGE IV                   3                 16
[1] 14  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                 T0+T1 T2 T3 T4
  20P LOSS MUTATED       4  5  5  5
  20P LOSS WILD-TYPE    59 66 69 62
D76V6, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                4                 59
  T2                   5                 66
  T3                   5                 69
  T4                   5                 62
[1] 4 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                  N0  N1  N2  N3
  20P LOSS MUTATED    10   1   3   4
  20P LOSS WILD-TYPE 158  60  35  43
D76V7, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               10                158
  N1                1                 60
  N2                3                 35
  N3                4                 43
[1] 4 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                  M0  M1 M1A M1B M1C
  20P LOSS MUTATED    18   0   1   0   2
  20P LOSS WILD-TYPE 288   4   2   4   7
D76V8, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                18                288
  M1                 0                  4
  M1A                1                  2
  M1B                0                  4
  M1C                2                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    10   5
  20P LOSS WILD-TYPE 119  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     10    5
  20P LOSS WILD-TYPE  119   82
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                10                119
  YES                5                 82
[1] 2 2
[1] FALSE
D76V10, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3  20
  20P LOSS WILD-TYPE  40 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3   20
  20P LOSS WILD-TYPE   40  284
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 3                 40
  YES               20                284
[1] 2 2
[1] FALSE
D76V11, continuous
D76V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     7  16
  20P LOSS WILD-TYPE 124 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      7   16
  20P LOSS WILD-TYPE  124  201
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                7                124
  MALE                 16                201
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         0    21
  20P LOSS WILD-TYPE     5                         1   305
D76V13, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   21                305
[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"
D76V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  20
  20P LOSS WILD-TYPE   5 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   20
  20P LOSS WILD-TYPE    5  314
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               20                314
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     4   2
  20Q LOSS WILD-TYPE 164 163
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                327 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                163 
$`20Q LOSS MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29G TCGA-ER-A19C TCGA-FS-A1ZE TCGA-WE-A8K5 TCGA-YG-AA3P 
       39.19         8.55         3.78        19.53         6.48         4.70 

$`20Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
        3.02         6.97         6.97        16.47         8.52       111.09 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       32.42        70.16       110.79        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       81.24        10.29        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        86.76        11.41        44.19         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        6.31        92.42        56.19        64.44        59.57       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       15.25        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.00         6.31         9.34       103.59        26.37        29.23 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       93.21        54.74        31.30        54.31        32.28        21.44 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       32.61        25.78       110.24        52.01        47.87        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       17.72        23.11        29.72        22.06        10.22        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
        4.18       142.45       108.79        38.93        75.65       124.47 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        5.72         9.90        11.31        13.22        14.60        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        10.03        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        7.00        17.56        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       23.15        19.00        13.35        13.22         0.20        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       10.55         6.31         8.12         1.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        60.23         4.34        15.85         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.18         7.99         9.90        37.97        11.15        62.79 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       36.85         1.08        39.62         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
        8.84         9.99        30.44         2.43        32.15         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        36.30         9.67        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       16.01        35.54        28.31        33.83        55.69         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
        1.15        13.02        34.98        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
        2.70         6.18        47.51         9.53        29.46         2.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       125.65       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       56.02        25.08        26.99        21.60        60.49        53.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       21.60        21.60        16.14        22.22         0.95        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       18.41        21.73        33.60        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       38.40         5.72        76.41        25.18         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.11       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       42.84        34.68         9.57        36.07         6.58        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       78.44        11.80         1.87         1.51        13.08        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       11.74         9.04         6.58        22.49         1.71         5.62 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74        15.72         6.71         3.58         5.36 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       13.28         2.20         4.70         3.29        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       11.01        23.80        14.24        15.52         7.33         7.30 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        3.39        20.38         8.22        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       49.15        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       53.85         3.22         7.36        28.73        14.20        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        5.98         6.41         2.27         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        17.33         9.90         7.23         0.85        11.61 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       44.28        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       12.16        14.70        11.84        10.65        14.50        14.50 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       14.50        15.81         0.43        11.05         5.79        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       164.19         8.98        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
       10.98       185.16        71.01        11.84         5.49         7.10 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       18.67        21.07        13.12         3.72         3.42        21.83 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        5.36         1.08        19.96         1.94        12.07         6.18 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        8.22         6.67         5.98 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              3.78               0.13 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             39.19             185.16 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             7.515             14.830 
[1] "3.8 - 39.2 (7.5)"   "0.1 - 185.2 (14.8)"
[1] "hr=" "1.1"
D77V2, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     4   2
  20Q LOSS WILD-TYPE 169 164
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                333 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                164 
$`20Q LOSS MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29G TCGA-ER-A19C TCGA-FS-A1ZE TCGA-WE-A8K5 TCGA-YG-AA3P 
      194.83        72.07        48.89        40.27        54.38        14.43 

$`20Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 
       17.03        61.02        12.99        16.57        16.67       112.04 
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.57        71.80       133.25        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       95.74        43.43       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        86.76        11.87        62.07       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       12.10       171.58        56.19        66.08        59.57       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
       58.06        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       24.53        13.87         9.34       103.59        39.75        45.30 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      174.84        55.73        56.35       145.12        32.94        22.62 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
       18.18       125.19        30.84        79.59        11.61        15.19 
TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN 
       58.52       228.99       170.20        89.13        95.24       161.00 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      137.79        29.06       129.63       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
        3.65         6.41        18.12        11.34        22.29        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        9.90        25.18        66.25        22.95        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.21        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       53.92        65.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
      215.44        15.68        13.87        10.16        17.85        68.25 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       54.02        17.29        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       27.22         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       68.15         4.96       133.81       151.27        91.56       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       13.55        63.35        80.61        47.84        13.97        63.78 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        55.92       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        36.82        39.29        86.14        59.28 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       161.03       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       54.74        79.66        75.48        90.97       126.81        13.91 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       14.30        55.59        44.88        94.82        21.67       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF 
       28.83        19.76        61.51        47.28       103.27       268.73 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       158.63       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
      167.90        47.54       248.65        43.23       134.40       162.48 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       71.21        53.26       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       54.51        13.81        23.47       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD 
       36.95        64.08        34.32        53.19       201.80        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       51.35       109.58       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
       50.76         9.17        77.75        98.40        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       26.37       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W 
       44.05       162.08        50.89        37.25         8.88       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       79.99        43.82        23.34        20.15        16.37        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       32.05       247.04        80.32        46.98        33.21         6.77 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21        15.72       210.08        15.16         7.00 
TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX 
       38.27        34.82        29.46        94.39       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       357.37        53.52        15.45         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       47.38        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      148.80        53.16        26.56        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       77.82        50.14        66.67        28.73       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       26.73        49.45        77.88         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
        0.16        19.30         9.90         7.23         2.04        11.74 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      139.89       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A8LK TCGA-GN-A8LL 
       32.48        39.58        46.36        12.62        50.10        21.37 
TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS TCGA-QB-AA9O 
       59.41        65.88       357.04       294.77         6.67        18.05 
TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O 
        0.33         0.69       212.22        63.02       121.08         4.01 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K6 
       42.08       219.16       105.04        24.03        38.56         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX 
       90.28        56.98        59.41        52.34         3.75        22.68 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
       43.73         2.20        30.18        10.36        15.16        36.03 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             14.43               0.16 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            194.83             369.93 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            51.635             50.140 
[1] "14.4 - 194.8 (51.6)" "0.2 - 369.9 (50.1)" 
[1] "hr=" "1.5"
D77V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20Q LOSS MUTATED                    3             0
  20Q LOSS WILD-TYPE                 58             5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20Q LOSS MUTATED                                           3
  20Q LOSS WILD-TYPE                                        69
                    vv
clus                 REGIONAL LYMPH NODE
  20Q LOSS MUTATED                     1
  20Q LOSS WILD-TYPE                 208
D77V4, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       3                 58
  PRIMARY TUMOR                                            0                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                3                 69
  REGIONAL LYMPH NODE                                      1                208
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  20Q LOSS MUTATED             0       0       1        0        0        0
  20Q LOSS WILD-TYPE          12       7      27       17       27       22
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20Q LOSS MUTATED           0         1         1         0          1
  20Q LOSS WILD-TYPE        14        18        11        35         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED            0          1        2
  20Q LOSS WILD-TYPE         32         57       17
D77V5, multiclass
             clus
vv            20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  I OR II NOS                0                 12
  STAGE 0                    0                  7
  STAGE I                    1                 27
  STAGE IA                   0                 17
  STAGE IB                   0                 27
  STAGE II                   0                 22
  STAGE IIA                  0                 14
  STAGE IIB                  1                 18
  STAGE IIC                  1                 11
  STAGE III                  0                 35
  STAGE IIIA                 1                 14
  STAGE IIIB                 0                 32
  STAGE IIIC                 1                 57
  STAGE IV                   2                 17
[1] 14  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                 T0+T1 T2 T3 T4
  20Q LOSS MUTATED       1  2  0  3
  20Q LOSS WILD-TYPE    62 69 74 64
D77V6, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                1                 62
  T2                   2                 69
  T3                   0                 74
  T4                   3                 64
[1] 4 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                  N0  N1  N2  N3
  20Q LOSS MUTATED     2   0   1   2
  20Q LOSS WILD-TYPE 166  61  37  45
D77V7, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                2                166
  N1                0                 61
  N2                1                 37
  N3                2                 45
[1] 4 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                  M0  M1 M1A M1B M1C
  20Q LOSS MUTATED     5   0   0   0   2
  20Q LOSS WILD-TYPE 301   4   3   4   7
D77V8, multiclass
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                 5                301
  M1                 0                  4
  M1A                0                  3
  M1B                0                  4
  M1C                2                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4   1
  20Q LOSS WILD-TYPE 125  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    1
  20Q LOSS WILD-TYPE  125   86
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 4                125
  YES                1                 86
[1] 2 2
[1] FALSE
D77V10, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   6
  20Q LOSS WILD-TYPE  42 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    6
  20Q LOSS WILD-TYPE   42  298
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 1                 42
  YES                6                298
[1] 2 2
[1] FALSE
D77V11, continuous
D77V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   6
  20Q LOSS WILD-TYPE 130 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    6
  20Q LOSS WILD-TYPE  130  211
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                130
  MALE                  6                211
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     6
  20Q LOSS WILD-TYPE     5                         1   320
D77V13, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    6                320
[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"
D77V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   6
  20Q LOSS WILD-TYPE   6 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    6
  20Q LOSS WILD-TYPE    6  328
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO                6                328
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    34  29
  21Q LOSS WILD-TYPE 134 136
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                63                270 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                136 
$`21Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q5 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL 
        6.97        32.42        68.22        86.76        36.16        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A8GN 
       56.19        64.44        46.32        25.78        17.72       124.47 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A180 
        9.90        11.31        10.03         0.20        10.55         8.12 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T 
        1.12        60.23         1.18         8.55        36.85        30.44 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        2.43        32.15         8.09        36.30        36.33        51.12 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MK 
       34.29        30.08        55.69         8.84        98.27       125.65 
TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A197 
       25.08        53.16        12.72        21.60        22.22        12.95 
TCGA-ER-A19E TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT 
       11.90         7.30        19.53         7.17        47.38        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A5DY TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
        8.68        27.39        17.33        44.28        10.13        15.42 
TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-AA1O 
       10.65        14.50        11.05        18.05         0.69         2.99 
TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YG-AA3O 
        3.72         5.36         6.18 

$`21Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
        3.02         6.97        16.47         8.52       111.09        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      110.79        28.08        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JF 
       85.32         8.38        21.14        88.50        11.41        44.19 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
        7.50         6.31        59.57       114.67        15.25        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       54.31        32.28        21.44        32.61       110.24        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
       47.87        13.68        23.11        29.72        22.06        10.22 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19         4.18       142.45       108.79        38.93        75.65 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       87.62        11.44         5.56        24.07         4.01        21.93 
TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        5.72        13.22        14.60        48.79        35.80        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       14.83        13.15         0.13        23.15        19.00        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       13.22         0.20        11.57         6.31         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
        5.13         4.31         4.34        15.85         9.21         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M 
        9.90        37.97        11.15        62.79         1.08        39.62 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 
        9.50        12.03         8.09         8.84         9.99        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       49.22         9.67        17.98        60.00        47.21        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       13.02        34.98        36.33         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        9.53        29.46         2.73        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       63.42       111.91        56.02        26.99        21.60        60.49 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       52.67         5.56       124.31       122.73        51.62         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 
       30.15        13.81        15.95         3.22        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14         0.95        27.35        18.41        21.73        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       31.40        18.61        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
        3.78         3.52        11.11       114.15        34.88         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       13.45        28.60        42.84        34.68         9.57        36.07 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        6.58        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        1.71         5.62        18.41        85.74        15.72         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
        3.58         5.36        13.28         2.20         4.70         3.29 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       64.47         3.45        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.33         3.39        20.38         8.22        11.08        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       12.92        12.89        52.08         8.65         8.81        49.15 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 
        0.82         5.23        53.85         3.22         7.36        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
       14.20        10.78         5.98         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.99         0.13         0.16         9.90         7.23         0.85 
TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       11.61        31.33        84.72        16.24        12.16        14.70 
TCGA-GN-A4U8 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS 
       11.84        14.50        14.50        15.81         0.43         5.79 
TCGA-RP-A693 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W 
        0.33       164.19         8.98        60.03        10.98       185.16 
TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM 
       71.01        11.84         5.49         6.48         7.10        18.67 
TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 
       21.07        13.12         3.42        21.83         1.08        19.96 
TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        1.94        12.07         4.70         8.22         6.67         5.98 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.20               0.13 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            125.65             185.16 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             18.05              14.50 
[1] "0.2 - 125.7 (18.1)" "0.1 - 185.2 (14.5)"
[1] "hr=" "1.2"
D78V2, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    34  30
  21Q LOSS WILD-TYPE 139 136
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                64                275 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                30                136 
$`21Q LOSS MUTATED`
TCGA-3N-A9WD TCGA-D3-A1Q5 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL 
       12.99       112.57       168.00        86.76        42.08       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A8GN 
       56.19        66.08        46.32        26.89        18.18       161.00 
TCGA-D9-A1JX TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-EB-A44R TCGA-EE-A17Y 
        6.41         9.90        25.18        20.38        10.16        27.22 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H 
       94.98        33.73       133.81        13.55        72.07        64.64 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 
      369.93        25.87       195.02        17.92        36.82        86.14 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 
       59.28        67.43        48.72       126.81        21.67       129.27 
TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JA 
      158.63        47.54       162.48       138.81        36.95        53.19 
TCGA-ER-A197 TCGA-ER-A19E TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM 
       13.94        13.02        27.72        40.27         9.70       101.26 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A5DY TCGA-GN-A262 TCGA-GN-A266 
       53.16        26.56        49.48        19.30       139.89        10.13 
TCGA-GN-A268 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-OD-A75X TCGA-QB-AA9O TCGA-RP-A694 
       62.79        12.62        59.41       294.77        18.05         0.69 
TCGA-W3-AA1O TCGA-WE-A8ZQ TCGA-WE-A8ZY TCGA-YG-AA3O 
        4.01        52.34        43.73        36.03 

$`21Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 
       17.03        61.02        16.57        16.67       112.04        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
      133.25        28.08        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JF 
      103.10        65.49        23.77       115.53        11.87        62.07 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
      113.52        12.10        59.57       130.72        58.06        46.98 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        22.62        63.81       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD 
      137.92       178.32       125.19        30.84        79.59        11.61 
TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM 
       15.19        58.52       228.99       170.20        89.13        95.24 
TCGA-D3-A8GP TCGA-D3-A8GQ TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A149 
      137.79        29.06       129.63       117.17       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC 
        3.65        18.12        11.34        22.29        11.11        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        48.89        36.03       117.21       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       17.85        68.25        54.02        17.29        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       12.20        29.82         8.65        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
        4.96       151.27        91.56       168.26        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       47.84        13.97        63.78         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 
       56.42        37.35        14.47        55.92        46.82       102.90 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.29       314.56       161.03       208.04        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48        90.97        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       44.88        94.82        28.83        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
      103.27       268.73       103.20        16.96       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      203.05       167.90       248.65        43.23       134.40        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        51.62         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        23.47       172.18       127.20        64.08        34.32 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       109.58       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       12.59        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T 
       61.05        44.05       162.08        50.89        37.25         8.88 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       31.27        32.05       247.04        80.32        46.98        33.21 
TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.77        92.98       174.21        15.72       210.08        15.16 
TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW 
        7.00        38.27        34.82        29.46        94.39       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       48.59       228.59       202.65        20.91        28.08         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       48.85       357.37        53.52        15.45        32.75        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY 
       23.93        74.73       133.55        11.41       148.80        27.09 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.02        77.82        50.14        66.67        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       12.43        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 
       47.54         0.16         9.90         7.23         2.04        11.74 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
      117.93        84.72        64.44        32.48        39.58        46.36 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-HR-A2OH TCGA-LH-A9QB TCGA-QB-A6FS TCGA-RP-A693 
       50.10        21.37        65.88       357.04         6.67         0.33 
TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 
      212.22        63.02       121.08        42.08       219.16       105.04 
TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN 
       24.03        38.56        54.38         8.61        90.28        56.98 
TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 
       59.41         3.75        22.68         2.20        30.18        10.36 
TCGA-WE-AAA4 TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       15.16        14.43        23.64        93.07        11.74 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.69               0.16 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            369.93             357.37 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             46.93              51.35 
[1] "0.7 - 369.9 (46.9)" "0.2 - 357.4 (51.4)"
[1] "hr=" "1"  
D78V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q LOSS MUTATED                    9             2
  21Q LOSS WILD-TYPE                 52             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  21Q LOSS MUTATED                                          15
  21Q LOSS WILD-TYPE                                        57
                    vv
clus                 REGIONAL LYMPH NODE
  21Q LOSS MUTATED                    38
  21Q LOSS WILD-TYPE                 171
D78V4, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       9                 52
  PRIMARY TUMOR                                            2                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               15                 57
  REGIONAL LYMPH NODE                                     38                171
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  21Q LOSS MUTATED             3       3       3        4        4        5
  21Q LOSS WILD-TYPE           9       4      25       13       23       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  21Q LOSS MUTATED           2         2         2         9          3
  21Q LOSS WILD-TYPE        12        17        10        26         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED            6          9        4
  21Q LOSS WILD-TYPE         26         49       15
D78V5, multiclass
             clus
vv            21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    3                  4
  STAGE I                    3                 25
  STAGE IA                   4                 13
  STAGE IB                   4                 23
  STAGE II                   5                 17
  STAGE IIA                  2                 12
  STAGE IIB                  2                 17
  STAGE IIC                  2                 10
  STAGE III                  9                 26
  STAGE IIIA                 3                 12
  STAGE IIIB                 6                 26
  STAGE IIIC                 9                 49
  STAGE IV                   4                 15
[1] 14  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                 T0+T1 T2 T3 T4
  21Q LOSS MUTATED       9 11 12 14
  21Q LOSS WILD-TYPE    54 60 62 53
D78V6, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1                9                 54
  T2                  11                 60
  T3                  12                 62
  T4                  14                 53
[1] 4 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                  N0  N1  N2  N3
  21Q LOSS MUTATED    29  14   7   6
  21Q LOSS WILD-TYPE 139  47  31  41
D78V7, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               29                139
  N1               14                 47
  N2                7                 31
  N3                6                 41
[1] 4 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                  M0  M1 M1A M1B M1C
  21Q LOSS MUTATED    57   0   1   0   3
  21Q LOSS WILD-TYPE 249   4   2   4   6
D78V8, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                57                249
  M1                 0                  4
  M1A                1                  2
  M1B                0                  4
  M1C                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    26  16
  21Q LOSS WILD-TYPE 103  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     26   16
  21Q LOSS WILD-TYPE  103   71
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                26                103
  YES               16                 71
[1] 2 2
[1] FALSE
D78V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     7  58
  21Q LOSS WILD-TYPE  36 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7   58
  21Q LOSS WILD-TYPE   36  246
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 7                 36
  YES               58                246
[1] 2 2
[1] FALSE
D78V11, continuous
D78V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    26  39
  21Q LOSS WILD-TYPE 105 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     26   39
  21Q LOSS WILD-TYPE  105  178
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               26                105
  MALE                 39                178
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       2                         1    59
  21Q LOSS WILD-TYPE     3                         0   267
D78V13, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   59                267
[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"
D78V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  63
  21Q LOSS WILD-TYPE   6 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   63
  21Q LOSS WILD-TYPE    6  271
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               63                271
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    12  23
  22Q LOSS WILD-TYPE 156 142
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                35                298 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                23                142 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A5GO 
        8.52        28.08        68.22        44.19        92.42        47.87 
TCGA-D3-A8GB TCGA-D3-A8GN TCGA-DA-A1I2 TCGA-EB-A44R TCGA-EE-A184 TCGA-EE-A29C 
       29.72       124.47        13.68         0.20         5.13        37.97 
TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A3JA 
       62.79        36.33         5.42        44.25        56.02        22.22 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19T TCGA-FR-A8YD 
        3.52        11.90        34.88        34.68         6.58         4.70 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-GF-A4EO 
       64.47         3.45        12.92         0.82        53.85         7.23 
TCGA-GN-A266 TCGA-GN-A4U9 TCGA-RP-A693 TCGA-W3-A825 TCGA-WE-A8ZQ 
       10.13        10.65         0.33         8.98         3.72 

$`22Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
        3.02         6.97         6.97        16.47       111.09        32.42 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       70.16       110.79        22.55        45.83        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       85.32         8.38        21.14        88.50        86.76        11.41 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
        7.50        36.16         6.31        56.19        64.44        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      114.67        15.25        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       13.32        24.00         6.31         9.34       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       29.23        93.21        54.74        31.30        54.31        32.28 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       21.44        32.61        25.78       110.24        52.01        13.68 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       17.72        23.11        22.06        10.22        15.19         4.18 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ 
      142.45       108.79        38.93        75.65        87.62        11.44 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
        5.56        24.07         4.01        21.93         5.72         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       11.31        13.22        14.60        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        39.19         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       14.83        13.15         0.13        23.15        19.00        13.35 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
       13.22         0.20        11.57        10.55         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        1.12         1.35        12.20         4.31        60.23         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
       15.85         9.21         1.18         7.99         9.90        11.15 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55        36.85         1.08        39.62         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        8.09         8.84         9.99        30.44         2.43        32.15 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.09        11.31        49.22        36.30         9.67        51.12 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        60.00        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       16.01        35.54        28.31        33.83        55.69         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.02        34.98        36.33         8.84        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH 
        6.18        47.51         9.53        29.46         2.73         7.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       14.56        63.42       125.65       111.91        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       21.60        60.49        53.16        52.67         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        51.62         3.68        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       12.72         3.22        22.92        21.60        21.60        16.14 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
        0.95        27.35        18.41        21.73        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       18.61        12.95        38.40         5.72        76.41        25.18 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        3.78        11.11       114.15         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       42.84         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A 
        6.58        22.49         1.71         5.62        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       15.72         6.71         3.58         5.36        13.28         2.20 
TCGA-FR-A8YE TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        3.29        11.01        23.80        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
        7.30         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        7.17        30.87        12.89        47.38        52.08         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
        8.81        49.15        40.64         8.68        27.39         5.23 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        3.22         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
        6.41         2.27         0.20         0.99         0.13         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 
       17.33         9.90         0.85        11.61        44.28        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       84.72        16.24        15.42        12.16        14.70        11.84 
TCGA-GN-A8LK TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X 
       14.50        14.50        14.50        15.81         0.43        11.05 
TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O 
        5.79        18.05         0.69       164.19        60.03         2.99 
TCGA-W3-AA1V TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 
       10.98       185.16        71.01        11.84         5.49         6.48 
TCGA-WE-A8K6 TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX 
        7.10        18.67        21.07        13.12         3.42        21.83 
TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        5.36         1.08        19.96         1.94        12.07         6.18 
TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
        4.70         8.22         6.67         5.98 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.20               0.13 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            124.47             185.16 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            13.680             14.765 
[1] "0.2 - 124.5 (13.7)" "0.1 - 185.2 (14.8)"
[1] "hr=" "1.3"
D79V2, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    13  23
  22Q LOSS WILD-TYPE 160 143
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                36                303 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                23                143 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A5GO 
       16.67        28.08       168.00        62.07       171.58       137.92 
TCGA-D3-A8GB TCGA-D3-A8GN TCGA-D9-A149 TCGA-DA-A1I2 TCGA-EB-A44R TCGA-EE-A184 
       30.84       161.00        54.67       176.55        10.16        68.15 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MM 
       47.84        63.78        86.14        13.91       103.20       167.90 
TCGA-EE-A3JA TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19T 
       53.19        12.59        13.02       152.35       162.08         8.88 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZY TCGA-FS-A4F0 
       29.46       216.92        48.59        47.38        27.09        77.82 
TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A4U9 TCGA-RP-A693 TCGA-W3-A825 TCGA-WE-A8ZQ 
        7.23        10.13        12.62         0.33        63.02        52.34 

$`22Q LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 
       17.03        61.02        12.99        16.57       112.04       112.57 
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 
       71.80       133.25        31.59        90.90        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      103.10        65.49        23.77       115.53        86.76        11.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
      113.52        42.08        12.10        56.19        66.08        59.57 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
      130.72        58.06        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       60.23        24.53        13.87         9.34       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       45.30       174.84        55.73        56.35       145.12        32.94 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       22.62        63.81        26.89       125.79       135.75       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI 
       18.18       125.19        79.59        11.61        15.19        58.52 
TCGA-D3-A8GJ TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GP TCGA-D3-A8GQ 
      228.99       170.20        89.13        95.24       137.79        29.06 
TCGA-D3-A8GR TCGA-D3-A8GS TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 
      129.63       117.17       151.53         3.65         6.41        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       11.34        22.29        11.11         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       22.95        48.89        36.03       117.21        20.38       194.83 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.93       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       17.85        68.25        54.02        17.29        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
       12.20        29.82        27.22         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       14.70        26.89         4.96       133.81       151.27        91.56 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
      168.26        13.55        63.35        80.61        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       64.64         2.60        56.84        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       14.47        55.92       369.93        25.87       195.02        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        36.82        39.29        59.28        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       161.03       208.04        48.72        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       79.66        75.48        90.97       126.81        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       44.88        94.82        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MF TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       268.73        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       158.63       203.05        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      134.40       162.48        71.21        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       51.62         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB 
      172.18       127.20        36.95        64.08        34.32       201.80 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        51.35       109.58       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       13.94        50.76         9.17        77.75        98.40        48.89 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93         6.44       131.51        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       50.89        37.25       148.18        79.99        43.82        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       20.15        16.37        31.27        32.05       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YE 
      210.08        15.16         7.00        38.27        34.82        94.39 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      228.59       202.65        20.91        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
       48.85       357.37        53.52        40.27        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        23.93       101.26        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F2 
      148.80        53.16        26.56        49.48        27.02        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       66.67        28.73       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       77.88         0.20        22.92        47.54         0.16        19.30 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         2.04        11.74       139.89       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A8LK 
       64.44        62.79        32.48        39.58        46.36        50.10 
TCGA-GN-A8LL TCGA-GN-A9SD TCGA-HR-A2OH TCGA-LH-A9QB TCGA-OD-A75X TCGA-QB-A6FS 
       21.37        59.41        65.88       357.04       294.77         6.67 
TCGA-QB-AA9O TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA1V 
       18.05         0.69       212.22       121.08         4.01        42.08 
TCGA-W3-AA1W TCGA-W3-AA21 TCGA-WE-A8JZ TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 
      219.16       105.04        24.03        38.56        54.38         8.61 
TCGA-WE-A8ZM TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-A8ZY 
       90.28        56.98        59.41         3.75        22.68        43.73 
TCGA-WE-AA9Y TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-YG-AA3P 
        2.20        30.18        10.36        15.16        36.03        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S TCGA-Z2-AA3V 
       23.64        93.07        11.74 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.33               0.16 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            216.92             369.93 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            52.765             50.100 
[1] "0.3 - 216.9 (52.8)" "0.2 - 369.9 (50.1)"
[1] "hr=" "1.4"
D79V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q LOSS MUTATED                    8             1
  22Q LOSS WILD-TYPE                 53             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  22Q LOSS MUTATED                                           7
  22Q LOSS WILD-TYPE                                        65
                    vv
clus                 REGIONAL LYMPH NODE
  22Q LOSS MUTATED                    21
  22Q LOSS WILD-TYPE                 188
D79V4, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       8                 53
  PRIMARY TUMOR                                            1                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                7                 65
  REGIONAL LYMPH NODE                                     21                188
[1] 4 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                 I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  22Q LOSS MUTATED             3       1       4        2        6        2
  22Q LOSS WILD-TYPE           9       6      24       15       21       20
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  22Q LOSS MUTATED           1         2         2         0          0
  22Q LOSS WILD-TYPE        13        17        10        35         15
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED            4          3        3
  22Q LOSS WILD-TYPE         28         55       16
D79V5, multiclass
             clus
vv            22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  I OR II NOS                3                  9
  STAGE 0                    1                  6
  STAGE I                    4                 24
  STAGE IA                   2                 15
  STAGE IB                   6                 21
  STAGE II                   2                 20
  STAGE IIA                  1                 13
  STAGE IIB                  2                 17
  STAGE IIC                  2                 10
  STAGE III                  0                 35
  STAGE IIIA                 0                 15
  STAGE IIIB                 4                 28
  STAGE IIIC                 3                 55
  STAGE IV                   3                 16
[1] 14  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                 T0+T1 T2 T3 T4
  22Q LOSS MUTATED       5 11  5  7
  22Q LOSS WILD-TYPE    58 60 69 60
D79V6, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1                5                 58
  T2                  11                 60
  T3                   5                 69
  T4                   7                 60
[1] 4 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                  N0  N1  N2  N3
  22Q LOSS MUTATED    25   4   2   4
  22Q LOSS WILD-TYPE 143  57  36  43
D79V7, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               25                143
  N1                4                 57
  N2                2                 36
  N3                4                 43
[1] 4 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                  M0  M1 M1A M1B M1C
  22Q LOSS MUTATED    33   0   1   1   1
  22Q LOSS WILD-TYPE 273   4   2   3   8
D79V8, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                33                273
  M1                 0                  4
  M1A                1                  2
  M1B                1                  3
  M1C                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    16   6
  22Q LOSS WILD-TYPE 113  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     16    6
  22Q LOSS WILD-TYPE  113   81
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                16                113
  YES                6                 81
[1] 2 2
[1] FALSE
D79V10, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     5  32
  22Q LOSS WILD-TYPE  38 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5   32
  22Q LOSS WILD-TYPE   38  272
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 5                 38
  YES               32                272
[1] 2 2
[1] FALSE
D79V11, continuous
D79V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    15  22
  22Q LOSS WILD-TYPE 116 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     15   22
  22Q LOSS WILD-TYPE  116  195
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               15                116
  MALE                 22                195
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         1    34
  22Q LOSS WILD-TYPE     4                         0   292
D79V13, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   34                292
[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"
D79V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     1  36
  22Q LOSS WILD-TYPE   6 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   36
  22Q LOSS WILD-TYPE    6  298
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               36                298
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    40  44
  XQ LOSS WILD-TYPE 128 121
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               84               249 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               44               121 
$`XQ LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JG 
      111.09        32.42        28.08        10.29        86.76         7.50 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       92.42        15.25        46.98        21.44        25.78       110.24 
TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GR TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-DA-A1HW 
       47.87        22.06         5.56        21.93         5.72        35.80 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       44.52        25.15        10.55         4.31         4.34        15.85 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29V 
        1.18        37.97        11.15        36.85         8.09         2.43 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MF 
        8.09        36.30        34.29         1.15        13.02         2.73 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH 
      125.65        56.02        53.16         3.68        13.81        12.72 
TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A2NE 
       16.14        31.40        11.90       114.15        13.45         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW 
       13.08        12.62        11.74         6.58         3.58        64.47 
TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       11.01         7.30        20.38        11.08        30.87        12.92 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.65         8.81        49.15         5.23        53.85         7.36 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A8LK 
       10.78         5.98         0.13         0.85        44.28        14.50 
TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1V TCGA-W3-AA1W TCGA-WE-A8JZ 
       14.50         0.43        11.05        10.98       185.16        11.84 
TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3P TCGA-Z2-A8RT TCGA-Z2-AA3S 
       18.67         5.36         1.08         4.70         8.22         6.67 

$`XQ LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
        3.02         6.97         6.97        16.47         8.52        70.16 
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      110.79        22.55        45.83        81.24        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH 
       21.14        88.50        68.22        11.41        44.19        36.16 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 
        6.31        56.19        64.44        59.57       114.67        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       82.29        61.38        13.32        24.00         6.31         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        26.37        29.23        93.21        54.74        31.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       54.31        32.28        32.61        52.01        13.68        17.72 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
       23.11        29.72        10.22        15.19         4.18       142.45 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      108.79        38.93        75.65       124.47        87.62        11.44 
TCGA-D3-A8GS TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       24.07         4.01         9.90        11.31        13.22        14.60 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       17.56        14.83        13.15         0.20         0.13        23.15 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       19.00        13.35        13.22         0.20        11.57         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B 
        8.12         1.12         1.35        12.20         5.13        60.23 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
        9.21         7.99         9.90        62.79         8.55         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       39.62         9.50        12.03         8.84         9.99        30.44 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       32.15        11.31        49.22         9.67        36.33        51.12 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        60.00        47.21        30.08        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GT 
       35.54        28.31        33.83        55.69         5.42        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       36.33         8.84        98.27         2.70         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        44.25         7.96        14.56        63.42 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      111.91        25.08        26.99        21.60        60.49        52.67 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG 
        5.56       124.31       122.73        51.62        30.15        15.95 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB 
        3.22        22.92        21.60        21.60        22.22         0.95 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       27.35        18.41        21.73        33.60        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       38.40         5.72        76.41        25.18         3.78         3.52 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
       11.11        34.88         4.21        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
        9.57        36.07         6.58        17.72        78.44        11.80 
TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN 
        1.87         9.04        22.49         1.71         5.62        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC 
       85.74        15.72         6.71         5.36        13.28         2.20 
TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.70         3.29         3.45        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK 
        7.33         3.39         8.22        19.53         7.17        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
       47.38        52.08        40.64         8.68        27.39         0.82 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
        3.22        28.73        14.20         6.41         2.27         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 
        0.99         0.16        17.33         9.90         7.23        11.61 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.13        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS 
       14.70        11.84        10.65        14.50        15.81         5.79 
TCGA-QB-AA9O TCGA-RP-A693 TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 
       18.05         0.33         0.69       164.19         8.98        60.03 
TCGA-W3-AA1O TCGA-W3-AA21 TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN 
        2.99        71.01         5.49         6.48         7.10        21.07 
TCGA-WE-A8ZO TCGA-WE-A8ZQ TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 
       13.12         3.72         3.42        21.83        19.96         1.94 
TCGA-WE-AAA4 TCGA-YG-AA3O TCGA-Z2-AA3V 
       12.07         6.18         5.98 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.13              0.13 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           185.16            164.19 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            12.82             15.95 
[1] "0.1 - 185.2 (12.8)" "0.1 - 164.2 (15.9)"
[1] "hr=" "1.2"
D80V2, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    42  44
  XQ LOSS WILD-TYPE 131 122
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               86               253 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               44               122 
$`XQ LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JC TCGA-D3-A2JG 
      112.04       112.57        28.08        43.43        86.76       113.52 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
      171.58        58.06        46.98        22.62        26.89       125.79 
TCGA-D3-A5GO TCGA-D3-A8GC TCGA-D3-A8GR TCGA-D9-A148 TCGA-D9-A1X3 TCGA-D9-A3Z3 
      137.92        79.59       129.63       151.53        18.12        22.29 
TCGA-D9-A4Z6 TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A17Y TCGA-EE-A185 
       11.11        36.03       107.34        53.92        27.22         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
      151.27        91.56        13.55        47.84        13.97        64.64 
TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR 
       37.35        25.87        17.92        36.82        67.43        14.30 
TCGA-EE-A2GS TCGA-EE-A2MF TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD 
       55.59       268.73       158.63       167.90       162.48         3.68 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A19E TCGA-ER-A19G 
       13.81       138.81        34.32        31.40        13.02       268.93 
TCGA-ER-A19L TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET 
      131.51        20.15        16.37        31.27        32.05        80.32 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF 
       15.16       216.92       228.59        27.72       357.37        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ 
       32.75        47.38       133.55        11.41       148.80        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A6C8 
       77.82        66.67        12.43        26.73        47.54         2.04 
TCGA-GN-A262 TCGA-GN-A8LK TCGA-GN-A8LL TCGA-LH-A9QB TCGA-OD-A75X TCGA-W3-AA1V 
      139.89        50.10        21.37       357.04       294.77        42.08 
TCGA-W3-AA1W TCGA-WE-A8JZ TCGA-WE-A8ZM TCGA-WE-A8ZY TCGA-WE-AA9Y TCGA-YG-AA3P 
      219.16        24.03        90.28        43.73         2.20        14.43 
TCGA-Z2-A8RT TCGA-Z2-AA3S 
       23.64        93.07 

$`XQ LOSS WILD-TYPE`
TCGA-3N-A9WB TCGA-3N-A9WC TCGA-3N-A9WD TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 
       17.03        61.02        12.99        16.57        16.67        71.80 
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
      133.25        31.59        90.90        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH 
       23.77       115.53       168.00        11.87        62.07        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 
       12.10        56.19        66.08        59.57       130.72        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
      166.52        86.93        60.23        24.53        13.87         9.34 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
      103.59        39.75        45.30       174.84        55.73        56.35 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
      145.12        32.94        63.81       135.75       178.32        18.18 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GD TCGA-D3-A8GE TCGA-D3-A8GI TCGA-D3-A8GJ 
      125.19        30.84        11.61        15.19        58.52       228.99 
TCGA-D3-A8GK TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D3-A8GN TCGA-D3-A8GP TCGA-D3-A8GQ 
      170.20        89.13        95.24       161.00       137.79        29.06 
TCGA-D3-A8GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 
      117.17        54.67         3.65         6.41        11.34         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        66.25        22.95        48.89       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
      194.83       176.55        35.93        61.18        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       68.09        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       10.16        17.85        68.25        54.02        17.29        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        6.35        12.20        29.82         8.65        94.98        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       14.70        26.89        68.15       133.81       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       80.61        63.78        72.07         2.60        56.84        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
       56.42        14.47        55.92       369.93       195.02        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        39.29        86.14        59.28       314.56       161.03 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      208.04        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       90.97       126.81        13.91        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
      129.27        28.83        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
      103.20        16.96       204.66        96.23       203.05        47.54 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      248.65        43.23       134.40        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73        51.62        54.51        23.47       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE 
       36.95        64.08        53.19       201.80        27.35        51.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      109.58       148.08        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H 
       77.75        98.40        48.89        12.59        26.37       152.35 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44        61.05        44.05       162.08        50.89        37.25 
TCGA-ER-A19T TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ES 
        8.88       148.18        79.99        43.82        23.34       247.04 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       46.98        33.21         6.77        92.98       174.21        15.72 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FR-A7UA TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE 
      210.08         7.00        38.27        34.82        29.46        94.39 
TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
       48.59       202.65        20.91        28.08         7.79        48.85 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       53.52        40.27         9.70        23.93       101.26        74.73 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 
       53.16        26.56        49.48        27.09        50.14        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV 
      174.84        49.45        77.88         0.20        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C9 TCGA-GN-A264 TCGA-GN-A265 
       19.30         9.90         7.23        11.74       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       10.13        64.44        62.79        32.48        39.58        46.36 
TCGA-GN-A4U9 TCGA-GN-A9SD TCGA-HR-A2OH TCGA-QB-A6FS TCGA-QB-AA9O TCGA-RP-A693 
       12.62        59.41        65.88         6.67        18.05         0.33 
TCGA-RP-A694 TCGA-W3-A824 TCGA-W3-A825 TCGA-W3-A828 TCGA-W3-AA1O TCGA-W3-AA21 
        0.69       212.22        63.02       121.08         4.01       105.04 
TCGA-WE-A8K1 TCGA-WE-A8K5 TCGA-WE-A8K6 TCGA-WE-A8ZN TCGA-WE-A8ZO TCGA-WE-A8ZQ 
       38.56        54.38         8.61        56.98        59.41        52.34 
TCGA-WE-A8ZT TCGA-WE-A8ZX TCGA-WE-AAA0 TCGA-WE-AAA3 TCGA-WE-AAA4 TCGA-YG-AA3O 
        3.75        22.68        30.18        10.36        15.16        36.03 
TCGA-Z2-AA3V 
       11.74 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2.04              0.16 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           357.37            369.93 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            47.18             51.62 
[1] "2.0 - 357.4 (47.2)" "0.2 - 369.9 (51.6)"
[1] "hr=" "1.1"
D80V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ LOSS MUTATED                   20             1
  XQ LOSS WILD-TYPE                 41             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  XQ LOSS MUTATED                                          16
  XQ LOSS WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  XQ LOSS MUTATED                    52
  XQ LOSS WILD-TYPE                 157
D80V4, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  DISTANT METASTASIS                                     20                41
  PRIMARY TUMOR                                           1                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              16                56
  REGIONAL LYMPH NODE                                    52               157
[1] 4 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                I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  XQ LOSS MUTATED             6       3       5        2        8        7
  XQ LOSS WILD-TYPE           6       4      23       15       19       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XQ LOSS MUTATED           3         9         2         5          3
  XQ LOSS WILD-TYPE        11        10        10        30         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED            6         16        6
  XQ LOSS WILD-TYPE         26         42       13
D80V5, multiclass
             clus
vv            XQ LOSS MUTATED XQ LOSS WILD-TYPE
  I OR II NOS               6                 6
  STAGE 0                   3                 4
  STAGE I                   5                23
  STAGE IA                  2                15
  STAGE IB                  8                19
  STAGE II                  7                15
  STAGE IIA                 3                11
  STAGE IIB                 9                10
  STAGE IIC                 2                10
  STAGE III                 5                30
  STAGE IIIA                3                12
  STAGE IIIB                6                26
  STAGE IIIC               16                42
  STAGE IV                  6                13
[1] 14  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                T0+T1 T2 T3 T4
  XQ LOSS MUTATED      13 15 22 18
  XQ LOSS WILD-TYPE    50 56 52 49
D80V6, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1              13                50
  T2                 15                56
  T3                 22                52
  T4                 18                49
[1] 4 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                 N0  N1  N2  N3
  XQ LOSS MUTATED    45  17   4  13
  XQ LOSS WILD-TYPE 123  44  34  34
D80V7, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              45               123
  N1              17                44
  N2               4                34
  N3              13                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"
                   vv
clus                 M0  M1 M1A M1B M1C
  XQ LOSS MUTATED    76   0   0   2   5
  XQ LOSS WILD-TYPE 230   4   3   2   4
D80V8, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               76               230
  M1                0                 4
  M1A               0                 3
  M1B               2                 2
  M1C               5                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V9, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   30 25
  XQ LOSS WILD-TYPE 99 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     30   25
  XQ LOSS WILD-TYPE   99   62
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               30                99
  YES              25                62
[1] 2 2
[1] FALSE
D80V10, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     8  81
  XQ LOSS WILD-TYPE  35 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8   81
  XQ LOSS WILD-TYPE   35  223
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                8                35
  YES              81               223
[1] 2 2
[1] FALSE
D80V11, continuous
D80V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    42  47
  XQ LOSS WILD-TYPE  89 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     42   47
  XQ LOSS WILD-TYPE   89  170
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              42                89
  MALE                47               170
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         0    83
  XQ LOSS WILD-TYPE     4                         1   243
D80V13, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  83               243
[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"
D80V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  84
  XQ LOSS WILD-TYPE   5 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   84
  XQ LOSS WILD-TYPE    5  250
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              84               250
[1] 2 2
[1] FALSE
