[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/10006254/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/10013813/transformed.cor.cli.txt"

nPatients in clinical file=295, in cluster file=299, common to both=281
[1] "Reduce the number of clustering variables from 80 to 79."
[1]  79 281
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               65               216 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               65               216 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              127               154 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              127               154 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               55               226 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               55               226 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               53               228 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               53               228 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               45               236 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               45               236 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               55               226 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               55               226 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               43               238 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               43               238 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               36               245 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               36               245 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               57               224 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               57               224 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               35               246 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               35               246 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              112               169 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              112               169 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               38               243 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               38               243 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              153               128 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              153               128 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              152               129 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              152               129 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               91               190 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               91               190 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              132               149 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              132               149 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               266 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               266 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               261 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               261 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                272 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                272 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                254 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                254 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                24                257 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                24                257 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                232 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                232 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                32                249 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                32                249 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                71                210 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                71                210 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                31                250 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                31                250 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                62                219 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                62                219 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                40                241 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                40                241 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                34                247 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                34                247 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                249 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                249 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                56                225 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                56                225 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                48                233 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                48                233 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                39                242 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                39                242 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                42                239 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                42                239 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                43                238 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                43                238 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               119                162 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               119                162 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               142                139 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               142                139 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                52                229 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                52                229 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               103                178 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               103                178 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               31               250 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               31               250 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               36               245 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               36               245 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               261 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               261 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               36               245 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               36               245 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               36               245 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               36               245 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               45               236 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               45               236 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               36               245 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               36               245 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               58               223 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               58               223 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               60               221 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               60               221 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               64               217 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               64               217 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               81               200 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               81               200 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               53               228 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               53               228 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              136               145 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              136               145 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               15               266 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               15               266 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               267 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               267 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               51               230 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               51               230 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               261 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               261 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              183                98 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              183                98 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              142               139 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              142               139 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               157                124 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               157                124 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               173                108 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               173                108 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                97                184 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                97                184 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               111                170 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               111                170 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                40                241 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                40                241 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                48                233 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                48                233 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                61                220 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                61                220 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                88                193 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                88                193 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                41                240 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                41                240 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                55                226 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                55                226 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                83                198 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                83                198 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                98                183 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                98                183 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                48                233 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                48                233 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                81                200 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                81                200 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                77                204 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                77                204 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                58                223 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                58                223 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                56                225 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                56                225 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                266 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                266 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                277 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                277 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                56                225 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                56                225 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                28                253 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                28                253 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               70               211 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               70               211 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DAYSTOSUBMITTEDSPECIMENDX"             
 [6] "PRIMARYSITEOFDESEASE"                  
 [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 281 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
          NA           NA         3408           NA           NA         4053 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
          NA           NA         2765         2912           NA           NA 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
          NA           NA         3514           NA         2126           NA 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
        1483           NA         1280           NA         5219         1709 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C1 TCGA-D3-A3C3 TCGA-D3-A3C6 
        2010         1372         3976           NA           NA           NA 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
        1429         1409         5065         2644           NA           NA 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
          NA           NA         3151         1209          653         4923 
TCGA-D3-A51F TCGA-D3-A51G TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
        1329           NA         1221         4012          559          305 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        1572          458         3374         4129         4195         5055 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
         226         3808         4609         1663          111          195 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
         345           99          301          766         2015           NA 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
        1487           NA         3565           NA         5926           NA 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
          NA         3265         1861           NA           NA          713 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
          NA          870           NA         6553          477          422 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
         309          543         1372         1065          108         1582 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 
         193          371           NA           NA           NA           NA 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
          NA           NA           NA           NA           NA         3335 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
          NA         2399           NA           NA           NA         2452 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
        1455           NA         1205           NA          979           NA 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1349           NA         1716         1136          440         1701 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       10523           NA         5218           NA           NA         3130 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
         743           NA         1787         1446         2051         9568 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
        4135         6328         1482         2717         1665         2423 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
        2296         2767         3101           NA          435         1691 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
        1365         2884           NA         3932           NA           NA 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
          NA         4403         6176           NA           NA         7563 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
          NA         3150         4151         1265         1620         3781 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
        3733          786          112         1658           NA          714 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
          NA           NA           NA           NA         1949           NA 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
          NA           NA         1016         3096         4504           NA 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
          NA           NA           NA           NA         2365           NA 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
          NA           NA           NA           NA         8180           NA 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A19P 
          NA           NA           NA         1340           NA           NA 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
          NA         1133           NA         2433           NA           NA 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
          NA          498          951          975           NA         2443 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FR-A69P 
        1429         1010         2828           NA         5299          149 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        6390          461          213           NA           NA           NA 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
          NA           NA         1225           NA           NA           NA 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
          NA           NA         3080           NA           NA           NA 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        4526         1617           NA         1505           NA           NA 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        2367           NA           NA           NA           NA          378 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
          NA         1504         2369            6          697         1446 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
           5           73          301          220          427         3664 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
          NA         2577           NA           NA           NA           NA 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
        1204         1410          384         8966          203 
Variable 1:'AGE':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=133,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=148,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=222,	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=112,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=29,	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=11,	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 281 columns, 2 survival variables, and 12 non-survival variables.
AGE, nv=66, 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 
22 31 60 55 57 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   53    60    55    57 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
22 31 60 55 57 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   53    60    55    57 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
141  51  32  37 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
141  51  32  37 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
141  51  32  37 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
141  51  32  37 
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=112, 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    28  34
  1P GAIN WILD-TYPE 109  99
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               62               208 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               34                99 
$`1P GAIN MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ 
       88.50        69.90        11.41        92.42        56.19       114.67 
TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
       15.25       103.59        47.87         4.01         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       13.22        10.03         6.64        10.55         8.12         1.12 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
       12.20        36.07        11.15        38.63         8.55         1.08 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GI TCGA-EE-A2GM 
        6.48         8.68         8.09        23.90        30.08        28.31 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MM 
        5.42        13.02        98.27         9.53        63.42        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AG 
       25.08        21.60        29.65         5.56       122.73        15.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G 
       21.60        22.22         5.72         3.52        11.11       114.15 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FS-A1YX 
        6.58         1.71        18.41        85.74         5.36         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F5 TCGA-GN-A266 
       23.80        30.87         8.65         8.68        28.73        10.13 
TCGA-GN-A267 TCGA-GN-A26A 
       16.24        12.16 

$`1P GAIN 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-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-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
        8.38        21.14        68.22        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
        6.31        64.44        45.11        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       61.38        13.32        24.00         6.31         9.34        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
        8.84        20.48        13.94        95.38        52.01         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        6.97        23.11         2.89        14.60        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       51.12        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15         4.93        22.36        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         0.00         0.00 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A184 
       13.22         0.20        11.57         6.31         1.35         5.13 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        9.90        37.97         4.41        27.12         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.09         8.84         9.99         2.43        11.31        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       47.21        19.43        16.01        35.54        33.83        30.84 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
        1.15        34.98        36.33         8.84         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       47.51        29.46        44.25         7.96        14.56       111.78 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      111.91        26.99        27.16        23.05       124.31        25.84 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        30.15        13.81        12.72         3.22        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         0.46        13.94        33.60 
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-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        3.78        11.90        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        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-A729 TCGA-FR-A7U8 TCGA-FS-A1YW 
        9.04        22.49         4.90         6.71         3.58        64.47 
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-A1ZJ 
       20.38         8.22        19.53        11.08         7.17        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.89        47.38        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-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
       12.85        24.85        31.33        84.72        15.42        14.70 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        11.05         5.79 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.08              0.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           122.73            124.31 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            13.12             14.22 
[1] "1.1 - 122.7 (13.1)" "0.0 - 124.3 (14.2)"
[1] "hr=" "1.1"
D1V2, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    29  34
  1P GAIN WILD-TYPE 113 100
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               63               213 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               34               100 
$`1P GAIN MUTATED`
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ 
      115.53        69.90        11.87       171.58        56.19       130.72 
TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
       58.06       103.59       137.92        11.34         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 
       66.25        20.38        68.09         3.55        27.22        94.98 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       33.73        26.89       109.64        13.97        39.62        72.07 
TCGA-EE-A29L TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GI 
        2.60       345.96       171.55        17.92        24.43        48.72 
TCGA-EE-A2GM TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ 
       75.48        13.91        55.59       129.27        47.28        96.23 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AB 
      167.90        47.54        43.23       103.56        53.26       122.73 
TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19F 
       23.47        64.08        53.19         9.17        12.59        26.37 
TCGA-ER-A19G TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U9 
      268.93        80.32        33.21        92.98       174.21         7.00 
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-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       10.13        64.44        32.48 

$`1P GAIN 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-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-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       65.49        23.77       168.00        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       12.10        66.08        45.11        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       86.93        60.23        24.53        13.87         9.34        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       10.03        51.68        15.06       110.93       135.75       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        3.25        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-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        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        45.11        35.01        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
       12.20        29.82         8.65        14.70        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       47.84        32.19        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
       14.47        55.92        25.87        46.82       102.90        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR 
       89.33        54.74        79.66        90.97       101.95        14.30 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82        21.67        28.83        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66       144.76       203.05 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
      248.65       136.47        41.59       124.31        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94        50.76        77.75        98.40        48.89 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       13.02       152.35         6.44       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-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-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY 
       46.98         4.90       210.08        15.16       216.92       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-A1ZJ TCGA-FS-A1ZK 
       53.52        40.27        15.45         9.70        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
      101.26        74.73        11.41       148.80        53.16        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-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         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 
      120.46       117.93        84.72        62.79        39.58        46.36 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2.60              0.16 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           345.96            357.37 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            53.19             47.38 
[1] "2.6 - 346.0 (53.2)" "0.2 - 357.4 (47.4)"
[1] "hr=" "1.1"
D1V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P GAIN MUTATED                    5             3
  1P GAIN WILD-TYPE                 32             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1P GAIN MUTATED                                          20
  1P GAIN WILD-TYPE                                        40
                   vv
clus                REGIONAL LYMPH NODE
  1P GAIN MUTATED                    37
  1P GAIN WILD-TYPE                 142
D1V4, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  DISTANT METASTASIS                                      5                32
  PRIMARY TUMOR                                           3                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              20                40
  REGIONAL LYMPH NODE                                    37               142
[1] 4 2
[1] 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       6        3        7        5
  1P GAIN WILD-TYPE           7       3      17        7       18       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1P GAIN MUTATED           0         1         2         8          8
  1P GAIN WILD-TYPE        10        13         8        24          6
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED            4          8        3
  1P GAIN WILD-TYPE         19         40        9
D1V5, multiclass
             clus
vv            1P GAIN MUTATED 1P GAIN WILD-TYPE
  I OR II NOS               3                 7
  STAGE 0                   3                 3
  STAGE I                   6                17
  STAGE IA                  3                 7
  STAGE IB                  7                18
  STAGE II                  5                12
  STAGE IIA                 0                10
  STAGE IIB                 1                13
  STAGE IIC                 2                 8
  STAGE III                 8                24
  STAGE IIIA                8                 6
  STAGE IIIB                4                19
  STAGE IIIC                8                40
  STAGE IV                  3                 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
  1P GAIN MUTATED       9 14 16 15
  1P GAIN WILD-TYPE    44 46 39 42
D1V6, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1               9                44
  T2                 14                46
  T3                 16                39
  T4                 15                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
  1P GAIN MUTATED    35  15   7   6
  1P GAIN WILD-TYPE 106  36  25  31
D1V7, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              35               106
  N1              15                36
  N2               7                25
  N3               6                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
  1P GAIN MUTATED    61   0   2   0   1
  1P GAIN WILD-TYPE 191   4   0   2   4
D1V8, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               61               191
  M1                0                 4
  M1A               2                 0
  M1B               0                 2
  M1C               1                 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"
D1V9, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   29 15
  1P GAIN WILD-TYPE 75 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     29   15
  1P GAIN WILD-TYPE   75   57
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               29                75
  YES              15                57
[1] 2 2
[1] FALSE
D1V10, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     6  59
  1P GAIN WILD-TYPE  28 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6   59
  1P GAIN WILD-TYPE   28  188
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                6                28
  YES              59               188
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    26  39
  1P GAIN WILD-TYPE  82 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     26   39
  1P GAIN WILD-TYPE   82  134
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              26                82
  MALE                39               134
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         0    64
  1P GAIN WILD-TYPE     4                         1   211
D1V13, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  64               211
[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     1  63
  1P GAIN WILD-TYPE   2 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   63
  1P GAIN WILD-TYPE    2  211
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              63               211
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   65 59
  1Q GAIN WILD-TYPE 72 74
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              124               146 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               59                74 
$`1Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC 
       16.47         8.52        81.24         8.38        88.50        69.90 
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE 
       11.41        92.42        56.19       114.67        15.25        13.32 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51K 
        6.31         9.34       103.59        26.37         5.39        17.72 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A3Z1 
       20.48        95.38        52.01        47.87        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 
        2.89         9.90        11.31        13.22        14.60        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       39.19         9.99        44.52        36.69         4.93         6.64 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Y 
        7.00        17.56         0.20         0.00        13.22        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20I 
        6.31         8.12         1.12         5.13        36.07         1.18 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M 
        9.90        11.15        38.63         8.55         1.08        27.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.84         9.99         6.48         8.68        49.22        23.90 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
        8.94        17.98        34.92        47.21        30.08        28.31 
TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MJ 
       33.83        13.02        36.33         2.70         9.53        63.42 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J7 
        5.56       122.73        25.84         3.68        15.95        21.60 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19D TCGA-ER-A19F 
       22.22        13.94        12.95         5.72         3.52        11.11 
TCGA-ER-A19G TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NH 
      114.15        34.68         9.57         1.87        13.08        11.74 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FS-A1YX 
        6.58         1.71        18.41        85.74         6.71         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH 
       23.80        14.24         7.30        20.38        11.08        30.87 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
       12.89        52.08         8.65        40.64         8.68         0.82 
TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
        5.23        28.73         2.27        10.13        16.24        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       14.70        11.84        10.65         5.79 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      111.09        32.42        70.16       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF 
       45.83        10.29        85.32        21.14        68.22        30.87 
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        45.11        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51F 
       46.32        82.29        61.38        24.00        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS 
       15.09        41.10         8.84        13.94         1.55         6.97 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A1IB 
       48.79        35.80        51.12        13.68        25.15        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A6L9 
       19.36        14.83        13.15         0.13         0.00         0.20 
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       11.57         1.35        12.20         4.31         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
        9.21         7.99        37.97         4.41         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.09         2.43         8.09        11.31         9.67        39.39 
TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP 
       34.29        19.43        16.01        35.54        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
        1.15        34.98         8.84        98.27         6.18        47.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       111.78       111.91 
TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       26.99       124.31        30.15        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
       22.92        21.60        16.14        27.35         0.46        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       31.40        18.61        38.40        76.41        25.18         3.78 
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-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       36.07        17.72        78.44        11.80         1.51        12.62 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
        9.04        22.49         4.90         3.58         5.36        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       11.01        15.52         7.33         3.39         8.22        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW 
        7.17        12.92        47.38         8.81        49.15        27.39 
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-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A268 TCGA-OD-A75X 
       15.42        11.05 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 0 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           122.73            124.31 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           13.150            15.255 
[1] "0.0 - 122.7 (13.2)" "0.0 - 124.3 (15.3)"
[1] "hr=" "1"  
D2V2, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   67 59
  1Q GAIN WILD-TYPE 75 75
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              126               150 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               59                75 
$`1Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JC 
       16.57        16.67        95.74        65.49       115.53        69.90 
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE 
       11.87       171.58        56.19       130.72        58.06        60.23 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51K 
       13.87         9.34       103.59        39.75        21.47        18.38 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A1JW 
       51.68       110.93       135.75       137.92       125.19         3.65 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       11.34         3.25         9.90        25.18        66.25        22.95 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       20.38       194.83        35.93       107.34        61.18        65.92 
TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL 
       68.09        10.49       215.44        10.16        35.01         3.55 
TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 
       52.01        27.22         8.65        94.98        33.73        68.15 
TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
      109.64        13.55        80.61        13.97        39.62        72.07 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
        2.60        44.35        14.47        55.92       345.96       171.55 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
      102.90        24.43        58.75       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       48.72        75.48        90.97        55.59        94.82        28.83 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
       47.28        96.23       167.90        47.54        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      136.47        41.59        53.26       122.73        25.84         3.68 
TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 
       23.47        64.08        53.19       101.79        13.94         9.17 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A2ND 
       12.59        26.37       268.93       162.08        50.89        23.34 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       16.37        32.05        80.32        33.21        92.98       174.21 
TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      210.08        48.59       202.65        20.91        27.72       357.37 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       15.45        32.75        23.93        74.73       133.55        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-GN-A266 
       26.56        27.09        27.02        28.73        77.88        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       64.44        32.48        39.58        46.36        12.62         6.67 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
      112.04       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF 
       90.90        43.43       103.10        23.77       168.00        48.76 
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        45.11        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51F 
       46.32       166.52        86.93        24.53       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GR TCGA-D3-A5GS 
       40.14       131.90        10.03        15.06       166.19         7.43 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
      151.53        54.67         6.41        48.89        36.03       117.21 
TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A44Q 
      176.55        53.92        23.44        28.60        15.68        13.87 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 
       17.85        45.11         6.35        12.20        29.82        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       26.89         4.96       151.27        78.87       168.26        63.35 
TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29V 
       47.84        32.19        18.61        56.42        37.35        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GJ 
       17.92        46.82        39.29        47.54        67.43        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
       54.74        79.66       101.95        13.91        14.30        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.27        19.76        61.51       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A3AA 
       16.96       204.66       144.76       203.05       248.65       124.31 
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-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       34.32        27.35        33.40       148.08        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H 
       50.76        77.75        98.40        48.89        13.02       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19W 
        6.44       131.51        61.05        44.05        37.25       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-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 
        4.90        15.16         7.00       216.92       228.59        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        7.79        48.85        53.52        40.27         9.70        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F2 
      101.26        11.41       148.80        49.48        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 
       66.67       174.84        12.43        26.73        49.45         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         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-OD-A75X 
       14.04       120.46       117.93        84.72        62.79       294.77 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             2.60              0.16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           357.37            294.77 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           49.805            47.460 
[1] "2.6 - 357.4 (49.8)" "0.2 - 294.8 (47.5)"
[1] "hr=" "1.1"
D2V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q GAIN MUTATED                   19             4
  1Q GAIN WILD-TYPE                 18             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1Q GAIN MUTATED                                          28
  1Q GAIN WILD-TYPE                                        32
                   vv
clus                REGIONAL LYMPH NODE
  1Q GAIN MUTATED                    75
  1Q GAIN WILD-TYPE                 104
D2V4, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     19                18
  PRIMARY TUMOR                                           4                 0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              28                32
  REGIONAL LYMPH NODE                                    75               104
[1] 4 2
[1] 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             3       2       9        5       14        9
  1Q GAIN WILD-TYPE           7       4      14        5       11        8
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1Q GAIN MUTATED           3         6         6        15         11
  1Q GAIN WILD-TYPE         7         8         4        17          3
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           12         18        6
  1Q GAIN WILD-TYPE         11         30        6
D2V5, multiclass
             clus
vv            1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  I OR II NOS               3                 7
  STAGE 0                   2                 4
  STAGE I                   9                14
  STAGE IA                  5                 5
  STAGE IB                 14                11
  STAGE II                  9                 8
  STAGE IIA                 3                 7
  STAGE IIB                 6                 8
  STAGE IIC                 6                 4
  STAGE III                15                17
  STAGE IIIA               11                 3
  STAGE IIIB               12                11
  STAGE IIIC               18                30
  STAGE IV                  6                 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
  1Q GAIN MUTATED      26 28 28 27
  1Q GAIN WILD-TYPE    27 32 27 30
D2V6, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              26                27
  T2                 28                32
  T3                 28                27
  T4                 27                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                N0 N1 N2 N3
  1Q GAIN MUTATED   67 22 20 14
  1Q GAIN WILD-TYPE 74 29 12 23
D2V7, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              67                74
  N1              22                29
  N2              20                12
  N3              14                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
  1Q GAIN MUTATED   118   1   2   0   3
  1Q GAIN WILD-TYPE 134   3   0   2   2
D2V8, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              118               134
  M1                1                 3
  M1A               2                 0
  M1B               0                 2
  M1C               3                 2
[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   52 32
  1Q GAIN WILD-TYPE 52 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     52   32
  1Q GAIN WILD-TYPE   52   40
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               52                52
  YES              32                40
[1] 2 2
[1] FALSE
D2V10, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    15 112
  1Q GAIN WILD-TYPE  19 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     15  112
  1Q GAIN WILD-TYPE   19  135
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               15                19
  YES             112               135
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   47 80
  1Q GAIN WILD-TYPE 61 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     47   80
  1Q GAIN WILD-TYPE   61   93
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              47                61
  MALE                80                93
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       2                         0   125
  1Q GAIN WILD-TYPE     3                         1   150
D2V13, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 125               150
[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     3 123
  1Q GAIN WILD-TYPE   0 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3  123
  1Q GAIN WILD-TYPE    0  151
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 0
  NOT HISPANIC OR LATINO             123               151
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    30  22
  2P GAIN WILD-TYPE 107 111
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               52               218 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               22               111 
$`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         5.39        52.01 
TCGA-D9-A6E9 TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SH 
        9.90        51.12        25.15        17.56        14.83         0.00 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q 
        9.21         7.99        11.15         1.08        27.12         8.09 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GM 
        8.84         6.48         8.68        49.22         8.94        28.31 
TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE 
       33.83        98.27         2.70        29.65         5.56        30.15 
TCGA-EE-A3AG TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G 
       15.95        33.60        12.95        25.18        11.90       114.15 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A2NC TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZK 
       34.88        42.84        11.80        18.41         8.22        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3I3 TCGA-OD-A75X 
       47.38         8.65         0.20        11.05 

$`2P GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.52       111.09        32.42       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       81.24        10.29        85.32         8.38        21.14        68.22 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       69.90        30.87         7.50        36.16         6.31        92.42 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE 
       45.11       114.67        15.25        46.98        46.32        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.00         9.34       103.59        26.37        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       95.38        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        2.89        11.31        13.22        14.60        48.79        35.80 
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-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q 
        4.93        22.36         6.64        19.36         7.00        13.15 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.20         0.13         0.00        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-A20I 
        5.13         4.31        36.07         4.34         5.13         1.18 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
        9.90        37.97        38.63         8.55         4.41         9.50 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
       12.03         9.99         2.43         8.09        11.31        23.90 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP 
       30.08        19.43        16.01        35.54        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
        1.15        13.02        34.98        36.33         8.84         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        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       111.78       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        27.16        23.05       124.31       122.73        25.84 
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         0.46        13.94 
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-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
        9.57        36.07        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-A3EV 
       13.08        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
        1.71        85.74         4.90         6.71         3.58         5.36 
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         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        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-QB-A6FS 
       10.65         5.79 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                0                 0 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           114.15            124.31 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           16.210            13.875 
[1] "0.0 - 114.2 (16.2)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1.3"
D3V2, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    31  22
  2P GAIN WILD-TYPE 111 112
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               53               223 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               22               112 
$`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        21.47       135.75 
TCGA-D9-A148 TCGA-D9-A6E9 TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
      151.53         9.90       117.21        53.92       215.44        15.68 
TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
       35.01       168.26        63.35        13.97         2.60        44.35 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
       37.35        14.47       345.96       171.55       102.90        58.75 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MU 
       75.48        90.97       129.27        28.83       103.56        53.26 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19E 
       54.51        23.47       148.08        13.94        98.40        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A2NC TCGA-FR-A3YN TCGA-FS-A1ZD 
      268.93       152.35        44.05        43.82        92.98        53.52 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3I3 TCGA-OD-A75X 
       23.93       101.26       133.55         0.20       294.77 

$`2P GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04       112.57       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       69.90        48.76       113.52        42.08        12.10       171.58 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE 
       45.11       130.72        58.06        46.98        46.32        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34       103.59        39.75       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 
      110.93       137.92       166.19         7.43       125.19        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC 
        3.65         6.41        11.34         3.25        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        48.89        36.03        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       107.34        61.18        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       28.60        10.49        13.87        10.16        17.85        45.11 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.55        52.01         6.35        12.20        29.82        27.22 
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-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B 
        4.96       109.64       151.27        78.87        13.55        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       47.84        39.62        72.07        32.19        18.61        56.42 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
       55.92        25.87        17.92        46.82        24.43        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       89.33        54.74        79.66       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       55.59        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       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 
      144.76       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 
      136.47        41.59       124.31       122.73        25.84         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        33.40       101.79        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-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25       148.18        79.99        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-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
      174.21         4.90       210.08        15.16         7.00       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         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       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-QB-A6FS 
        6.67 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.20              0.16 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           345.96            357.37 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            58.75             46.98 
[1] "0.2 - 346.0 (58.8)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.5"
D3V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P GAIN MUTATED                    8             1
  2P GAIN WILD-TYPE                 29             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2P GAIN MUTATED                                          15
  2P GAIN WILD-TYPE                                        45
                   vv
clus                REGIONAL LYMPH NODE
  2P GAIN MUTATED                    30
  2P GAIN WILD-TYPE                 149
D3V4, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  DISTANT METASTASIS                                      8                29
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              15                45
  REGIONAL LYMPH NODE                                    30               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
  2P GAIN MUTATED             3       2       5        3        5        2
  2P GAIN WILD-TYPE           7       4      18        7       20       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2P GAIN MUTATED           2         1         2         5          4
  2P GAIN WILD-TYPE         8        13         8        27         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED            4          9        1
  2P GAIN WILD-TYPE         19         39       11
D3V5, multiclass
             clus
vv            2P GAIN MUTATED 2P GAIN WILD-TYPE
  I OR II NOS               3                 7
  STAGE 0                   2                 4
  STAGE I                   5                18
  STAGE IA                  3                 7
  STAGE IB                  5                20
  STAGE II                  2                15
  STAGE IIA                 2                 8
  STAGE IIB                 1                13
  STAGE IIC                 2                 8
  STAGE III                 5                27
  STAGE IIIA                4                10
  STAGE IIIB                4                19
  STAGE IIIC                9                39
  STAGE IV                  1                11
[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  7 11
  2P GAIN WILD-TYPE    44 43 48 46
D3V6, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1               9                44
  T2                 17                43
  T3                  7                48
  T4                 11                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
  2P GAIN MUTATED    30   9   6   7
  2P GAIN WILD-TYPE 111  42  26  30
D3V7, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              30               111
  N1               9                42
  N2               6                26
  N3               7                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
  2P GAIN MUTATED    52   1   0   1   0
  2P GAIN WILD-TYPE 200   3   2   1   5
D3V8, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               52               200
  M1                1                 3
  M1A               0                 2
  M1B               1                 1
  M1C               0                 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"
D3V9, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   19 16
  2P GAIN WILD-TYPE 85 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     19   16
  2P GAIN WILD-TYPE   85   56
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               19                85
  YES              16                56
[1] 2 2
[1] FALSE
D3V10, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     4  51
  2P GAIN WILD-TYPE  30 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4   51
  2P GAIN WILD-TYPE   30  196
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                4                30
  YES              51               196
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    20  35
  2P GAIN WILD-TYPE  88 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     20   35
  2P GAIN WILD-TYPE   88  138
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              20                88
  MALE                35               138
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0    55
  2P GAIN WILD-TYPE     5                         1   220
D3V13, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  55               220
[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  54
  2P GAIN WILD-TYPE   3 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   54
  2P GAIN WILD-TYPE    3  220
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              54               220
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    31  18
  2Q GAIN WILD-TYPE 106 115
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               49               221 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               18               115 
$`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        69.90        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         5.39 
TCGA-D3-A5GN TCGA-D9-A6E9 TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
       52.01         9.90        51.12        25.15        17.56        14.83 
TCGA-EB-A5SH TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q 
        0.00         9.21         7.99         1.08        27.12         8.09 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GM 
        8.84         6.48         8.68        49.22         8.94        28.31 
TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AE 
       33.83        98.27         2.70        29.65         5.56        30.15 
TCGA-EE-A3AG TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19N 
       15.95        33.60        25.18        11.90       114.15        42.84 
TCGA-ER-A2NC TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A4F5 TCGA-FW-A3I3 
       11.80        18.41         8.22        47.38        28.73         0.20 
TCGA-OD-A75X 
       11.05 

$`2Q GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.52       111.09        32.42       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       81.24        10.29        85.32         8.38        21.14        68.22 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       30.87         7.50        36.16         6.31        92.42        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF 
      114.67        15.25        46.98        46.32        13.32        24.00 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        26.37        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       41.10        17.72         8.84        20.48        13.94        95.38 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       47.87         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
       11.31        13.22        14.60        48.79        35.80        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       39.19        13.68         9.99        44.52        36.69         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R 
       22.36         6.64        19.36         7.00        13.15         0.20 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.13         0.00        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-A29B 
        4.31        36.07         4.34         5.13         1.18         9.90 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       37.97        11.15        38.63         8.55         4.41         9.50 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
       12.03         9.99         2.43         8.09        11.31        23.90 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP 
       30.08        19.43        16.01        35.54        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
        1.15        13.02        34.98        36.33         8.84         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        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       111.78       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        27.16        23.05       124.31       122.73        25.84 
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         0.46        13.94 
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-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.78         3.52        11.11        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       28.60        34.68         9.57        36.07        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-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        6.58        22.49         1.71        85.74         4.90         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        3.58         5.36        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-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-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-A3R5 
       14.20        10.78         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         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       12.16        14.70        11.84        10.65         5.79 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                0                 0 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           114.15            124.31 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            18.41             13.45 
[1] "0.0 - 114.2 (18.4)" "0.0 - 124.3 (13.4)"
[1] "hr=" "1.7"
D4V2, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    32  18
  2Q GAIN WILD-TYPE 110 116
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               50               226 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               18               116 
$`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        69.90        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        21.47 
TCGA-D3-A5GN TCGA-D9-A6E9 TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
      135.75         9.90       117.21        53.92       215.44        15.68 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29L TCGA-EE-A29M 
       35.01         3.55       168.26        63.35         2.60        44.35 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A6 
       37.35        14.47       345.96       171.55       102.90        58.75 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MR TCGA-EE-A2MU 
       75.48        90.97       129.27        28.83       103.56        53.26 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G 
       54.51        23.47       148.08        98.40        13.02       268.93 
TCGA-ER-A19N TCGA-ER-A2NC TCGA-FR-A3YN TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A4F5 
       44.05        43.82        92.98        53.52       101.26        28.73 
TCGA-FW-A3I3 TCGA-OD-A75X 
        0.20       294.77 

$`2Q GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04       112.57       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       48.76       113.52        42.08        12.10       171.58        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        58.06        46.98        46.32        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        9.34       103.59        39.75       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      131.90        18.38        10.03        51.68        15.06       110.93 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      137.92       166.19         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC 
        3.65         6.41        11.34         3.25        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       22.95        48.89        36.03        20.38       194.83       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       107.34        61.18        65.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       28.60        10.49        13.87        10.16        17.85        45.11 
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-A29B TCGA-EE-A29C 
      109.64       151.27        78.87        13.55        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       13.97        39.62        72.07        32.19        18.61        56.42 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 
       55.92        25.87        17.92        46.82        24.43        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       89.33        54.74        79.66       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       55.59        44.88        94.82        21.67        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       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 
      144.76       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 
      136.47        41.59       124.31       122.73        25.84         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        33.40       101.79        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-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      162.08        50.89        37.25       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-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       46.98        33.21       174.21         4.90       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        7.00       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-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
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-QB-A6FS 
       39.58        46.36        12.62         6.67 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.20              0.16 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           345.96            357.37 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            57.47             47.13 
[1] "0.2 - 346.0 (57.5)" "0.2 - 357.4 (47.1)"
[1] "hr=" "1.7"
D4V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q GAIN MUTATED                    6             1
  2Q GAIN WILD-TYPE                 31             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2Q GAIN MUTATED                                          15
  2Q GAIN WILD-TYPE                                        45
                   vv
clus                REGIONAL LYMPH NODE
  2Q GAIN MUTATED                    31
  2Q GAIN WILD-TYPE                 148
D4V4, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      6                31
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              15                45
  REGIONAL LYMPH NODE                                    31               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
  2Q GAIN MUTATED             3       2       5        3        6        1
  2Q GAIN WILD-TYPE           7       4      18        7       19       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2Q GAIN MUTATED           2         1         2         7          4
  2Q GAIN WILD-TYPE         8        13         8        25         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED            3          8        1
  2Q GAIN WILD-TYPE         20         40       11
D4V5, multiclass
             clus
vv            2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  I OR II NOS               3                 7
  STAGE 0                   2                 4
  STAGE I                   5                18
  STAGE IA                  3                 7
  STAGE IB                  6                19
  STAGE II                  1                16
  STAGE IIA                 2                 8
  STAGE IIB                 1                13
  STAGE IIC                 2                 8
  STAGE III                 7                25
  STAGE IIIA                4                10
  STAGE IIIB                3                20
  STAGE IIIC                8                40
  STAGE IV                  1                11
[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      10 18  6  9
  2Q GAIN WILD-TYPE    43 42 49 48
D4V6, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              10                43
  T2                 18                42
  T3                  6                49
  T4                  9                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
  2Q GAIN MUTATED    29   8   7   6
  2Q GAIN WILD-TYPE 112  43  25  31
D4V7, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              29               112
  N1               8                43
  N2               7                25
  N3               6                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
  2Q GAIN MUTATED    51   1   0   0   0
  2Q GAIN WILD-TYPE 201   3   2   2   5
D4V8, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               51               201
  M1                1                 3
  M1A               0                 2
  M1B               0                 2
  M1C               0                 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"
D4V9, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   19 14
  2Q GAIN WILD-TYPE 85 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     19   14
  2Q GAIN WILD-TYPE   85   58
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               19                85
  YES              14                58
[1] 2 2
[1] FALSE
D4V10, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     5  48
  2Q GAIN WILD-TYPE  29 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5   48
  2Q GAIN WILD-TYPE   29  199
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                5                29
  YES              48               199
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    21  32
  2Q GAIN WILD-TYPE  87 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     21   32
  2Q GAIN WILD-TYPE   87  141
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              21                87
  MALE                32               141
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0    53
  2Q GAIN WILD-TYPE     5                         1   222
D4V13, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  53               222
[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  52
  2Q GAIN WILD-TYPE   3 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   52
  2Q GAIN WILD-TYPE    3  222
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              52               222
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    27  15
  3P GAIN WILD-TYPE 110 118
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               42               228 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               15               118 
$`3P GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV 
        8.38        30.87        82.29        61.38       103.59         5.39 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       52.01         1.55         4.93         7.00        17.56        14.83 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H 
        0.00         0.00         8.12         5.13        36.07         9.21 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GI 
        1.08        27.12         8.84         6.48         8.68        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-A19S 
       21.60        22.22        13.94        33.60       114.15        36.07 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-GN-A266 
        6.58         1.71        23.80        12.89         3.22        10.13 

$`3P GAIN 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-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF 
      114.67        15.25        46.98        46.32        13.32        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        6.31         9.34        26.37        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       41.10        17.72         8.84        20.48        13.94        95.38 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       47.87         6.97        23.11         4.01         2.89         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-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A44R 
       25.15        22.36         6.64        19.36        13.15         0.20 
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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
        1.12         1.35        12.20         4.31         4.34         5.13 
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        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        8.55         4.41         9.50        12.03         8.09         9.99 
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        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        47.21 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR 
       19.43        16.01        35.54        28.31        30.84         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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       63.42       111.78       111.91        56.02        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       29.65        27.16        23.05       124.31       122.73        25.84 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        3.68        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 
       21.60        16.14        27.35         0.46        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-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.90        11.11        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       28.60        42.84        34.68         9.57        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-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        9.04        22.49        18.41        85.74         4.90         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
        3.58         5.36        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         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        14.70        11.84        10.65        11.05         5.79 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.00              0.13 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           114.15            124.31 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            11.51             14.40 
[1] "0.0 - 114.2 (11.5)" "0.1 - 124.3 (14.4)"
[1] "hr=" "1.3"
D5V2, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    28  15
  3P GAIN WILD-TYPE 114 119
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               43               233 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               15               119 
$`3P GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MR TCGA-D3-A3MV 
       65.49        48.76       166.52        86.93       103.59        21.47 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
      135.75       166.19        65.92        10.49       215.44        15.68 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A20B 
       45.11        35.01         3.55        94.98        68.15       109.64 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W 
      168.26         2.60        44.35        14.47       345.96       171.55 
TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A2MU 
       48.72        90.97        13.91        21.67       248.65        53.26 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A19G 
       54.51        36.95        53.19       101.79       148.08       268.93 
TCGA-ER-A19S TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F2 
       37.25        80.32        33.21       202.65        23.93        50.14 
TCGA-GN-A266 
       10.13 

$`3P GAIN 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-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3CF 
      130.72        58.06        46.98        46.32        60.23        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.87         9.34        39.75       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      131.90        18.38        10.03        51.68        15.06       110.93 
TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      137.92         7.43       125.19       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         3.25         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-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-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN 
       68.09        28.60        13.87        10.16        17.85        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-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       14.70        26.89         4.96       151.27        78.87        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        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       32.19        18.61        56.42        37.35        55.92        25.87 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
       47.54        67.43       314.56       135.95       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        75.48       101.95        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       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 
      144.76       203.05       167.90        47.54        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      136.47        41.59       124.31       122.73        25.84         3.68 
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-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       34.32        27.35        33.40        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02        26.37       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-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-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       46.98        92.98       174.21         4.90       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        7.00       216.92        48.59       228.59        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-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        32.75        47.38       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-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         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       39.58        46.36        12.62       294.77         6.67 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2.60              0.16 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           345.96            357.37 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            54.51             46.98 
[1] "2.6 - 346.0 (54.5)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.9"
D5V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P GAIN MUTATED                    8             0
  3P GAIN WILD-TYPE                 29             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3P GAIN MUTATED                                          12
  3P GAIN WILD-TYPE                                        48
                   vv
clus                REGIONAL LYMPH NODE
  3P GAIN MUTATED                    25
  3P GAIN WILD-TYPE                 154
D5V4, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  DISTANT METASTASIS                                      8                29
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              12                48
  REGIONAL LYMPH NODE                                    25               154
[1] 4 2
[1] 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             3       1       5        5        5        2
  3P GAIN WILD-TYPE           7       5      18        5       20       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3P GAIN MUTATED           1         0         2         6          1
  3P GAIN WILD-TYPE         9        14         8        26         13
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED            5          3        1
  3P GAIN WILD-TYPE         18         45       11
D5V5, multiclass
             clus
vv            3P GAIN MUTATED 3P GAIN WILD-TYPE
  I OR II NOS               3                 7
  STAGE 0                   1                 5
  STAGE I                   5                18
  STAGE IA                  5                 5
  STAGE IB                  5                20
  STAGE II                  2                15
  STAGE IIA                 1                 9
  STAGE IIB                 0                14
  STAGE IIC                 2                 8
  STAGE III                 6                26
  STAGE IIIA                1                13
  STAGE IIIB                5                18
  STAGE IIIC                3                45
  STAGE IV                  1                11
[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      10 15  4  8
  3P GAIN WILD-TYPE    43 45 51 49
D5V6, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1              10                43
  T2                 15                45
  T3                  4                51
  T4                  8                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
  3P GAIN MUTATED    28   8   3   2
  3P GAIN WILD-TYPE 113  43  29  35
D5V7, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              28               113
  N1               8                43
  N2               3                29
  N3               2                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
  3P GAIN MUTATED    41   0   1   0   0
  3P GAIN WILD-TYPE 211   4   1   2   5
D5V8, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               41               211
  M1                0                 4
  M1A               1                 1
  M1B               0                 2
  M1C               0                 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"
D5V9, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   17  9
  3P GAIN WILD-TYPE 87 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     17    9
  3P GAIN WILD-TYPE   87   63
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               17                87
  YES               9                63
[1] 2 2
[1] FALSE
D5V10, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     4  41
  3P GAIN WILD-TYPE  30 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   41
  3P GAIN WILD-TYPE   30  206
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                4                30
  YES              41               206
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    19  26
  3P GAIN WILD-TYPE  89 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     19   26
  3P GAIN WILD-TYPE   89  147
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              19                89
  MALE                26               147
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0    45
  3P GAIN WILD-TYPE     5                         1   230
D5V13, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  45               230
[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  45
  3P GAIN WILD-TYPE   3 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   45
  3P GAIN WILD-TYPE    3  229
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              45               229
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    31  21
  3Q GAIN WILD-TYPE 106 112
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               52               218 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               21               112 
$`3Q GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 
        8.38        88.50        30.87        92.42        56.19        15.25 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A6EC 
       82.29       103.59         5.39        52.01         1.55        13.22 
TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EE-A180 
        4.93         7.00        17.56        14.83         0.00         8.12 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29M 
        1.35         5.13        36.07         5.13         9.21        27.12 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GI TCGA-EE-A2GN TCGA-EE-A2GP 
        8.84         6.48         8.68        30.08        33.83         5.42 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA 
        8.84        98.27       111.91        26.99         5.56       124.31 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
       30.15        21.60        21.60        22.22        13.94        33.60 
TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1Z0 
      114.15        28.60         1.87         6.58         1.71        23.80 
TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-GN-A266 TCGA-GN-A26A 
       12.89         3.22        10.13        12.16 

$`3Q GAIN 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-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        22.55        45.83        81.24        10.29        85.32 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        68.22        69.90        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
        6.31        64.44        45.11       114.67        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       61.38        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 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       20.48        13.94        95.38        47.87         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
        4.01         2.89         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-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       44.52        36.69        25.15        22.36         6.64        19.36 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       13.15         0.20         0.13         0.00        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       11.57        10.55         6.31         1.12        12.20         4.31 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        4.34         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       38.63         8.55         4.41         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.09         9.99         2.43         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 
       30.84         1.15        13.02        34.98        36.33         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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       14.56        63.42       111.78        56.02        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       29.65        27.16        23.05       122.73        25.84         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       13.81        15.95        12.72         3.22        22.92        16.14 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35         0.46        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-A19N TCGA-ER-A19P 
       11.11        34.88         4.21        13.45        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
        9.57        36.07        17.72        78.44        11.80         1.51 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN 
       13.08        12.62        11.74         9.04        22.49        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       85.74         4.90         6.71         3.58         5.36        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.45        11.01        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-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        12.92        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-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         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-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        16.24        15.42        14.70        11.84        10.65 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                 0 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           124.31            122.73 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           14.385            14.070 
[1] "0.0 - 124.3 (14.4)" "0.0 - 122.7 (14.1)"
[1] "hr=" "1.3"
D6V2, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    32  21
  3Q GAIN WILD-TYPE 110 113
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               53               223 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               21               113 
$`3Q GAIN MUTATED`
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3C6 
       65.49       115.53        48.76       171.58        56.19        58.06 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A6EC 
      166.52       103.59        21.47       135.75       166.19        66.25 
TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL 
       65.92        10.49       215.44        15.68        45.11         3.55 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       94.98        14.70        68.15       109.64        78.87       168.26 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2GI TCGA-EE-A2GN 
       44.35        14.47       345.96       171.55        48.72        90.97 
TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU 
       13.91        21.67       129.27       203.05       248.65        53.26 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH 
      124.31        54.51        36.95        64.08        53.19       101.79 
TCGA-EE-A3JI TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3PL 
      148.08       268.93        61.05        23.34        80.32        33.21 
TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-GN-A266 TCGA-GN-A26A 
      202.65        23.93        50.14        10.13        32.48 

$`3Q GAIN 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-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
       28.08        31.59        90.90        95.74        43.43       103.10 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       168.00        69.90        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       12.10        66.08        45.11       130.72        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       86.93        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 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU 
       51.68        15.06       110.93       137.92         7.43       125.19 
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         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        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-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       17.85        35.01        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C 
       27.22         8.65        33.73        26.89         4.96       151.27 
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        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         2.60        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        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
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       101.95 
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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       144.76       167.90        47.54        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
      136.47        41.59       122.73        25.84         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD 
       23.47       138.81       172.18       127.20        34.32        27.35 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       33.40        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-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-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       31.27        32.05       247.04        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
        4.90       210.08        15.16         7.00       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         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       64.44        62.79        39.58        46.36        12.62       294.77 
TCGA-QB-A6FS 
        6.67 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             3.55              0.16 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           345.96            357.37 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            65.49             45.11 
[1] "3.5 - 346.0 (65.5)" "0.2 - 357.4 (45.1)"
[1] "hr=" "1.8"
D6V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q GAIN MUTATED                   10             1
  3Q GAIN WILD-TYPE                 27             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3Q GAIN MUTATED                                          14
  3Q GAIN WILD-TYPE                                        46
                   vv
clus                REGIONAL LYMPH NODE
  3Q GAIN MUTATED                    30
  3Q GAIN WILD-TYPE                 149
D6V4, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     10                27
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              14                46
  REGIONAL LYMPH NODE                                    30               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
  3Q GAIN MUTATED             4       1       8        5        7        3
  3Q GAIN WILD-TYPE           6       5      15        5       18       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3Q GAIN MUTATED           1         0         1         7          4
  3Q GAIN WILD-TYPE         9        14         9        25         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED            5          4        1
  3Q GAIN WILD-TYPE         18         44       11
D6V5, multiclass
             clus
vv            3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  I OR II NOS               4                 6
  STAGE 0                   1                 5
  STAGE I                   8                15
  STAGE IA                  5                 5
  STAGE IB                  7                18
  STAGE II                  3                14
  STAGE IIA                 1                 9
  STAGE IIB                 0                14
  STAGE IIC                 1                 9
  STAGE III                 7                25
  STAGE IIIA                4                10
  STAGE IIIB                5                18
  STAGE IIIC                4                44
  STAGE IV                  1                11
[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      15 19  7  6
  3Q GAIN WILD-TYPE    38 41 48 51
D6V6, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              15                38
  T2                 19                41
  T3                  7                48
  T4                  6                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
  3Q GAIN MUTATED    33  14   3   2
  3Q GAIN WILD-TYPE 108  37  29  35
D6V7, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              33               108
  N1              14                37
  N2               3                29
  N3               2                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
  3Q GAIN MUTATED    52   0   1   0   0
  3Q GAIN WILD-TYPE 200   4   1   2   5
D6V8, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               52               200
  M1                0                 4
  M1A               1                 1
  M1B               0                 2
  M1C               0                 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"
D6V9, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   25  8
  3Q GAIN WILD-TYPE 79 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     25    8
  3Q GAIN WILD-TYPE   79   64
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               25                79
  YES               8                64
[1] 2 2
[1] FALSE
D6V10, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5  50
  3Q GAIN WILD-TYPE  29 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5   50
  3Q GAIN WILD-TYPE   29  197
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                5                29
  YES              50               197
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    23  32
  3Q GAIN WILD-TYPE  85 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     23   32
  3Q GAIN WILD-TYPE   85  141
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              23                85
  MALE                32               141
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         0    55
  3Q GAIN WILD-TYPE     5                         1   220
D6V13, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  55               220
[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  55
  3Q GAIN WILD-TYPE   3 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   55
  3Q GAIN WILD-TYPE    3  219
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              55               219
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    24  19
  4P GAIN WILD-TYPE 113 114
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               43               227 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19               114 
$`4P GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51N 
        8.52        15.25        46.98        13.32        26.37         8.84 
TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IB 
       23.11         9.90        11.31        48.79        39.19        22.36 
TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29P 
       17.56         0.00         5.13         5.13         8.55        12.03 
TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA 
       39.39        30.08         5.42        63.42        26.99       124.31 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A19H TCGA-ER-A3ET TCGA-ER-A3PL 
        3.22        21.60        22.22        34.88         6.58         1.71 
TCGA-FR-A3YN TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       18.41         3.45        12.92        12.89        47.38         8.65 
TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 
        8.68         3.22        28.73         7.23        31.33        15.42 
TCGA-GN-A26D 
       14.70 

$`4P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       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-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       45.11       114.67        46.32        82.29        61.38        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       15.09        41.10        17.72        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87         1.55         6.97         4.01         2.89 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       13.22        14.60        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
        9.99        44.52        36.69        25.15         4.93         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       19.36         7.00        14.83        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00        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        36.07 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.34         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        38.63         4.41         1.08        27.12         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         6.48         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        34.92        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        30.84         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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.78       111.91        56.02        25.08        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16        23.05         5.56       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        13.81        15.95        12.72        22.92        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        27.35         0.46        13.94        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-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-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P 
       12.62        11.74         9.04        22.49        85.74         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        6.71         3.58         5.36        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-A1ZP 
        8.22        19.53        11.08         7.17        30.87        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-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       53.85         7.36        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         0.43 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        9.90        12.85        24.85        84.72        10.13        16.24 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        11.84        10.65        11.05         5.79 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                 0 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           124.31            122.73 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            14.70             13.94 
[1] "0.0 - 124.3 (14.7)" "0.0 - 122.7 (13.9)"
[1] "hr=" "1"  
D7V2, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    24  19
  4P GAIN WILD-TYPE 118 115
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               43               233 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19               115 
$`4P GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A51N 
       16.67        58.06        46.98        60.23        39.75        10.03 
TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1IB 
      125.19         9.90        25.18        48.89       194.83        23.44 
TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29P 
      215.44        35.01        68.15        78.87        72.07        56.42 
TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2MJ TCGA-EE-A2MP TCGA-EE-A3AA 
       47.54        48.72        13.91        96.23       248.65       124.31 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A19H TCGA-ER-A3ET TCGA-ER-A3PL 
      172.18        64.08        53.19       152.35        80.32        33.21 
TCGA-FR-A3YN TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       92.98        48.59        47.38        23.93       101.26       133.55 
TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A268 
       26.56        50.14        28.73         7.23       117.93        62.79 
TCGA-GN-A26D 
       39.58 

$`4P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       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-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       45.11       130.72        46.32       166.52        86.93        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       40.14       131.90        18.38        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92       166.19         7.43       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
        3.65         6.41        11.34         3.25        66.25        22.95 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.21        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       61.18        53.92        65.92        68.09        28.60        10.49 
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        45.11         3.55 
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       109.64 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27       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        39.62        32.19         2.60        44.35        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       345.96        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       135.95       208.04        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       101.95        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      144.76       203.05       167.90        47.54        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      136.47        41.59        53.26       122.73        25.84         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-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        27.35        33.40       101.79       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-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-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
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-FR-A44A TCGA-FR-A69P 
       31.27        32.05       247.04        46.98       174.21         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      210.08        15.16         7.00       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-A1ZP 
       53.52        40.27        15.45         9.70        32.75        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        53.16        49.48        27.09        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        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         2.40 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        9.90        14.04       120.46        84.72        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        46.36        12.62       294.77         6.67 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             7.23              0.16 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           248.65            357.37 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            53.19             46.82 
[1] "7.2 - 248.7 (53.2)" "0.2 - 357.4 (46.8)"
[1] "hr=" "1.2"
D7V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P GAIN MUTATED                    4             2
  4P GAIN WILD-TYPE                 33             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4P GAIN MUTATED                                          12
  4P GAIN WILD-TYPE                                        48
                   vv
clus                REGIONAL LYMPH NODE
  4P GAIN MUTATED                    25
  4P GAIN WILD-TYPE                 154
D7V4, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  DISTANT METASTASIS                                      4                33
  PRIMARY TUMOR                                           2                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              12                48
  REGIONAL LYMPH NODE                                    25               154
[1] 4 2
[1] 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             1       0       5        1        7        1
  4P GAIN WILD-TYPE           9       6      18        9       18       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4P GAIN MUTATED           0         1         5         6          4
  4P GAIN WILD-TYPE        10        13         5        26         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED            3          4        2
  4P GAIN WILD-TYPE         20         44       10
D7V5, multiclass
             clus
vv            4P GAIN MUTATED 4P GAIN WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   5                18
  STAGE IA                  1                 9
  STAGE IB                  7                18
  STAGE II                  1                16
  STAGE IIA                 0                10
  STAGE IIB                 1                13
  STAGE IIC                 5                 5
  STAGE III                 6                26
  STAGE IIIA                4                10
  STAGE IIIB                3                20
  STAGE IIIC                4                44
  STAGE IV                  2                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
  4P GAIN MUTATED      10 13  4 12
  4P GAIN WILD-TYPE    43 47 51 45
D7V6, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1              10                43
  T2                 13                47
  T3                  4                51
  T4                 12                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
  4P GAIN MUTATED    25   7   5   4
  4P GAIN WILD-TYPE 116  44  27  33
D7V7, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              25               116
  N1               7                44
  N2               5                27
  N3               4                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
  4P GAIN MUTATED    38   0   1   0   1
  4P GAIN WILD-TYPE 214   4   1   2   4
D7V8, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               38               214
  M1                0                 4
  M1A               1                 1
  M1B               0                 2
  M1C               1                 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"
D7V9, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   16 11
  4P GAIN WILD-TYPE 88 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     16   11
  4P GAIN WILD-TYPE   88   61
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               16                88
  YES              11                61
[1] 2 2
[1] FALSE
D7V10, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     7  36
  4P GAIN WILD-TYPE  27 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      7   36
  4P GAIN WILD-TYPE   27  211
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                7                27
  YES              36               211
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    19  24
  4P GAIN WILD-TYPE  89 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     19   24
  4P GAIN WILD-TYPE   89  149
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              19                89
  MALE                24               149
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         0    43
  4P GAIN WILD-TYPE     5                         1   232
D7V13, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  43               232
[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     0  43
  4P GAIN WILD-TYPE   3 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   43
  4P GAIN WILD-TYPE    3  231
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              43               231
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    19  17
  4Q GAIN WILD-TYPE 118 116
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               36               234 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               116 
$`4Q GAIN MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A5GU TCGA-D9-A6EA TCGA-DA-A1HV 
       15.25        13.32        26.37        23.11        11.31        48.79 
TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20F 
       39.19        22.36        17.56         0.00         5.13         5.13 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2MJ 
       11.15         8.55        12.03        39.39         5.42        63.42 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
       26.99        29.65         3.68         3.22        21.60        22.22 
TCGA-ER-A19H TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       34.88         1.71        18.41         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 

$`4Q GAIN 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-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        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       64.44        45.11       114.67        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         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       20.48        13.94        95.38        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        6.97         4.01         2.89         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-A5UN 
       14.83        13.15         0.20         0.13         0.00        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-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H 
        1.35        12.20         4.31        36.07         4.34         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
        1.18         7.99         9.90        37.97        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08        27.12         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 
        6.48         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        34.29        17.98        34.92 
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-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83        30.84         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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       56.02        25.08        21.60        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        25.84        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       12.72        22.92        21.60        16.14        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        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-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-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-A2NH TCGA-ER-A3ES 
        1.87         1.51        13.08        12.62        11.74         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        6.58        22.49        85.74         4.90         6.71         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        5.36        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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        12.89        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-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        0.43         9.90        12.85        24.85        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       16.24        12.16        11.84        10.65        11.05         5.79 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                 0 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            63.42            124.31 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           15.335            13.875 
[1] "0.0 - 63.4 (15.3)"  "0.0 - 124.3 (13.9)"
[1] "hr=" "1.1"
D8V2, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    19  17
  4Q GAIN WILD-TYPE 123 117
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               36               240 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               117 
$`4Q GAIN MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A5GU TCGA-D9-A6EA TCGA-DA-A1HV 
       58.06        60.23        39.75       125.19        25.18        48.89 
TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EE-A184 TCGA-EE-A20F 
      194.83        23.44       215.44        35.01        68.15        78.87 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GP TCGA-EE-A2MJ 
       13.97        72.07        56.42        47.54        13.91        96.23 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
      248.65       103.56         3.68       172.18        64.08        53.19 
TCGA-ER-A19H TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ 
      152.35        33.21        92.98        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 

$`4Q GAIN 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-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        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.08        45.11       130.72        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        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       51.68        15.06       110.93       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
        7.43       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
        3.25         9.90        66.25        22.95        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-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       65.92        68.09        28.60        10.49        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       10.16        17.85        45.11         3.55        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-A20H 
       14.70        26.89         4.96       109.64       151.27       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       13.55        63.35        80.61        47.84        39.62        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        2.60        44.35        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 
      345.96        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        39.29        58.75        67.43       314.56       135.95 
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       101.95        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54        43.23       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      124.31       122.73        25.84        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
      138.81       127.20        36.95        34.32        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       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-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-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-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-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       80.32        46.98       174.21         4.90       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        7.00       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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       15.45         9.70        32.75        47.38        23.93        74.73 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41       148.80        53.16        49.48        27.09        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-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        2.40         9.90        14.04       120.46        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       64.44        32.48        46.36        12.62       294.77         6.67 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3.68              0.16 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           248.65            357.37 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           59.145            46.980 
[1] "3.7 - 248.7 (59.1)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.2"
D8V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q GAIN MUTATED                    3             1
  4Q GAIN WILD-TYPE                 34             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4Q GAIN MUTATED                                          10
  4Q GAIN WILD-TYPE                                        50
                   vv
clus                REGIONAL LYMPH NODE
  4Q GAIN MUTATED                    22
  4Q GAIN WILD-TYPE                 157
D8V4, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      3                34
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              10                50
  REGIONAL LYMPH NODE                                    22               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
  4Q GAIN MUTATED             1       0       5        0        7        0
  4Q GAIN WILD-TYPE           9       6      18       10       18       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4Q GAIN MUTATED           0         1         3         5          2
  4Q GAIN WILD-TYPE        10        13         7        27         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED            3          5        1
  4Q GAIN WILD-TYPE         20         43       11
D8V5, multiclass
             clus
vv            4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   5                18
  STAGE IA                  0                10
  STAGE IB                  7                18
  STAGE II                  0                17
  STAGE IIA                 0                10
  STAGE IIB                 1                13
  STAGE IIC                 3                 7
  STAGE III                 5                27
  STAGE IIIA                2                12
  STAGE IIIB                3                20
  STAGE IIIC                5                43
  STAGE IV                  1                11
[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       7 13  3  9
  4Q GAIN WILD-TYPE    46 47 52 48
D8V6, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               7                46
  T2                 13                47
  T3                  3                52
  T4                  9                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
  4Q GAIN MUTATED    21   5   5   3
  4Q GAIN WILD-TYPE 120  46  27  34
D8V7, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              21               120
  N1               5                46
  N2               5                27
  N3               3                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 GAIN MUTATED    32   0   1   0   0
  4Q GAIN WILD-TYPE 220   4   1   2   5
D8V8, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               32               220
  M1                0                 4
  M1A               1                 1
  M1B               0                 2
  M1C               0                 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"
D8V9, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   14 10
  4Q GAIN WILD-TYPE 90 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     14   10
  4Q GAIN WILD-TYPE   90   62
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               14                90
  YES              10                62
[1] 2 2
[1] FALSE
D8V10, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5  31
  4Q GAIN WILD-TYPE  29 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5   31
  4Q GAIN WILD-TYPE   29  216
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                5                29
  YES              31               216
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    13  23
  4Q GAIN WILD-TYPE  95 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     13   23
  4Q GAIN WILD-TYPE   95  150
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              13                95
  MALE                23               150
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         0    36
  4Q GAIN WILD-TYPE     5                         1   239
D8V13, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  36               239
[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     0  36
  4Q GAIN WILD-TYPE   3 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   36
  4Q GAIN WILD-TYPE    3  238
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              36               238
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    34  20
  5P GAIN WILD-TYPE 103 113
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               54               216 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               113 
$`5P GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP 
        8.52        32.42        30.87         6.31        56.19        45.11 
TCGA-D3-A3C6 TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR 
       15.25        26.37        80.22         8.84        52.01         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-EE-A180 
        6.97        23.11         9.90        11.31        13.22         8.12 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
        1.12        36.07         9.21         6.48         8.68        11.31 
TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA 
       28.31        98.27         2.70        26.99        27.16       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19B 
      122.73        30.15         3.22        22.22        33.60        25.18 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A3PL 
        3.78       114.15        28.60        42.84        34.68         1.71 
TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZQ 
       85.74         5.36         3.45        19.53        12.89         8.65 
TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U9 
       28.73         0.20         0.13         7.23        84.72        10.65 

$`5P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47       111.09        70.16       110.79        28.08        22.55 
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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        69.90        11.41         7.50        36.16 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       92.42        64.44       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-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
        5.39        42.71        15.09        41.10        17.72        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EG 
       13.94        95.38        47.87         4.01         2.89        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-A5UN TCGA-EB-A6L9 
        0.20         0.13         0.00         0.00        13.22         0.20 
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-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.31         4.34         5.13         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        38.63         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        2.43         8.09        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        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        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
        1.15        13.02        34.98        36.33         8.84         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       63.42       111.78       111.91        56.02        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       29.65        23.05         5.56        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35         0.46        13.94        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       34.88         4.21        13.45         9.57        36.07        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-FR-A3YN TCGA-FR-A69P 
       11.74         9.04         6.58        22.49        18.41         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        6.71         3.58        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         0.43 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        9.90        12.85        24.85        31.33        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       15.42        12.16        14.70        11.84        11.05         5.79 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.13              0.00 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           124.31            114.67 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            17.39             13.94 
[1] "0.1 - 124.3 (17.4)" "0.0 - 114.7 (13.9)"
[1] "hr=" "1.5"
D9V2, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    36  20
  5P GAIN WILD-TYPE 106 114
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               56               220 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               114 
$`5P GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP 
       16.67       112.57        48.76        12.10        56.19        45.11 
TCGA-D3-A3C6 TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR 
       58.06        39.75       161.85        10.03       135.75       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-D9-A6EA 
        7.43       125.19       151.53         3.65         9.90        25.18 
TCGA-D9-A6EC TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29T 
       66.25        94.98        33.73       109.64       168.26       345.96 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP 
      171.55        46.82        75.48       129.27        28.83       248.65 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JA 
      136.47       124.31       122.73        54.51       172.18        53.19 
TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19M TCGA-ER-A19N 
      148.08        98.40        48.89       268.93        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZE 
      162.08        33.21       174.21         7.00        48.59        40.27 
TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO 
       23.93       133.55        28.73         0.20        47.54         7.23 
TCGA-GN-A265 TCGA-GN-A4U9 
       84.72        12.62 

$`5P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57       112.04        71.80       133.25        28.08        31.59 
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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        69.90        11.87       113.52        42.08 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
      171.58        66.08       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-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       21.47        43.69        40.14       131.90        18.38        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 
       15.06       110.93       137.92        54.67         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        3.25        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-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.16        17.85        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.55        52.01         6.35        12.20        29.82        27.22 
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-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       78.87        13.55        63.35        80.61        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       56.42        37.35        14.47        55.92        25.87        17.92 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       208.04        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       101.95        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      203.05       167.90        47.54        43.23       103.56        41.59 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       53.26        25.84         3.68        13.81        23.47       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        36.95        64.08        34.32        27.35        33.40 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      101.79        31.40        35.44        13.94        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J 
       77.75        12.59        13.02        26.37       152.35         6.44 
TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      131.51        50.89        37.25       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-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       80.32        46.98        92.98         4.90       210.08        15.16 
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         2.40         9.90        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       39.58        46.36       294.77         6.67 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.20              0.16 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           345.96            357.37 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           57.125            46.670 
[1] "0.2 - 346.0 (57.1)" "0.2 - 357.4 (46.7)"
[1] "hr=" "1.8"
D9V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P GAIN MUTATED                    8             3
  5P GAIN WILD-TYPE                 29             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5P GAIN MUTATED                                           8
  5P GAIN WILD-TYPE                                        52
                   vv
clus                REGIONAL LYMPH NODE
  5P GAIN MUTATED                    38
  5P GAIN WILD-TYPE                 141
D9V4, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  DISTANT METASTASIS                                      8                29
  PRIMARY TUMOR                                           3                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               8                52
  REGIONAL LYMPH NODE                                    38               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
  5P GAIN MUTATED             3       1       7        2        6        6
  5P GAIN WILD-TYPE           7       5      16        8       19       11
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5P GAIN MUTATED           1         0         3         5          3
  5P GAIN WILD-TYPE         9        14         7        27         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED            1          5        4
  5P GAIN WILD-TYPE         22         43        8
D9V5, multiclass
             clus
vv            5P GAIN MUTATED 5P GAIN WILD-TYPE
  I OR II NOS               3                 7
  STAGE 0                   1                 5
  STAGE I                   7                16
  STAGE IA                  2                 8
  STAGE IB                  6                19
  STAGE II                  6                11
  STAGE IIA                 1                 9
  STAGE IIB                 0                14
  STAGE IIC                 3                 7
  STAGE III                 5                27
  STAGE IIIA                3                11
  STAGE IIIB                1                22
  STAGE IIIC                5                43
  STAGE IV                  4                 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
  5P GAIN MUTATED      13 12 12  8
  5P GAIN WILD-TYPE    40 48 43 49
D9V6, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              13                40
  T2                 12                48
  T3                 12                43
  T4                  8                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
  5P GAIN MUTATED    34   7   4   6
  5P GAIN WILD-TYPE 107  44  28  31
D9V7, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              34               107
  N1               7                44
  N2               4                28
  N3               6                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
  5P GAIN MUTATED    48   1   1   1   2
  5P GAIN WILD-TYPE 204   3   1   1   3
D9V8, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               48               204
  M1                1                 3
  M1A               1                 1
  M1B               1                 1
  M1C               2                 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"
D9V9, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   23  7
  5P GAIN WILD-TYPE 81 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     23    7
  5P GAIN WILD-TYPE   81   65
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               23                81
  YES               7                65
[1] 2 2
[1] FALSE
D9V10, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     9  48
  5P GAIN WILD-TYPE  25 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      9   48
  5P GAIN WILD-TYPE   25  199
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                9                25
  YES              48               199
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    24  33
  5P GAIN WILD-TYPE  84 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     24   33
  5P GAIN WILD-TYPE   84  140
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              24                84
  MALE                33               140
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       0                         0    57
  5P GAIN WILD-TYPE     5                         1   218
D9V13, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  57               218
[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     0  57
  5P GAIN WILD-TYPE   3 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0   57
  5P GAIN WILD-TYPE    3  217
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              57               217
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    22  11
  5Q GAIN WILD-TYPE 115 122
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               33               237 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               11               122 
$`5Q GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3MU TCGA-D3-A51K 
        8.52        30.87        56.19        45.11        26.37        17.72 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-EE-A180 TCGA-EE-A181 
        1.55         6.97        23.11         9.90         8.12         1.12 
TCGA-EE-A20B TCGA-EE-A29W TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE 
       36.07         8.68        26.99        27.16       124.31        30.15 
TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19C TCGA-ER-A19N TCGA-ER-A19P 
        3.22        22.22        33.60         3.78        42.84        34.68 
TCGA-ER-A3PL TCGA-FR-A7U9 TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A4F5 TCGA-FW-A3TU 
        1.71         5.36         8.22        12.89        28.73         0.13 
TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U9 
        7.23        84.72        10.65 

$`5Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       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        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 
       36.16         6.31        92.42        64.44       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-A3MV TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       15.09        41.10         8.84        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC 
       52.01        47.87         4.01         2.89        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-A5UN 
       13.15         0.20         0.13         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
        0.20        11.57        10.55         6.31         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31         4.34         5.13         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        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         6.48         2.43         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        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        30.84         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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       21.60        29.65        23.05         5.56       122.73        25.84 
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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       21.60        16.14        27.35         0.46        13.94        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-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-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       13.45        28.60         9.57        36.07        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         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        6.71         3.58        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-GN-A262 
        0.99         0.16         0.43         9.90        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        10.13        16.24        15.42        12.16        14.70 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        11.05         5.79 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.13              0.00 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           124.31            122.73 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            17.72             13.94 
[1] "0.1 - 124.3 (17.7)" "0.0 - 122.7 (13.9)"
[1] "hr=" "1.5"
D10V2, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    24  11
  5Q GAIN WILD-TYPE 118 123
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               35               241 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               11               123 
$`5Q GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3MU TCGA-D3-A51K 
       16.67        48.76        56.19        45.11        39.75        18.38 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 
      166.19         7.43       125.19       151.53         3.65         9.90 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29W TCGA-EE-A2MP TCGA-EE-A2MS 
       94.98        33.73       109.64       171.55       248.65       136.47 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19C 
      124.31        54.51       172.18        53.19       148.08        48.89 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A3PL TCGA-FR-A7U9 TCGA-FS-A1ZD TCGA-FS-A1ZK 
       44.05       162.08        33.21         7.00        53.52        23.93 
TCGA-FS-A4F5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U9 
       28.73        47.54         7.23        84.72        12.62 

$`5Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       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        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 
       42.08        12.10       171.58        66.08       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-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       40.14       131.90        10.03        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      135.75       137.92        54.67         6.41        11.34         3.25 
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        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       35.01         3.55        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       27.22         8.65        14.70        26.89        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        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        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       44.35        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
      345.96        25.87        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
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-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       90.97       101.95        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       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 
      144.76       203.05       167.90        47.54        43.23       103.56 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       41.59        53.26       122.73        25.84         3.68        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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       27.35        33.40       101.79        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-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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       46.98        92.98       174.21         4.90       210.08        15.16 
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-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        2.40         9.90        14.04       120.46       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X 
       64.44        62.79        32.48        39.58        46.36       294.77 
TCGA-QB-A6FS 
        6.67 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             3.65              0.16 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           248.65            357.37 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            48.89             47.54 
[1] "3.6 - 248.7 (48.9)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.7"
D10V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q GAIN MUTATED                    4             1
  5Q GAIN WILD-TYPE                 33             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5Q GAIN MUTATED                                           4
  5Q GAIN WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  5Q GAIN MUTATED                    26
  5Q GAIN WILD-TYPE                 153
D10V4, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      4                33
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                56
  REGIONAL LYMPH NODE                                    26               153
[1] 4 2
[1] 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             0       1       3        2        4        4
  5Q GAIN WILD-TYPE          10       5      20        8       21       13
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5Q GAIN MUTATED           1         0         1         4          2
  5Q GAIN WILD-TYPE         9        14         9        28         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED            1          3        2
  5Q GAIN WILD-TYPE         22         45       10
D10V5, multiclass
             clus
vv            5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   1                 5
  STAGE I                   3                20
  STAGE IA                  2                 8
  STAGE IB                  4                21
  STAGE II                  4                13
  STAGE IIA                 1                 9
  STAGE IIB                 0                14
  STAGE IIC                 1                 9
  STAGE III                 4                28
  STAGE IIIA                2                12
  STAGE IIIB                1                22
  STAGE IIIC                3                45
  STAGE IV                  2                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
  5Q GAIN MUTATED       9  8  7  3
  5Q GAIN WILD-TYPE    44 52 48 54
D10V6, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               9                44
  T2                  8                52
  T3                  7                48
  T4                  3                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
  5Q GAIN MUTATED    18   5   3   4
  5Q GAIN WILD-TYPE 123  46  29  33
D10V7, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              18               123
  N1               5                46
  N2               3                29
  N3               4                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
  5Q GAIN MUTATED    28   0   1   1   1
  5Q GAIN WILD-TYPE 224   4   1   1   4
D10V8, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               28               224
  M1                0                 4
  M1A               1                 1
  M1B               1                 1
  M1C               1                 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"
D10V9, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   14  5
  5Q GAIN WILD-TYPE 90 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     14    5
  5Q GAIN WILD-TYPE   90   67
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               14                90
  YES               5                67
[1] 2 2
[1] FALSE
D10V10, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     6  29
  5Q GAIN WILD-TYPE  28 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      6   29
  5Q GAIN WILD-TYPE   28  218
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                6                28
  YES              29               218
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    12  23
  5Q GAIN WILD-TYPE  96 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     12   23
  5Q GAIN WILD-TYPE   96  150
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              12                96
  MALE                23               150
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         0    35
  5Q GAIN WILD-TYPE     5                         1   240
D10V13, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  35               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"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  34
  5Q GAIN WILD-TYPE   2 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   34
  5Q GAIN WILD-TYPE    2  240
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              34               240
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   49 58
  6P GAIN WILD-TYPE 88 75
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              107               163 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               58                75 
$`6P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
       16.47         8.52       110.79        45.83        81.24         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MR 
       21.14        30.87        64.44        15.25        61.38       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU 
       26.37        80.22        13.94        52.01        47.87        23.11 
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         0.00         0.00         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        36.07         9.21         9.90        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD 
        8.84         9.99         8.09         9.67        39.39        17.98 
TCGA-EE-A2GH TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       47.21        33.83         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
       36.33        29.46        14.56       111.78        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        27.16         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-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        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-FS-A1Z0 
       11.80        13.08         9.04        22.49         1.71        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       14.24        20.38        19.53        12.92        12.89        52.08 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
        8.68         0.82         5.23         3.22        28.73        14.20 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A266 
        2.27         0.20         0.13         7.23        31.33        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-QB-A6FS 
       16.24        12.16        14.70        10.65         5.79 

$`6P GAIN WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
      111.09        32.42        70.16        28.08        22.55        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
       85.32        88.50        68.22        69.90        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
       36.16         6.31        92.42        56.19        45.11       114.67 
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-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        9.34         5.39        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 
        8.84        20.48        95.38         1.55         6.97         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY 
        2.89        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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A182 
       13.22         0.20        11.57        10.55         8.12         1.35 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
        4.34         5.13         1.18         7.99        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         9.50 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.09         6.48         2.43         8.68        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       23.90         8.94        34.29        34.92        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 
       16.01        35.54        28.31        30.84         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18        47.51         9.53        44.25         7.96 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC 
       63.42       111.91        29.65        23.05       122.73        25.84 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       30.15        12.72        22.92        27.35         0.46        13.94 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       31.40        18.61        38.40        76.41        25.18         3.52 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19W TCGA-ER-A1A1 
       11.11       114.15        34.88        13.45        17.72        78.44 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-FR-A3YN 
        1.87         1.51        12.62        11.74         6.58        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       85.74         4.90         6.71         3.58         5.36        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
        3.45        11.01        15.52         7.33         7.30         3.39 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        8.22        11.08         7.17        30.87        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.81        49.15        40.64        27.39        53.85         7.36 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
       10.78         5.98         6.41         0.99         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 
        9.90        12.85        24.85        84.72        15.42        11.84 
TCGA-OD-A75X 
       11.05 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.00              0.16 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           124.31            122.73 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            13.94             14.60 
[1] "0.0 - 124.3 (13.9)" "0.2 - 122.7 (14.6)"
[1] "hr=" "1.3"
D11V2, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   52 58
  6P GAIN WILD-TYPE 90 76
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              110               166 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               58                76 
$`6P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
       16.57        16.67       133.25        90.90        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JF TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MR 
       23.77        48.76        66.08        58.06        86.93       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GU 
       39.75       161.85        15.06       135.75       137.92       125.19 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1I0 
      151.53        54.67         3.65         9.90        48.89        20.38 
TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
      176.55        65.92        10.49        17.85        45.11        35.01 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        33.73        26.89        68.15         4.96       109.64 
TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X 
      168.26        80.61        56.42        14.47        55.92        17.92 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GN TCGA-EE-A2GP 
       39.29        47.54       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-A2MI 
       14.30        55.59        44.88        94.82       103.27       204.66 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      144.76       167.90        47.54       248.65        43.23       136.47 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       53.26       124.31         3.68        13.81        23.47       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 
       36.95        64.08        34.32        53.19       148.08        13.94 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
        9.17        48.89        13.02         6.44        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ES 
      162.08        50.89        37.25        43.82        16.37       247.04 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZE 
       46.98        33.21       202.65        20.91       357.37        40.27 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       47.38        23.93        74.73        26.56        27.09        27.02 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU 
       50.14        28.73       174.84        77.88         0.20        47.54 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        7.23       117.93        10.13        64.44        32.48        39.58 
TCGA-GN-A4U9 TCGA-QB-A6FS 
       12.62         6.67 

$`6P GAIN WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
      112.04       112.57        71.80        28.08        31.59        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG 
      103.10       115.53       168.00        69.90        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08        12.10       171.58        56.19        45.11       130.72 
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-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        9.34        21.47        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A1JX 
       10.03        51.68       110.93       166.19         7.43         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW 
       11.34         3.25        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         3.55        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        78.87        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        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29V 
        2.60        44.35        18.61        37.35       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC 
      171.55        46.82       102.90        24.43        58.75        67.43 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      135.95        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
      101.95        21.67       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR 
       47.28       103.20        16.96        96.23       203.05       103.56 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J4 
       41.59       122.73        25.84        54.51       138.81       127.20 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35        33.40       101.79        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       77.75        98.40        12.59        26.37       268.93       152.35 
TCGA-ER-A19L TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
      131.51       148.18        79.99        23.34        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       32.05        80.32        92.98       174.21         4.90       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 
       15.16         7.00       216.92        48.59       228.59        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.79        27.72        48.85        53.52        15.45         9.70 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       32.75       101.26       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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       22.92         0.16         2.40         9.90        14.04       120.46 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-OD-A75X 
       84.72        62.79        46.36       294.77 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.20              0.16 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           357.37            345.96 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           47.540            48.215 
[1] "0.2 - 357.4 (47.5)" "0.2 - 346.0 (48.2)"
[1] "hr=" "1.1"
D11V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P GAIN MUTATED                   19             2
  6P GAIN WILD-TYPE                 18             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6P GAIN MUTATED                                          24
  6P GAIN WILD-TYPE                                        36
                   vv
clus                REGIONAL LYMPH NODE
  6P GAIN MUTATED                    66
  6P GAIN WILD-TYPE                 113
D11V4, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  DISTANT METASTASIS                                     19                18
  PRIMARY TUMOR                                           2                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              24                36
  REGIONAL LYMPH NODE                                    66               113
[1] 4 2
[1] 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      12        4       15        7
  6P GAIN WILD-TYPE           8       4      11        6       10       10
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6P GAIN MUTATED           3         6         7        10          6
  6P GAIN WILD-TYPE         7         8         3        22          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED            7         13        5
  6P GAIN WILD-TYPE         16         35        7
D11V5, multiclass
             clus
vv            6P GAIN MUTATED 6P GAIN WILD-TYPE
  I OR II NOS               2                 8
  STAGE 0                   2                 4
  STAGE I                  12                11
  STAGE IA                  4                 6
  STAGE IB                 15                10
  STAGE II                  7                10
  STAGE IIA                 3                 7
  STAGE IIB                 6                 8
  STAGE IIC                 7                 3
  STAGE III                10                22
  STAGE IIIA                6                 8
  STAGE IIIB                7                16
  STAGE IIIC               13                35
  STAGE IV                  5                 7
[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      20 29 16 29
  6P GAIN WILD-TYPE    33 31 39 28
D11V6, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1              20                33
  T2                 29                31
  T3                 16                39
  T4                 29                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
  6P GAIN MUTATED   65 17  8 13
  6P GAIN WILD-TYPE 76 34 24 24
D11V7, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              65                76
  N1              17                34
  N2               8                24
  N3              13                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
  6P GAIN MUTATED    97   3   2   1   0
  6P GAIN WILD-TYPE 155   1   0   1   5
D11V8, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               97               155
  M1                3                 1
  M1A               2                 0
  M1B               1                 1
  M1C               0                 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"
D11V9, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   43 28
  6P GAIN WILD-TYPE 61 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     43   28
  6P GAIN WILD-TYPE   61   44
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               43                61
  YES              28                44
[1] 2 2
[1] FALSE
D11V10, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    16  96
  6P GAIN WILD-TYPE  18 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     16   96
  6P GAIN WILD-TYPE   18  151
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               16                18
  YES              96               151
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    47  65
  6P GAIN WILD-TYPE  61 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     47   65
  6P GAIN WILD-TYPE   61  108
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              47                61
  MALE                65               108
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         0   111
  6P GAIN WILD-TYPE     4                         1   164
D11V13, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 111               164
[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     1 111
  6P GAIN WILD-TYPE   2 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1  111
  6P GAIN WILD-TYPE    2  163
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO             111               163
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    17  20
  6Q GAIN WILD-TYPE 120 113
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               37               233 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               20               113 
$`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        80.22        47.87         9.90 
TCGA-DA-A1I0 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A29B TCGA-EE-A29R TCGA-EE-A2GS 
       10.03         0.00         0.00         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       111.78        25.08        27.16 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 
        3.22        21.60        16.14        22.22        33.60        12.95 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2NC 
        3.78        11.90        28.60         9.57        36.07        11.80 
TCGA-ER-A3EV TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A3TU 
       22.49        12.89         3.22        14.20         0.20         0.13 
TCGA-GN-A266 
       10.13 

$`6Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47       111.09        32.42        70.16        28.08        22.55 
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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
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         5.39 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       13.94        95.38        52.01         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        4.01         2.89        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-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-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C 
        4.34         5.13         9.21         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        38.63         8.55         4.41         1.08        27.12 
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         6.48         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        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-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       30.84         5.42         1.15        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18        47.51         9.53        44.25         7.96 
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        29.65 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 
       30.15        13.81        15.95        12.72        22.92        21.60 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35         0.46        13.94        31.40        18.61        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W 
       34.88         4.21        13.45        42.84        34.68        17.72 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        9.04         6.58         1.71        18.41        85.74         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        6.71         3.58         5.36        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-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-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        7.36        28.73        10.78         5.98         6.41         2.27 
TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.99         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        10.65        11.05         5.79 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.00              0.13 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           111.78            124.31 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            13.02             14.24 
[1] "0.0 - 111.8 (13.0)" "0.1 - 124.3 (14.2)"
[1] "hr=" "1.2"
D12V2, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    18  20
  6Q GAIN WILD-TYPE 124 114
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               38               238 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               20               114 
$`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       161.85       137.92        54.67 
TCGA-D9-A6E9 TCGA-DA-A1I0 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A29B TCGA-EE-A29R 
        9.90        20.38        45.11        35.01        80.61        14.47 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MN 
       55.59        44.88       103.27       204.66       144.76        47.54 
TCGA-EE-A2MS TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JI 
      136.47       172.18        36.95        34.32        53.19       148.08 
TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S 
       13.94        48.89        13.02        61.05        50.89        37.25 
TCGA-ER-A2NC TCGA-ER-A3EV TCGA-FS-A1ZK TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FW-A3I3 
       43.82        46.98        23.93        50.14       174.84         0.20 
TCGA-FW-A3TU TCGA-GN-A266 
       47.54        10.13 

$`6Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57       112.04       112.57        71.80        28.08        31.59 
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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
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        21.47 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       15.06       110.93       135.75       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA 
      151.53         3.65         6.41        11.34         3.25        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-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       13.87        10.16        17.85         3.55        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       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       78.87       168.26        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 
       39.62        72.07        32.19         2.60        44.35        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       345.96        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       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       101.95 
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-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ 
       19.76        61.51        47.28       103.20        16.96        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       103.56        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JD 
       13.81        23.47       138.81       127.20        64.08        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
       33.40       101.79        31.40        35.44        50.76         9.17 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       77.75        98.40        12.59        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 
        6.44       131.51        44.05       162.08       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-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       80.32        33.21        92.98       174.21         4.90       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       15.16         7.00       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-A1ZH TCGA-FS-A1ZJ 
       53.52        40.27        15.45         9.70        32.75        47.38 
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-A4F4 
       26.56        49.48        27.09        27.02        77.82        66.67 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       28.73        12.43        26.73        49.45        77.88        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
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-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.20              0.16 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           204.66            357.37 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           48.215            47.690 
[1] "0.2 - 204.7 (48.2)" "0.2 - 357.4 (47.7)"
[1] "hr=" "1.1"
D12V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q GAIN MUTATED                    7             1
  6Q GAIN WILD-TYPE                 30             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6Q GAIN MUTATED                                           9
  6Q GAIN WILD-TYPE                                        51
                   vv
clus                REGIONAL LYMPH NODE
  6Q GAIN MUTATED                    20
  6Q GAIN WILD-TYPE                 159
D12V4, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      7                30
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               9                51
  REGIONAL LYMPH NODE                                    20               159
[1] 4 2
[1] 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       5        0        7        3
  6Q GAIN WILD-TYPE           9       6      18       10       18       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6Q GAIN MUTATED           1         2         3         4          2
  6Q GAIN WILD-TYPE         9        12         7        28         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED            1          1        2
  6Q GAIN WILD-TYPE         22         47       10
D12V5, multiclass
             clus
vv            6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   0                 6
  STAGE I                   5                18
  STAGE IA                  0                10
  STAGE IB                  7                18
  STAGE II                  3                14
  STAGE IIA                 1                 9
  STAGE IIB                 2                12
  STAGE IIC                 3                 7
  STAGE III                 4                28
  STAGE IIIA                2                12
  STAGE IIIB                1                22
  STAGE IIIC                1                47
  STAGE IV                  2                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
  6Q GAIN MUTATED       2 11  5 14
  6Q GAIN WILD-TYPE    51 49 50 43
D12V6, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               2                51
  T2                 11                49
  T3                  5                50
  T4                 14                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                 N0  N1  N2  N3
  6Q GAIN MUTATED    26   6   0   1
  6Q GAIN WILD-TYPE 115  45  32  36
D12V7, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              26               115
  N1               6                45
  N2               0                32
  N3               1                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
  6Q GAIN MUTATED    32   1   1   0   0
  6Q GAIN WILD-TYPE 220   3   1   2   5
D12V8, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               32               220
  M1                1                 3
  M1A               1                 1
  M1B               0                 2
  M1C               0                 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"
D12V9, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   19  8
  6Q GAIN WILD-TYPE 85 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     19    8
  6Q GAIN WILD-TYPE   85   64
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               19                85
  YES               8                64
[1] 2 2
[1] FALSE
D12V10, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3  35
  6Q GAIN WILD-TYPE  31 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   35
  6Q GAIN WILD-TYPE   31  212
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                3                31
  YES              35               212
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    17  21
  6Q GAIN WILD-TYPE  91 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     17   21
  6Q GAIN WILD-TYPE   91  152
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              17                91
  MALE                21               152
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         0    38
  6Q GAIN WILD-TYPE     5                         1   237
D12V13, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  38               237
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  38
  6Q GAIN WILD-TYPE   3 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   38
  6Q GAIN WILD-TYPE    3  236
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              38               236
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   73 73
  7P GAIN WILD-TYPE 64 60
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              146               124 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               73                60 
$`7P 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        69.90        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        45.11       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-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       41.10         8.84        20.48        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       23.11         2.89         9.90        11.31        13.22        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
       44.52        36.69        25.15         4.93         6.64        17.56 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
       13.15         0.13        13.22         0.20        10.55         8.12 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
        1.12        36.07         9.21         7.99        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
       38.63         9.50        12.03         6.48         8.68        11.31 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
        8.94        39.39        34.92        47.21        30.08        19.43 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
       35.54        28.31        33.83        30.84         5.42        98.27 
TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN 
        2.70         7.96        63.42       111.78        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       26.99        21.60        29.65        27.16         5.56       124.31 
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-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
       22.92        21.60        21.60        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-A2ND TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       36.07         1.87        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        4.90         6.71         5.36         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-GN-A264 TCGA-GN-A265 
       14.20         0.20         0.43         7.23        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-QB-A6FS 
       10.65         5.79 

$`7P GAIN WILD-TYPE`
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-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO 
        8.38        68.22        30.87        36.16         6.31        64.44 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.32        24.00         5.39        80.22        42.71        15.09 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-DA-A1I1 
       17.72        13.94        95.38        47.87         4.01        39.19 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG 
       22.36        19.36         7.00        14.83         0.20         0.00 
TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        0.00        11.57         6.31         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29G 
        4.31         4.34         5.13         1.18         9.90         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08        27.12         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
        2.43         8.09        49.22        23.90         9.67        34.29 
TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       17.98        16.01         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        8.84         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3J8 
       14.56       111.91        23.05       122.73        25.84        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
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-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS 
       19.53        11.08        12.92        12.89        52.08        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       40.64         8.68        27.39        53.85         7.36        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-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-OD-A75X 
        9.90        12.85        24.85        11.05 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.13              0.00 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           124.31            122.73 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           15.335            13.050 
[1] "0.1 - 124.3 (15.3)" "0.0 - 122.7 (13.1)"
[1] "hr=" "1.1"
D13V2, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   76 74
  7P GAIN WILD-TYPE 66 60
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              150               126 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               74                60 
$`7P 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        69.90        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        45.11       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-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
      131.90        10.03        51.68       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 
      125.19       151.53        54.67         6.41         3.25         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-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-A1IC TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UL 
       65.92        68.09       215.44        13.87        17.85         3.55 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B 
       52.01        12.20        27.22        94.98        33.73       109.64 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N 
      168.26        63.35        47.84        13.97        39.62        18.61 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB 
       56.42       345.96       171.55        46.82        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM 
      135.95       208.04        48.72        89.33        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH 
       90.97       101.95        13.91       129.27        28.83        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       144.76       167.90        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE 
      103.56       136.47        53.26       124.31         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-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
       64.08        13.94         9.17        98.40        48.89        13.02 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2ND 
      268.93       152.35         6.44       162.08        37.25        23.34 
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         4.90       210.08 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC 
        7.00        48.59        20.91        28.08         7.79       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52         9.70        32.75       101.26       133.55        11.41 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 
       27.09        27.02        50.14        28.73       174.84         0.20 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.40         7.23       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       62.79        32.48        39.58        46.36        12.62         6.67 

$`7P GAIN WILD-TYPE`
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-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO 
       65.49       168.00        48.76        42.08        12.10        66.08 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       60.23        24.53        21.47       161.85        43.69        40.14 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A1JW TCGA-D9-A3Z1 
       18.38        15.06       110.93       137.92         3.65        11.34 
TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R 
      194.83        23.44        28.60        10.49        15.68        10.16 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       45.11        35.01         6.35        29.82         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       151.27        78.87        13.55 
TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q 
       80.61        72.07        32.19         2.60        44.35        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        55.92        25.87        17.92       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS 
       39.29        67.43       314.56        54.74        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-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MT TCGA-EE-A3AB 
      103.27       103.20       204.66       203.05        41.59       122.73 
TCGA-EE-A3AC TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       25.84        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D 
      148.08        31.40        35.44        50.76        77.75        12.59 
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
       26.37       131.51        61.05        44.05        50.89       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        43.82        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      247.04        80.32        15.16       216.92       228.59       202.65 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       27.72        48.85        40.27        15.45        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 
       74.73       148.80        53.16        26.56        49.48        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       66.67        12.43        26.73        49.45        77.88        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-OD-A75X 
       47.54         0.16         9.90        14.04       120.46       294.77 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.20              0.16 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           357.37            314.56 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            50.91             44.20 
[1] "0.2 - 357.4 (50.9)" "0.2 - 314.6 (44.2)"
[1] "hr=" "1.1"
D13V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P GAIN MUTATED                   15             3
  7P GAIN WILD-TYPE                 22             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7P GAIN MUTATED                                          36
  7P GAIN WILD-TYPE                                        24
                   vv
clus                REGIONAL LYMPH NODE
  7P GAIN MUTATED                    98
  7P GAIN WILD-TYPE                  81
D13V4, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  DISTANT METASTASIS                                     15                22
  PRIMARY TUMOR                                           3                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              36                24
  REGIONAL LYMPH NODE                                    98                81
[1] 4 2
[1] 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             8       1      15        5        7        9
  7P GAIN WILD-TYPE           2       5       8        5       18        8
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7P GAIN MUTATED           5         4         7        21         11
  7P GAIN WILD-TYPE         5        10         3        11          3
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           13         24        9
  7P GAIN WILD-TYPE         10         24        3
D13V5, multiclass
             clus
vv            7P GAIN MUTATED 7P GAIN WILD-TYPE
  I OR II NOS               8                 2
  STAGE 0                   1                 5
  STAGE I                  15                 8
  STAGE IA                  5                 5
  STAGE IB                  7                18
  STAGE II                  9                 8
  STAGE IIA                 5                 5
  STAGE IIB                 4                10
  STAGE IIC                 7                 3
  STAGE III                21                11
  STAGE IIIA               11                 3
  STAGE IIIB               13                10
  STAGE IIIC               24                24
  STAGE IV                  9                 3
[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      33 28 32 31
  7P GAIN WILD-TYPE    20 32 23 26
D13V6, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              33                20
  T2                 28                32
  T3                 32                23
  T4                 31                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7P GAIN MUTATED   72 35 15 21
  7P GAIN WILD-TYPE 69 16 17 16
D13V7, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              72                69
  N1              35                16
  N2              15                17
  N3              21                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  7P GAIN MUTATED   134   3   2   1   4
  7P GAIN WILD-TYPE 118   1   0   1   1
D13V8, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              134               118
  M1                3                 1
  M1A               2                 0
  M1B               1                 1
  M1C               4                 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"
D13V9, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   58 37
  7P GAIN WILD-TYPE 46 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     58   37
  7P GAIN WILD-TYPE   46   35
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               58                46
  YES              37                35
[1] 2 2
[1] FALSE
D13V10, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    22 131
  7P GAIN WILD-TYPE  12 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     22  131
  7P GAIN WILD-TYPE   12  116
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               22                12
  YES             131               116
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   64 89
  7P GAIN WILD-TYPE 44 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     64   89
  7P GAIN WILD-TYPE   44   84
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              64                44
  MALE                89                84
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       4                         0   149
  7P GAIN WILD-TYPE     1                         1   126
D13V13, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 149               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"
D13V14, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     2 149
  7P GAIN WILD-TYPE   1 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2  149
  7P GAIN WILD-TYPE    1  125
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO             149               125
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   72 73
  7Q GAIN WILD-TYPE 65 60
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              145               125 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               73                60 
$`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        69.90        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        45.11       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 
        5.39        41.10        20.48        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       23.11         2.89         9.90        11.31        13.22        14.60 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
       44.52        36.69        25.15         4.93         6.64        17.56 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
       14.83        13.15        13.22         0.20        10.55         8.12 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        1.12        12.20        36.07         9.21         7.99        37.97 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 
       38.63         9.50        12.03         6.48         8.68        11.31 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL 
        8.94        39.39        34.92        47.21        30.08        35.54 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH 
       28.31        30.84         5.42        98.27         2.70         7.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       63.42       111.78        56.02        26.99        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       27.16         5.56       124.31        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD 
       12.72         3.22        22.92        21.60        21.60        27.35 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E 
       31.40        12.95         5.72        25.18         3.78        11.90 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2ND 
      114.15        34.88         4.21        34.68        36.07         1.87 
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         4.90         6.71 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC 
        5.36         3.45        14.24        15.52         7.33        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        8.22        11.08         7.17        30.87        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 
        8.81        49.15         0.82         5.23         3.22        28.73 
TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 
       14.20         0.20         0.43         7.23        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-QB-A6FS 
        5.79 

$`7Q GAIN WILD-TYPE`
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-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO 
        8.38        68.22        30.87        36.16         6.31        64.44 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
       13.32        24.00        80.22        42.71        15.09        17.72 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-DA-A1I1 
        8.84        13.94        95.38        47.87         4.01        39.19 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       22.36        19.36         7.00         0.20         0.13         0.00 
TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
        0.00        11.57         6.31         1.35         5.13         4.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
        4.34         5.13         1.18         9.90        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08        27.12         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
        2.43         8.09        49.22        23.90         9.67        34.29 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS 
       17.98        19.43        16.01        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-A2MG TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MT 
       29.46        44.25        14.56       111.91        25.08        23.05 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      122.73        25.84         3.68        16.14        22.22         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D 
       13.94        33.60        18.61        38.40        76.41         3.52 
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W 
       11.11        13.45        28.60        42.84         9.57        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44        11.80         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        9.04         6.58         3.58        64.47        11.01        23.80 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
        7.30         3.39        19.53        12.92        12.89        52.08 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       40.64         8.68        27.39        53.85         7.36        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-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U8 TCGA-OD-A75X 
        9.90        12.85        24.85        11.84        11.05 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.2               0.0 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           124.31            122.73 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            15.42             12.92 
[1] "0.2 - 124.3 (15.4)" "0.0 - 122.7 (12.9)"
[1] "hr=" "1.1"
D14V2, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   75 74
  7Q GAIN WILD-TYPE 67 60
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              149               127 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               74                60 
$`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        69.90        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        45.11       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 
       21.47       131.90        51.68       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 
      125.19       151.53        54.67         6.41         3.25         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-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-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5UL 
       65.92        68.09       215.44        15.68        13.87         3.55 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
       52.01        12.20        27.22        94.98        33.73        26.89 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N 
      109.64       168.26        63.35        47.84        39.62        18.61 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB 
       56.42       345.96       171.55        46.82        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO 
      135.95       208.04        48.72        79.66        75.48       101.95 
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       144.76 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
      167.90       248.65        43.23       103.56       136.47        53.26 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        54.51        13.81        23.47       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A197 
      127.20        36.95        64.08        27.35        31.40        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
        9.17        98.40        48.89        13.02       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3EV TCGA-ER-A3PL 
        6.44       162.08        37.25        23.34        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YX 
       92.98       174.21         4.90       210.08         7.00        48.59 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       20.91        28.08         7.79       357.37        53.52        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
        9.70        32.75       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FW-A3I3 
       27.09        27.02        50.14        28.73       174.84         0.20 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        2.40         7.23       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-QB-A6FS 
       62.79        32.48        39.58        12.62         6.67 

$`7Q GAIN WILD-TYPE`
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-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO 
       65.49       168.00        48.76        42.08        12.10        66.08 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
       60.23        24.53       161.85        43.69        40.14        18.38 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A1JW TCGA-D9-A3Z1 
       10.03        15.06       110.93       137.92         3.65        11.34 
TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5KH 
      194.83        23.44        28.60        10.49        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       45.11        35.01         6.35        29.82         8.65        14.70 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B 
       68.15         4.96       151.27        78.87        13.55        80.61 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q 
       13.97        72.07        32.19         2.60        44.35        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
       14.47        55.92        25.87        17.92       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GN 
       39.29        67.43       314.56        89.33        54.74        90.97 
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-A2MG TCGA-EE-A2MI TCGA-EE-A2ML 
       61.51        47.28       103.27       103.20       204.66       203.05 
TCGA-EE-A2MN TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3J8 
       47.54        41.59       122.73        25.84         3.68        34.32 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       53.19        33.40       101.79       148.08        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       77.75        12.59        26.37       131.51        61.05        44.05 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FS-A1YW 
       31.27        32.05       247.04        80.32        15.16       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZJ 
      228.59       202.65        27.72        48.85        40.27        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F0 
       23.93        74.73        53.16        26.56        49.48        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 
       66.67        12.43        26.73        49.45        77.88        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A4U8 
       47.54         0.16         9.90        14.04       120.46        46.36 
TCGA-OD-A75X 
      294.77 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.20              0.16 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           357.37            314.56 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            50.14             45.11 
[1] "0.2 - 357.4 (50.1)" "0.2 - 314.6 (45.1)"
[1] "hr=" "1.1"
D14V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q GAIN MUTATED                   16             3
  7Q GAIN WILD-TYPE                 21             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7Q GAIN MUTATED                                          36
  7Q GAIN WILD-TYPE                                        24
                   vv
clus                REGIONAL LYMPH NODE
  7Q GAIN MUTATED                    96
  7Q GAIN WILD-TYPE                  83
D14V4, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     16                21
  PRIMARY TUMOR                                           3                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              36                24
  REGIONAL LYMPH NODE                                    96                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
  7Q GAIN MUTATED             8       2      14        4        7       10
  7Q GAIN WILD-TYPE           2       4       9        6       18        7
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7Q GAIN MUTATED           4         5         8        20         11
  7Q GAIN WILD-TYPE         6         9         2        12          3
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           15         23        8
  7Q GAIN WILD-TYPE          8         25        4
D14V5, multiclass
             clus
vv            7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  I OR II NOS               8                 2
  STAGE 0                   2                 4
  STAGE I                  14                 9
  STAGE IA                  4                 6
  STAGE IB                  7                18
  STAGE II                 10                 7
  STAGE IIA                 4                 6
  STAGE IIB                 5                 9
  STAGE IIC                 8                 2
  STAGE III                20                12
  STAGE IIIA               11                 3
  STAGE IIIB               15                 8
  STAGE IIIC               23                25
  STAGE IV                  8                 4
[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      29 29 32 32
  7Q GAIN WILD-TYPE    24 31 23 25
D14V6, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              29                24
  T2                 29                31
  T3                 32                23
  T4                 32                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                N0 N1 N2 N3
  7Q GAIN MUTATED   73 32 18 20
  7Q GAIN WILD-TYPE 68 19 14 17
D14V7, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              73                68
  N1              32                19
  N2              18                14
  N3              20                17
[1] 4 2
[1] 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   135   3   2   1   3
  7Q GAIN WILD-TYPE 117   1   0   1   2
D14V8, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              135               117
  M1                3                 1
  M1A               2                 0
  M1B               1                 1
  M1C               3                 2
[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   58 37
  7Q GAIN WILD-TYPE 46 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     58   37
  7Q GAIN WILD-TYPE   46   35
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               58                46
  YES              37                35
[1] 2 2
[1] FALSE
D14V10, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    21 131
  7Q GAIN WILD-TYPE  13 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     21  131
  7Q GAIN WILD-TYPE   13  116
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               21                13
  YES             131               116
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   65 87
  7Q GAIN WILD-TYPE 43 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     65   87
  7Q GAIN WILD-TYPE   43   86
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              65                43
  MALE                87                86
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       3                         0   149
  7Q GAIN WILD-TYPE     2                         1   126
D14V13, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 149               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"
D14V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 148
  7Q GAIN WILD-TYPE   1 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  148
  7Q GAIN WILD-TYPE    1  126
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 1
  NOT HISPANIC OR LATINO             148               126
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   44 45
  8P GAIN WILD-TYPE 93 88
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               89               181 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               45                88 
$`8P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN 
       70.16        22.55        85.32        69.90        30.87        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
       64.44        45.11        61.38        13.32       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6EC TCGA-D9-A6EG 
        5.39         1.55         6.97        23.11        13.22        14.60 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 
       35.80        51.12        39.19        13.68         9.99        17.56 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A181 
       13.15         0.20         0.13         0.00        10.55         1.12 
TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2GD TCGA-EE-A2GE 
       36.07        11.15         8.55         8.84        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
       47.21        35.54        28.31        33.83        30.84         5.42 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A3AB 
       98.27         2.70         6.18         7.96        29.65       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
        3.68        30.15        22.92        21.60        21.60        22.22 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        3.78       114.15        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A2NF TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       42.84        11.80        13.08        85.74         6.71         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD 
        5.36        64.47         3.45        15.52         7.33         8.22 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY 
       12.89        47.38        52.08         8.65         8.81         0.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
        3.22         7.36        28.73         2.27         0.20         0.16 
TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        9.90        10.13        16.24        12.16        14.70 

$`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        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       17.72         8.84        20.48        13.94        95.38        52.01 
TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       47.87         4.01         2.89         9.90        11.31        48.79 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       10.03        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UN 
        6.64        19.36         7.00        14.83         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
        0.20        11.57         6.31         8.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        7.99         9.90        37.97        38.63         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       27.12         9.50        12.03         8.09         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ 
        9.67         8.94        39.39        34.29        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       16.01         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51         9.53        29.46        44.25        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      111.78       111.91        56.02        25.08        26.99        21.60 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
       27.16        23.05         5.56       124.31        25.84        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       15.95        12.72         3.22        16.14        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
       34.68         9.57        36.07        17.72        78.44         1.87 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        1.51        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        1.71        18.41         4.90        11.01        23.80        14.24 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.30         3.39        20.38        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       30.87        12.92        49.15        40.64         8.68        27.39 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        5.23        53.85        14.20        10.78         5.98         6.41 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.99         0.13         0.43         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       31.33        84.72        15.42        11.84        10.65        11.05 
TCGA-QB-A6FS 
        5.79 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 0 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           122.73            124.31 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            14.60             13.94 
[1] "0.0 - 122.7 (14.6)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1"  
D15V2, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   44 45
  8P GAIN WILD-TYPE 98 89
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               89               187 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               45                89 
$`8P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN 
       71.80        31.59       103.10        69.90        48.76        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU 
       66.08        45.11        86.93        60.23       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A6EC TCGA-D9-A6EG 
       21.47       166.19         7.43       125.19        66.25        22.95 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 
       36.03       117.21       194.83       176.55        35.93       215.44 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A181 
       13.87        10.16        17.85        35.01        27.22        33.73 
TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A2GD TCGA-EE-A2GE 
      109.64        13.97        72.07        14.47       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
      208.04        79.66        75.48        90.97       101.95        13.91 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A3AB 
      129.27        28.83        19.76        16.96       103.56       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA 
        3.68        54.51       127.20        36.95        64.08        53.19 
TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       48.89       268.93       152.35         6.44       131.51        61.05 
TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A2NF TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       44.05        43.82        16.37       174.21       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD 
        7.00       216.92        48.59        28.08         7.79        53.52 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZY 
       23.93       101.26        74.73       133.55        11.41        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV 
       50.14        66.67        28.73        77.88         0.20         0.16 
TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        9.90        10.13        64.44        32.48        39.58 

$`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       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       18.38        10.03        51.68        15.06       110.93       135.75 
TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      137.92       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 
        3.25         9.90        25.18        48.89        20.38       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-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       10.49        15.68        45.11         3.55        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       12.20        29.82         8.65        94.98        14.70        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        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       63.35        80.61        47.84        39.62        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       44.35        18.61        56.42        37.35        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.29        58.75        47.54        67.43        48.72        89.33 
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-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51        47.28       103.27       103.20       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
      136.47        41.59        53.26       124.31        25.84        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
       23.47       138.81       172.18        34.32        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      162.08        50.89        37.25       148.18        79.99        23.34 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       33.21        92.98         4.90       228.59       202.65        20.91 
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-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       32.75        47.38       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       27.02        77.82       174.84        12.43        26.73        49.45 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       22.92        47.54         2.40         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      117.93        84.72        62.79        46.36        12.62       294.77 
TCGA-QB-A6FS 
        6.67 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.16              2.40 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           314.56            357.37 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            53.19             47.28 
[1] "0.2 - 314.6 (53.2)" "2.4 - 357.4 (47.3)"
[1] "hr=" "1"  
D15V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P GAIN MUTATED                    7             2
  8P GAIN WILD-TYPE                 30             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8P GAIN MUTATED                                          29
  8P GAIN WILD-TYPE                                        31
                   vv
clus                REGIONAL LYMPH NODE
  8P GAIN MUTATED                    53
  8P GAIN WILD-TYPE                 126
D15V4, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  DISTANT METASTASIS                                      7                30
  PRIMARY TUMOR                                           2                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              29                31
  REGIONAL LYMPH NODE                                    53               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
  8P GAIN MUTATED             2       1       9        2        6        9
  8P GAIN WILD-TYPE           8       5      14        8       19        8
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8P GAIN MUTATED           4         2         4        15          6
  8P GAIN WILD-TYPE         6        12         6        17          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED            6         17        3
  8P GAIN WILD-TYPE         17         31        9
D15V5, multiclass
             clus
vv            8P GAIN MUTATED 8P GAIN WILD-TYPE
  I OR II NOS               2                 8
  STAGE 0                   1                 5
  STAGE I                   9                14
  STAGE IA                  2                 8
  STAGE IB                  6                19
  STAGE II                  9                 8
  STAGE IIA                 4                 6
  STAGE IIB                 2                12
  STAGE IIC                 4                 6
  STAGE III                15                17
  STAGE IIIA                6                 8
  STAGE IIIB                6                17
  STAGE IIIC               17                31
  STAGE IV                  3                 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
  8P GAIN MUTATED      21 18 20 19
  8P GAIN WILD-TYPE    32 42 35 38
D15V6, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              21                32
  T2                 18                42
  T3                 20                35
  T4                 19                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
  8P GAIN MUTATED   43 21 11 12
  8P GAIN WILD-TYPE 98 30 21 25
D15V7, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              43                98
  N1              21                30
  N2              11                21
  N3              12                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
  8P GAIN MUTATED    84   2   0   0   1
  8P GAIN WILD-TYPE 168   2   2   2   4
D15V8, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               84               168
  M1                2                 2
  M1A               0                 2
  M1B               0                 2
  M1C               1                 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"
D15V9, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   29 28
  8P GAIN WILD-TYPE 75 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     29   28
  8P GAIN WILD-TYPE   75   44
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               29                75
  YES              28                44
[1] 2 2
[1] FALSE
D15V10, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    13  78
  8P GAIN WILD-TYPE  21 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     13   78
  8P GAIN WILD-TYPE   21  169
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               13                21
  YES              78               169
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    32  59
  8P GAIN WILD-TYPE  76 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     32   59
  8P GAIN WILD-TYPE   76  114
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              32                76
  MALE                59               114
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       4                         0    87
  8P GAIN WILD-TYPE     1                         1   188
D15V13, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  87               188
[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     0  89
  8P GAIN WILD-TYPE   3 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   89
  8P GAIN WILD-TYPE    3  185
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              89               185
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   66 63
  8Q GAIN WILD-TYPE 71 70
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              129               141 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               63                70 
$`8Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.47       111.09        70.16        22.55        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO 
       85.32        88.50        69.90        30.87        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       45.11        15.25        82.29        61.38        13.32         6.31 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J 
        9.34       103.59        26.37         5.39        80.22        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       17.72         8.84        52.01         1.55         6.97        23.11 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.22        14.60        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       13.68         9.99         7.00        17.56        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
        0.00         0.00         0.20        10.55         6.31         1.12 
TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29T 
       36.07        37.97        38.63         8.55         8.84         6.48 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GM 
        9.67        17.98        34.92        47.21        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       33.83        30.84         5.42        13.02        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA TCGA-EE-A3AB 
        6.18         7.96        25.08        29.65       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
        3.68        30.15        15.95         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G TCGA-ER-A19H 
       21.60        22.22        12.95         3.78       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        13.45        28.60        42.84         9.57        36.07 
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-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        6.71         3.58         5.36        64.47         3.45        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZK TCGA-FS-A1ZM 
       23.80        15.52         7.33         8.22        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-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD 
        0.82         3.22         7.36        28.73        14.20         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
        0.20         0.16         9.90        10.13        16.24        12.16 
TCGA-GN-A26D TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.05         5.79 

$`8Q GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 
        8.52        32.42       110.79        28.08        45.83         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       21.14        68.22        11.41         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF TCGA-D3-A51F 
       92.42       114.67        46.98        46.32        24.00        42.71 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A3Z1 
       15.09        20.48        13.94        95.38        47.87         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 
        2.89         9.90        11.31        48.79        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 
       25.15         4.93        22.36         6.64        19.36        14.83 
TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
        0.13        13.22        11.57         8.12         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        5.13         4.31         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        7.99         9.90        11.15         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
        9.50        12.03         8.09         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09        11.31        49.22        23.90         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GT 
       34.29        30.08        19.43        16.01         1.15        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       36.33         8.84        47.51         9.53        29.46        44.25 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
       14.56        63.42       111.78       111.91        56.02        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF 
       21.60        27.16        23.05         5.56        25.84        13.81 
TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       12.72        16.14        27.35         0.46        13.94        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-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 
        3.52        11.90        11.11        34.68        17.72        78.44 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN 
        1.51        12.62        11.74         9.04         1.71        18.41 
TCGA-FR-A69P TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
        4.90        14.24         7.30         3.39        20.38        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       11.08         7.17        30.87        12.92        27.39         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
       53.85        10.78         5.98         6.41         0.99         0.13 
TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        0.43         7.23        12.85        24.85        31.33        84.72 
TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 
       15.42        11.84        10.65 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.00              0.13 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           124.31            114.67 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            14.60             13.94 
[1] "0.0 - 124.3 (14.6)" "0.1 - 114.7 (13.9)"
[1] "hr=" "1.1"
D16V2, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   67 63
  8Q GAIN WILD-TYPE 75 71
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              130               146 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               63                71 
$`8Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.57       112.04        71.80        31.59        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO 
      103.10       115.53        69.90        48.76        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML 
       45.11        58.06       166.52        86.93        60.23        13.87 
TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51J 
        9.34       103.59        39.75        21.47       161.85       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       18.38        10.03       135.75       166.19         7.43       125.19 
TCGA-D9-A1JW TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        3.65        66.25        22.95        36.03       117.21        20.38 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44Q 
      194.83       176.55        35.93        10.49       215.44        13.87 
TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
       10.16        45.11        35.01        12.20        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R 
       33.73       109.64        47.84        39.62        72.07        14.47 
TCGA-EE-A29T TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL 
      345.96        39.29       314.56       135.95       208.04        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 
       75.48        90.97       101.95        13.91        55.59       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA 
       28.83        19.76        16.96        47.54       103.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73         3.68        54.51        23.47       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19G 
       36.95        64.08        53.19        13.94        48.89       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q 
      152.35         6.44       131.51        61.05        44.05        50.89 
TCGA-ER-A19S TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ET TCGA-ER-A3EV 
       37.25        43.82        23.34        16.37        80.32        46.98 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
      174.21       210.08        15.16         7.00       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZK 
      228.59       202.65        28.08         7.79        53.52        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-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       26.56        27.09        50.14        66.67        28.73       174.84 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A267 
       77.88         0.20         0.16         9.90        10.13        64.44 
TCGA-GN-A26A TCGA-GN-A26D TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        39.58       294.77         6.67 

$`8Q GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 
       16.67       112.57       133.25        28.08        90.90        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       168.00        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CF TCGA-D3-A51F 
      171.58       130.72        46.98        46.32        24.53        43.69 
TCGA-D3-A51H TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A148 
       40.14        51.68        15.06       110.93       137.92       151.53 
TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
       54.67         6.41        11.34         3.25         9.90        25.18 
TCGA-DA-A1HV TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       48.89       107.34        61.18        53.92        65.92        23.44 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EB-A5UN 
       68.09        28.60        15.68        17.85         3.55        52.01 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        6.35        29.82        94.98        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.96       151.27        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       80.61        13.97        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       56.42        37.35        55.92        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        24.43        58.75        47.54        67.43 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU 
       48.72        89.33        54.74        14.30        44.88        94.82 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
       21.67        61.51        47.28       103.27       103.20       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ 
       96.23       144.76       203.05       167.90       248.65        43.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH 
      136.47        41.59        53.26        25.84        13.81       138.81 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       35.44        50.76         9.17        77.75        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE 
       13.02        26.37       162.08       148.18        79.99        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P 
       31.27        32.05       247.04        33.21        92.98         4.90 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF 
       20.91        27.72        48.85       357.37        40.27        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
        9.70        32.75        47.38        49.48        27.02        77.82 
TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY 
       12.43        26.73        49.45        22.92        47.54         2.40 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        7.23        14.04       120.46       117.93        84.72        62.79 
TCGA-GN-A4U8 TCGA-GN-A4U9 
       46.36        12.62 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.16              2.40 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           345.96            357.37 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           50.515            46.900 
[1] "0.2 - 346.0 (50.5)" "2.4 - 357.4 (46.9)"
[1] "hr=" "1.2"
D16V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q GAIN MUTATED                   14             2
  8Q GAIN WILD-TYPE                 23             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8Q GAIN MUTATED                                          38
  8Q GAIN WILD-TYPE                                        22
                   vv
clus                REGIONAL LYMPH NODE
  8Q GAIN MUTATED                    77
  8Q GAIN WILD-TYPE                 102
D16V4, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  DISTANT METASTASIS                                     14                23
  PRIMARY TUMOR                                           2                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              38                22
  REGIONAL LYMPH NODE                                    77               102
[1] 4 2
[1] 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             4       1      12        3       11       10
  8Q GAIN WILD-TYPE           6       5      11        7       14        7
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8Q GAIN MUTATED           5         4         5        21          9
  8Q GAIN WILD-TYPE         5        10         5        11          5
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           10         21        5
  8Q GAIN WILD-TYPE         13         27        7
D16V5, multiclass
             clus
vv            8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  I OR II NOS               4                 6
  STAGE 0                   1                 5
  STAGE I                  12                11
  STAGE IA                  3                 7
  STAGE IB                 11                14
  STAGE II                 10                 7
  STAGE IIA                 5                 5
  STAGE IIB                 4                10
  STAGE IIC                 5                 5
  STAGE III                21                11
  STAGE IIIA                9                 5
  STAGE IIIB               10                13
  STAGE IIIC               21                27
  STAGE IV                  5                 7
[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      33 30 24 24
  8Q GAIN WILD-TYPE    20 30 31 33
D16V6, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              33                20
  T2                 30                30
  T3                 24                31
  T4                 24                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
  8Q GAIN MUTATED   61 27 18 18
  8Q GAIN WILD-TYPE 80 24 14 19
D16V7, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              61                80
  N1              27                24
  N2              18                14
  N3              18                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
  8Q GAIN MUTATED   121   2   1   0   2
  8Q GAIN WILD-TYPE 131   2   1   2   3
D16V8, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              121               131
  M1                2                 2
  M1A               1                 1
  M1B               0                 2
  M1C               2                 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"
D16V9, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   45 33
  8Q GAIN WILD-TYPE 59 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     45   33
  8Q GAIN WILD-TYPE   59   39
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               45                59
  YES              33                39
[1] 2 2
[1] FALSE
D16V10, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    21 111
  8Q GAIN WILD-TYPE  13 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     21  111
  8Q GAIN WILD-TYPE   13  136
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               21                13
  YES             111               136
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   50 82
  8Q GAIN WILD-TYPE 58 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     50   82
  8Q GAIN WILD-TYPE   58   91
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              50                58
  MALE                82                91
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       4                         0   128
  8Q GAIN WILD-TYPE     1                         1   147
D16V13, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 128               147
[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     1 129
  8Q GAIN WILD-TYPE   2 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1  129
  8Q GAIN WILD-TYPE    2  145
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO             129               145
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     8   7
  9P GAIN WILD-TYPE 129 126
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               255 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7               126 
$`9P GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A5GN TCGA-D3-A5GS TCGA-EB-A5SH 
       22.55        45.83        88.50        52.01         6.97         0.00 
TCGA-EE-A184 TCGA-EE-A2M5 TCGA-ER-A19G TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ET 
        5.13         8.84       114.15        11.80        13.08         6.58 
TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A4F8 
       23.80        12.92        14.20 

$`9P GAIN 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-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        69.90        11.41        30.87         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        45.11       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         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       20.48        13.94        95.38        47.87         1.55        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01         2.89         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-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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.20         0.13         0.00        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        36.07         4.34         5.13         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        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         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         6.48         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        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        30.84         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-A2MG TCGA-EE-A2MH 
        6.18        47.51         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       111.78       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        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        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-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       36.07        17.72        78.44         1.87         1.51        12.62 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       11.74         9.04        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
        4.90         6.71         3.58         5.36        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-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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        2.27         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       10.65        11.05         5.79 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 0 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           114.15            124.31 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            13.08             14.24 
[1] "0.0 - 114.2 (13.1)" "0.0 - 124.3 (14.2)"
[1] "hr=" "1.1"
D17V2, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     8   7
  9P GAIN WILD-TYPE 134 127
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               261 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7               127 
$`9P GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JA TCGA-D3-A5GN TCGA-D3-A5GS TCGA-EB-A5SH 
       31.59        90.90       115.53       135.75         7.43        35.01 
TCGA-EE-A184 TCGA-EE-A2M5 TCGA-ER-A19G TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3ET 
       68.15        21.67       268.93        43.82        16.37        80.32 
TCGA-FS-A1Z0 TCGA-FS-A1ZJ TCGA-FS-A4F8 
      202.65        47.38       174.84 

$`9P GAIN 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-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       28.08        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        69.90        11.87        48.76       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        45.11       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        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       51.68        15.06       110.93       137.92       166.19       125.19 
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         3.25 
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 
       45.11         3.55        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       109.64       151.27        78.87       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        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        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       345.96        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       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       101.95        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-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       144.76       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       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        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-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       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-A19W TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       37.25       148.18        79.99        23.34        20.15        31.27 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
        4.90       210.08        15.16         7.00       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-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-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-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        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         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             7.43              0.16 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           268.93            357.37 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            68.15             47.54 
[1] "7.4 - 268.9 (68.2)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.4"
D17V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P GAIN MUTATED                    3             1
  9P GAIN WILD-TYPE                 34             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9P GAIN MUTATED                                           2
  9P GAIN WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  9P GAIN MUTATED                     9
  9P GAIN WILD-TYPE                 170
D17V4, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  DISTANT METASTASIS                                      3                34
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                58
  REGIONAL LYMPH NODE                                     9               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
  9P GAIN MUTATED             0       0       4        1        3        0
  9P GAIN WILD-TYPE          10       6      19        9       22       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9P GAIN MUTATED           0         0         0         1          2
  9P GAIN WILD-TYPE        10        14        10        31         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED            1          1        1
  9P GAIN WILD-TYPE         22         47       11
D17V5, multiclass
             clus
vv            9P GAIN MUTATED 9P GAIN WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   4                19
  STAGE IA                  1                 9
  STAGE IB                  3                22
  STAGE II                  0                17
  STAGE IIA                 0                10
  STAGE IIB                 0                14
  STAGE IIC                 0                10
  STAGE III                 1                31
  STAGE IIIA                2                12
  STAGE IIIB                1                22
  STAGE IIIC                1                47
  STAGE IV                  1                11
[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  1  3
  9P GAIN WILD-TYPE    49 54 54 54
D17V6, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               4                49
  T2                  6                54
  T3                  1                54
  T4                  3                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
  9P GAIN MUTATED    10   3   1   1
  9P GAIN WILD-TYPE 131  48  31  36
D17V7, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              10               131
  N1               3                48
  N2               1                31
  N3               1                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
  9P GAIN MUTATED    14   0   0   0   1
  9P GAIN WILD-TYPE 238   4   2   2   4
D17V8, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               14               238
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               1                 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"
D17V9, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    9  3
  9P GAIN WILD-TYPE 95 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      9    3
  9P GAIN WILD-TYPE   95   69
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                9                95
  YES               3                69
[1] 2 2
[1] FALSE
D17V10, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  15
  9P GAIN WILD-TYPE  34 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   15
  9P GAIN WILD-TYPE   34  232
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                0                34
  YES              15               232
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     6   9
  9P GAIN WILD-TYPE 102 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6    9
  9P GAIN WILD-TYPE  102  164
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               6               102
  MALE                 9               164
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         0    15
  9P GAIN WILD-TYPE     5                         1   260
D17V13, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  15               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"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  15
  9P GAIN WILD-TYPE   3 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   15
  9P GAIN WILD-TYPE    3  259
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               259
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     7  13
  9Q GAIN WILD-TYPE 130 120
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               250 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               13               120 
$`9Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A3ML TCGA-D3-A5GN TCGA-D3-A5GR 
       22.55        88.50        68.22         6.31        52.01         1.55 
TCGA-D3-A5GS TCGA-EE-A184 TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A3J3 TCGA-ER-A19G 
        6.97         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-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-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-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        69.90        11.41        30.87         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        45.11       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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.00         9.34       103.59        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.94        95.38        47.87        23.11         4.01         2.89 
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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.00         0.00        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-A185 
        6.31         8.12         1.12         1.35        12.20         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         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        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         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         6.48         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        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        30.84         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-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51        29.46        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 
      111.78       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 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        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-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.90        11.11        34.88         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        1.51        12.62        11.74         9.04         6.58        22.49 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
        1.71        18.41         4.90         6.71         3.58         5.36 
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-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-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       30.87        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-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 
        0.43         9.90         7.23        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        11.05         5.79 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.55              0.00 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           114.15            124.31 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            12.36             14.58 
[1] "1.6 - 114.2 (12.4)" "0.0 - 124.3 (14.6)"
[1] "hr=" "1.4"
D18V2, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     7  13
  9Q GAIN WILD-TYPE 135 121
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               256 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               13               121 
$`9Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A3ML TCGA-D3-A5GN TCGA-D3-A5GR 
       31.59       115.53       168.00        13.87       135.75       166.19 
TCGA-D3-A5GS TCGA-EE-A184 TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A3J3 TCGA-ER-A19G 
        7.43        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-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-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-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77        69.90        11.87        48.76       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        45.11       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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       24.53         9.34       103.59        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
       15.06       110.93       137.92       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         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-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.16        17.85        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.55        52.01         6.35        12.20        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-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
      109.64       151.27        78.87       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        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        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       345.96        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       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       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        94.82       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51       103.27       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 
      144.76       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 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        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-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       13.02        26.37       152.35         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-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        31.27        32.05       247.04        80.32        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       33.21        92.98         4.90       210.08        15.16         7.00 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      216.92       228.59        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-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-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-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             7.43              0.16 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           268.93            357.37 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            58.37             47.54 
[1] "7.4 - 268.9 (58.4)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1"  
D18V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q GAIN MUTATED                    4             1
  9Q GAIN WILD-TYPE                 33             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9Q GAIN MUTATED                                           3
  9Q GAIN WILD-TYPE                                        57
                   vv
clus                REGIONAL LYMPH NODE
  9Q GAIN MUTATED                    12
  9Q GAIN WILD-TYPE                 167
D18V4, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      4                33
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               3                57
  REGIONAL LYMPH NODE                                    12               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
  9Q GAIN MUTATED             0       1       5        1        3        2
  9Q GAIN WILD-TYPE          10       5      18        9       22       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9Q GAIN MUTATED           0         0         0         1          2
  9Q GAIN WILD-TYPE        10        14        10        31         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED            1          2        1
  9Q GAIN WILD-TYPE         22         46       11
D18V5, multiclass
             clus
vv            9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   1                 5
  STAGE I                   5                18
  STAGE IA                  1                 9
  STAGE IB                  3                22
  STAGE II                  2                15
  STAGE IIA                 0                10
  STAGE IIB                 0                14
  STAGE IIC                 0                10
  STAGE III                 1                31
  STAGE IIIA                2                12
  STAGE IIIB                1                22
  STAGE IIIC                2                46
  STAGE IV                  1                11
[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  7  3  2
  9Q GAIN WILD-TYPE    47 53 52 55
D18V6, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               6                47
  T2                  7                53
  T3                  3                52
  T4                  2                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
  9Q GAIN MUTATED    13   3   2   2
  9Q GAIN WILD-TYPE 128  48  30  35
D18V7, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              13               128
  N1               3                48
  N2               2                30
  N3               2                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
  9Q GAIN MUTATED    19   0   0   0   1
  9Q GAIN WILD-TYPE 233   4   2   2   4
D18V8, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               19               233
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               1                 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"
D18V9, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   12  3
  9Q GAIN WILD-TYPE 92 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     12    3
  9Q GAIN WILD-TYPE   92   69
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               12                92
  YES               3                69
[1] 2 2
[1] FALSE
D18V10, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  20
  9Q GAIN WILD-TYPE  34 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   20
  9Q GAIN WILD-TYPE   34  227
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                34
  YES              20               227
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     9  11
  9Q GAIN WILD-TYPE  99 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      9   11
  9Q GAIN WILD-TYPE   99  162
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               9                99
  MALE                11               162
[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   256
D18V13, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  19               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"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  20
  9Q GAIN WILD-TYPE   3 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   20
  9Q GAIN WILD-TYPE    3  254
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              20               254
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     5   4
  10P GAIN WILD-TYPE 132 129
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                261 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                129 
$`10P GAIN MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A51N TCGA-D9-A6EC TCGA-DA-A1HY TCGA-EE-A29D 
       15.25       103.59         8.84        13.22        51.12        11.15 
TCGA-ER-A19C TCGA-ER-A19M TCGA-FW-A3I3 
        3.78        28.60         0.20 

$`10P GAIN 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-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        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       64.44        45.11       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-A3MU 
       61.38        13.32        24.00         6.31         9.34        26.37 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       20.48        13.94        95.38        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         9.90        11.31 
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-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-A5UN TCGA-EB-A6L9 
        0.20         0.13         0.00         0.00        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        36.07         4.34         5.13 
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        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        8.55         4.41         1.08        27.12         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         6.48         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        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        30.84 
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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       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        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        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-A19N TCGA-ER-A19P 
      114.15        34.88         4.21        13.45        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        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         4.90         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        3.58         5.36        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-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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       10.65        11.05         5.79 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               0.2                0.0 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            103.59             124.31 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             13.22              14.20 
[1] "0.2 - 103.6 (13.2)" "0.0 - 124.3 (14.2)"
[1] "hr=" "1.1"
D19V2, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     5   4
  10P GAIN WILD-TYPE 137 130
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                267 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                130 
$`10P GAIN MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3MR TCGA-D3-A51N TCGA-D9-A6EC TCGA-DA-A1HY TCGA-EE-A29D 
       58.06       103.59        10.03        66.25       117.21        13.97 
TCGA-ER-A19C TCGA-ER-A19M TCGA-FW-A3I3 
       48.89        61.05         0.20 

$`10P GAIN 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-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        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.08        45.11       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-A3MU 
       86.93        60.23        24.53        13.87         9.34        39.75 
TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       51.68        15.06       110.93       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       11.34         3.25         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 
       45.11        35.01         3.55        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       109.64       151.27        78.87 
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        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        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       345.96        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       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       101.95 
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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       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       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        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-A19N TCGA-ER-A19P 
      268.93       152.35         6.44       131.51        44.05       162.08 
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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98        33.21        92.98       174.21         4.90       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       15.16         7.00       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-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-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-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       50.14        66.67        28.73       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         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.20               0.16 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            117.21             357.37 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             58.06              47.54 
[1] "0.2 - 117.2 (58.1)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.1"
D19V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10P GAIN MUTATED                    1             1
  10P GAIN WILD-TYPE                 36             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10P GAIN MUTATED                                           1
  10P GAIN WILD-TYPE                                        59
                    vv
clus                 REGIONAL LYMPH NODE
  10P GAIN MUTATED                     6
  10P GAIN WILD-TYPE                 173
D19V4, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  DISTANT METASTASIS                                       1                 36
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                1                 59
  REGIONAL LYMPH NODE                                      6                173
[1] 4 2
[1] 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          10       6      22       10       23       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10P GAIN MUTATED           0         0         0         1          1
  10P GAIN WILD-TYPE        10        14        10        31         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED            0          2        2
  10P GAIN WILD-TYPE         23         46       10
D19V5, multiclass
             clus
vv            10P GAIN MUTATED 10P GAIN WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    0                  6
  STAGE I                    1                 22
  STAGE IA                   0                 10
  STAGE IB                   2                 23
  STAGE II                   0                 17
  STAGE IIA                  0                 10
  STAGE IIB                  0                 14
  STAGE IIC                  0                 10
  STAGE III                  1                 31
  STAGE IIIA                 1                 13
  STAGE IIIB                 0                 23
  STAGE IIIC                 2                 46
  STAGE IV                   2                 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 GAIN MUTATED       2  4  2  1
  10P GAIN WILD-TYPE    51 56 53 56
D19V6, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1                2                 51
  T2                   4                 56
  T3                   2                 53
  T4                   1                 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
  10P GAIN MUTATED     3   3   0   2
  10P GAIN WILD-TYPE 138  48  32  35
D19V7, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                3                138
  N1                3                 48
  N2                0                 32
  N3                2                 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
  10P GAIN MUTATED     7   1   0   0   1
  10P GAIN WILD-TYPE 245   3   2   2   4
D19V8, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                 7                245
  M1                 1                  3
  M1A                0                  2
  M1B                0                  2
  M1C                1                  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"
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4   2
  10P GAIN WILD-TYPE 100  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    2
  10P GAIN WILD-TYPE  100   70
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 4                100
  YES                2                 70
[1] 2 2
[1] FALSE
D19V10, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3   6
  10P GAIN WILD-TYPE  31 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    6
  10P GAIN WILD-TYPE   31  241
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 3                 31
  YES                6                241
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4   5
  10P GAIN WILD-TYPE 104 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    5
  10P GAIN WILD-TYPE  104  168
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                4                104
  MALE                  5                168
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0     9
  10P GAIN WILD-TYPE     5                         1   266
D19V13, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    9                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"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0   9
  10P GAIN WILD-TYPE   3 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    9
  10P GAIN WILD-TYPE    3  265
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                9                265
[1] 2 2
[1] FALSE

Clustering(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    13  12
  11P GAIN WILD-TYPE 124 121
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                25                245 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                12                121 
$`11P GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC 
       69.90        30.87        45.11        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         6.48         8.68        39.39        47.21 
TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A3JI TCGA-ER-A19N TCGA-FS-A1YX 
        5.42         8.84        47.51        33.60        42.84         3.45 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-GN-A266 TCGA-GN-A268 
        3.39         8.22        49.15         3.22        10.13        15.42 
TCGA-GN-A26D 
       14.70 

$`11P GAIN 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-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-A2JD TCGA-D3-A2JG 
        8.38        21.14        88.50        68.22        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-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       15.25        46.98        46.32        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         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       95.38        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
        4.01         2.89         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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.00         0.00        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 
       36.07         4.34         5.13         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        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         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        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
        9.67         8.94        34.29        17.98        34.92        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        30.84 
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-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
        6.18         9.53        29.46        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       111.78       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        29.65        27.16        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         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-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       22.22        27.35         0.46        13.94        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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       13.45        28.60        34.68         9.57        36.07        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-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       85.74         4.90         6.71         3.58         5.36        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-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-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT 
       12.89        47.38        52.08         8.65         8.81        40.64 
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-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         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23        12.85        24.85        31.33        84.72        16.24 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        11.84        10.65        11.05         5.79 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              3.22               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             82.29             124.31 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             13.32              14.20 
[1] "3.2 - 82.3 (13.3)"  "0.0 - 124.3 (14.2)"
[1] "hr=" "1"  
D20V2, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    13  12
  11P GAIN WILD-TYPE 129 122
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                25                251 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                12                122 
$`11P GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC 
       69.90        48.76        45.11       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       345.96       171.55        47.54       208.04 
TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A3JI TCGA-ER-A19N TCGA-FS-A1YX 
       13.91        21.67        61.51       148.08        44.05        48.59 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-GN-A266 TCGA-GN-A268 
       48.85        53.52       148.80        50.14        10.13        62.79 
TCGA-GN-A26D 
       39.58 

$`11P GAIN 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-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-A2JD TCGA-D3-A2JG 
       65.49        23.77       115.53       168.00        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-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.98        46.32        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        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      110.93       135.75       137.92       166.19         7.43       125.19 
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         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        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-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.16        17.85        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.55        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 
      109.64       151.27        78.87       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        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
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        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       39.29        58.75        67.43       314.56       135.95        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       101.95 
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-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       19.76        47.28       103.27       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       144.76       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       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         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-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       53.19        27.35        33.40       101.79        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-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      131.51        61.05       162.08        50.89        37.25       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-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
      174.21         4.90       210.08        15.16         7.00       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-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-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT 
       23.93       101.26        74.73       133.55        11.41        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       26.56        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         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        7.23        14.04       120.46       117.93        84.72        64.44 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        46.36        12.62       294.77         6.67 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             10.13               0.16 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            345.96             357.37 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             53.52              46.98 
[1] "10.1 - 346.0 (53.5)" "0.2 - 357.4 (47.0)" 
[1] "hr=" "1.2"
D20V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P GAIN MUTATED                    3             1
  11P GAIN WILD-TYPE                 34             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11P GAIN MUTATED                                           4
  11P GAIN WILD-TYPE                                        56
                    vv
clus                 REGIONAL LYMPH NODE
  11P GAIN MUTATED                    19
  11P GAIN WILD-TYPE                 160
D20V4, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  DISTANT METASTASIS                                       3                 34
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                4                 56
  REGIONAL LYMPH NODE                                     19                160
[1] 4 2
[1] 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       5        1        0        2
  11P GAIN WILD-TYPE           7       5      18        9       25       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11P GAIN MUTATED           1         1         2         3          1
  11P GAIN WILD-TYPE         9        13         8        29         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED            3          1        0
  11P GAIN WILD-TYPE         20         47       12
D20V5, multiclass
             clus
vv            11P GAIN MUTATED 11P GAIN WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    1                  5
  STAGE I                    5                 18
  STAGE IA                   1                  9
  STAGE IB                   0                 25
  STAGE II                   2                 15
  STAGE IIA                  1                  9
  STAGE IIB                  1                 13
  STAGE IIC                  2                  8
  STAGE III                  3                 29
  STAGE IIIA                 1                 13
  STAGE IIIB                 3                 20
  STAGE IIIC                 1                 47
  STAGE IV                   0                 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
  11P GAIN MUTATED       5  9  2  5
  11P GAIN WILD-TYPE    48 51 53 52
D20V6, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                5                 48
  T2                   9                 51
  T3                   2                 53
  T4                   5                 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
  11P GAIN MUTATED    17   4   2   1
  11P GAIN WILD-TYPE 124  47  30  36
D20V7, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               17                124
  N1                4                 47
  N2                2                 30
  N3                1                 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
  11P GAIN MUTATED    24   0   0   0   0
  11P GAIN WILD-TYPE 228   4   2   2   5
D20V8, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                24                228
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                0                  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"
D20V9, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    9  5
  11P GAIN WILD-TYPE 95 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      9    5
  11P GAIN WILD-TYPE   95   67
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 9                 95
  YES                5                 67
[1] 2 2
[1] FALSE
D20V10, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6  21
  11P GAIN WILD-TYPE  28 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6   21
  11P GAIN WILD-TYPE   28  226
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 6                 28
  YES               21                226
[1] 2 2
[1] FALSE
D20V11, continuous
D20V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     9  18
  11P GAIN WILD-TYPE  99 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      9   18
  11P GAIN WILD-TYPE   99  155
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                9                 99
  MALE                 18                155
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0    27
  11P GAIN WILD-TYPE     5                         1   248
D20V13, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   27                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"
D20V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  27
  11P GAIN WILD-TYPE   3 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   27
  11P GAIN WILD-TYPE    3  247
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               27                247
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    12  10
  11Q GAIN WILD-TYPE 125 123
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                22                248 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                123 
$`11Q GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC 
       69.90        30.87        45.11        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         8.68        47.21         5.42         8.84        47.51 
TCGA-EE-A3JI TCGA-ER-A19N TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZD 
       33.60        42.84         6.71         3.45         3.39         8.22 
TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A268 
       49.15         3.22         7.23        15.42 

$`11Q GAIN 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-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-A2JD TCGA-D3-A2JG 
        8.38        21.14        88.50        68.22        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-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       15.25        46.98        46.32        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         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       95.38        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
        4.01         2.89         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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.00         0.00        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-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         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        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         6.48         2.43         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        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        30.84         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       36.33        98.27         2.70         6.18         9.53        29.46 
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       111.78       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        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
       13.94        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-A19M TCGA-ER-A19P 
      114.15        34.88         4.21        13.45        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        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-A7U8 
       22.49         1.71        18.41        85.74         4.90         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        5.36        64.47        11.01        23.80        14.24        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.33         7.30        20.38        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-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        40.64         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         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-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        0.43         9.90        12.85        24.85        31.33        84.72 
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-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              3.22               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             82.29             124.31 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.27              14.22 
[1] "3.2 - 82.3 (13.3)"  "0.0 - 124.3 (14.2)"
[1] "hr=" "1.1"
D21V2, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    12  10
  11Q GAIN WILD-TYPE 130 124
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                22                254 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                124 
$`11Q GAIN MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D9-A6EC 
       69.90        48.76        45.11       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       171.55       208.04        13.91        21.67        61.51 
TCGA-EE-A3JI TCGA-ER-A19N TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZD 
      148.08        44.05       210.08        48.59        48.85        53.52 
TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A268 
      148.80        50.14         7.23        62.79 

$`11Q GAIN 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-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-A2JD TCGA-D3-A2JG 
       65.49        23.77       115.53       168.00        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-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.98        46.32        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        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
      110.93       135.75       137.92       166.19         7.43       125.19 
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         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        25.18        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-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.16        17.85        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.55        52.01         6.35        12.20        29.82        27.22 
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-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       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        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       14.47        55.92       345.96        25.87        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48        90.97       101.95        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       94.82       129.27        28.83        19.76        47.28       103.27 
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       144.76       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       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      101.79        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-A19M TCGA-ER-A19P 
      268.93       152.35         6.44       131.51        61.05       162.08 
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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       46.98        33.21        92.98       174.21         4.90        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        7.00       216.92       228.59       202.65        20.91        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.79        27.72       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-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       11.41        53.16        26.56        49.48        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-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        2.40         9.90        14.04       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        64.44        32.48        39.58        46.36        12.62 
TCGA-OD-A75X TCGA-QB-A6FS 
      294.77         6.67 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              7.23               0.16 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            210.08             357.37 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            56.875             47.130 
[1] "7.2 - 210.1 (56.9)" "0.2 - 357.4 (47.1)"
[1] "hr=" "1.3"
D21V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q GAIN MUTATED                    2             1
  11Q GAIN WILD-TYPE                 35             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11Q GAIN MUTATED                                           3
  11Q GAIN WILD-TYPE                                        57
                    vv
clus                 REGIONAL LYMPH NODE
  11Q GAIN MUTATED                    18
  11Q GAIN WILD-TYPE                 161
D21V4, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       2                 35
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                3                 57
  REGIONAL LYMPH NODE                                     18                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
  11Q GAIN MUTATED             3       1       6        1        0        2
  11Q GAIN WILD-TYPE           7       5      17        9       25       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11Q GAIN MUTATED           1         1         1         2          1
  11Q GAIN WILD-TYPE         9        13         9        30         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED            2          1        0
  11Q GAIN WILD-TYPE         21         47       12
D21V5, multiclass
             clus
vv            11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    1                  5
  STAGE I                    6                 17
  STAGE IA                   1                  9
  STAGE IB                   0                 25
  STAGE II                   2                 15
  STAGE IIA                  1                  9
  STAGE IIB                  1                 13
  STAGE IIC                  1                  9
  STAGE III                  2                 30
  STAGE IIIA                 1                 13
  STAGE IIIB                 2                 21
  STAGE IIIC                 1                 47
  STAGE IV                   0                 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
  11Q GAIN MUTATED       6  8  2  3
  11Q GAIN WILD-TYPE    47 52 53 54
D21V6, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                6                 47
  T2                   8                 52
  T3                   2                 53
  T4                   3                 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
  11Q GAIN MUTATED    16   3   2   1
  11Q GAIN WILD-TYPE 125  48  30  36
D21V7, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               16                125
  N1                3                 48
  N2                2                 30
  N3                1                 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
  11Q GAIN MUTATED    22   0   0   0   0
  11Q GAIN WILD-TYPE 230   4   2   2   5
D21V8, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                22                230
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                0                  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"
D21V9, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    9  3
  11Q GAIN WILD-TYPE 95 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      9    3
  11Q GAIN WILD-TYPE   95   69
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 9                 95
  YES                3                 69
[1] 2 2
[1] FALSE
D21V10, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     6  18
  11Q GAIN WILD-TYPE  28 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6   18
  11Q GAIN WILD-TYPE   28  229
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 6                 28
  YES               18                229
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     9  15
  11Q GAIN WILD-TYPE  99 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      9   15
  11Q GAIN WILD-TYPE   99  158
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                9                 99
  MALE                 15                158
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0    24
  11Q GAIN WILD-TYPE     5                         1   251
D21V13, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   24                251
[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
  11Q GAIN MUTATED     0  24
  11Q GAIN WILD-TYPE   3 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   24
  11Q GAIN WILD-TYPE    3  250
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               24                250
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    21  27
  12P GAIN WILD-TYPE 116 106
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                48                222 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                27                106 
$`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-D9-A6E9 
       13.32        24.00         5.39        52.01        23.11         9.90 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A44Q 
       13.22        35.80        36.69         4.93        17.56        13.15 
TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29X 
        0.13        10.55         8.12         9.21        11.15         8.09 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GU TCGA-EE-A2M5 
        9.67         8.94        39.39        47.21        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI 
       98.27       124.31         3.68        21.60         0.46        33.60 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3ET 
       25.18         3.78         4.21        13.45        28.60         6.58 
TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-GN-A267 TCGA-GN-A26A 
        1.71         6.71        47.38         8.68        16.24        12.16 

$`12P GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.52       111.09        32.42       110.79        28.08        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        69.90        11.41        30.87         7.50        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        45.11       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       46.32        82.29         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 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        95.38        47.87         1.55         6.97 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
        4.01         2.89        11.31        14.60        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       10.03        39.19        13.68         9.99        44.52        25.15 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R 
       22.36         6.64        19.36         7.00        14.83         0.20 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
        0.00         0.00        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        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.34         5.13         1.18         7.99         9.90        37.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       38.63         8.55         4.41         1.08        27.12         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         6.48         2.43 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD 
        8.68        11.31        49.22        23.90        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        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        30.84         5.42         1.15        13.02        34.98 
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       111.78       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        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
        5.56       122.73        25.84        30.15        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       12.72         3.22        22.92        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35        13.94        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-A19G 
        5.72        76.41         3.52        11.90        11.11       114.15 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       34.88        42.84        34.68         9.57        36.07        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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       11.74         9.04        22.49        18.41        85.74         4.90 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        3.58         5.36        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-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-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.89        52.08         8.65         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-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         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        31.33        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       15.42        14.70        11.84        10.65        11.05         5.79 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.13               0.00 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            124.31             122.73 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            13.385             14.220 
[1] "0.1 - 124.3 (13.4)" "0.0 - 122.7 (14.2)"
[1] "hr=" "1.2"
D22V2, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    22  27
  12P GAIN WILD-TYPE 120 107
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                227 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                27                107 
$`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-D9-A6E9 
       60.23        24.53        21.47       135.75       125.19         9.90 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A44Q 
       66.25        36.03        61.18        65.92       215.44        13.87 
TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29D 
       17.85         3.55        27.22        94.98       168.26        13.97 
TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GU 
       17.92        39.29        58.75        47.54       208.04        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3J5 TCGA-EE-A3JE 
       21.67       129.27       124.31         3.68        36.95        33.40 
TCGA-EE-A3JI TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
      148.08        98.40        48.89         6.44       131.51        61.05 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1ZM TCGA-FS-A1ZU TCGA-GN-A267 
       80.32        33.21       210.08       101.26        26.56        64.44 
TCGA-GN-A26A 
       32.48 

$`12P GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04       112.57       133.25        28.08        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        69.90        11.87        48.76       113.52        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        45.11       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       46.32       166.52        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 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       110.93       137.92       166.19         7.43 
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         3.25 
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-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
      176.55        35.93       107.34        53.92        23.44        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH 
       28.60        10.49        15.68        10.16        45.11        35.01 
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       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
       78.87        13.55        63.35        80.61        47.84        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       72.07        32.19         2.60        44.35        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       345.96        25.87       171.55 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       46.82       102.90        24.43        67.43       314.56       135.95 
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-A2M7 
      101.95        13.91        14.30        55.59        44.88        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       144.76       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       103.56       136.47        41.59        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84        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-A3JD 
      172.18       127.20        64.08        34.32        53.19        27.35 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 
      101.79        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-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-A2NG TCGA-ER-A2NH 
       43.82        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
      247.04        46.98        92.98       174.21         4.90        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        7.00       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-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         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       14.04       120.46       117.93        84.72        10.13        62.79 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       39.58        46.36        12.62       294.77         6.67 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              3.55               0.16 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            215.44             357.37 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             58.06              47.38 
[1] "3.5 - 215.4 (58.1)" "0.2 - 357.4 (47.4)"
[1] "hr=" "1.2"
D22V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P GAIN MUTATED                    4             2
  12P GAIN WILD-TYPE                 33             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12P GAIN MUTATED                                          13
  12P GAIN WILD-TYPE                                        47
                    vv
clus                 REGIONAL LYMPH NODE
  12P GAIN MUTATED                    30
  12P GAIN WILD-TYPE                 149
D22V4, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  DISTANT METASTASIS                                       4                 33
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 47
  REGIONAL LYMPH NODE                                     30                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
  12P GAIN MUTATED             0       0       8        2        5        0
  12P GAIN WILD-TYPE          10       6      15        8       20       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12P GAIN MUTATED           0         0         2        10          5
  12P GAIN WILD-TYPE        10        14         8        22          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED            8          5        2
  12P GAIN WILD-TYPE         15         43       10
D22V5, multiclass
             clus
vv            12P GAIN MUTATED 12P GAIN WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    0                  6
  STAGE I                    8                 15
  STAGE IA                   2                  8
  STAGE IB                   5                 20
  STAGE II                   0                 17
  STAGE IIA                  0                 10
  STAGE IIB                  0                 14
  STAGE IIC                  2                  8
  STAGE III                 10                 22
  STAGE IIIA                 5                  9
  STAGE IIIB                 8                 15
  STAGE IIIC                 5                 43
  STAGE IV                   2                 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
  12P GAIN MUTATED      15 13  8  8
  12P GAIN WILD-TYPE    38 47 47 49
D22V6, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               15                 38
  T2                  13                 47
  T3                   8                 47
  T4                   8                 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
  12P GAIN MUTATED    19  19   4   5
  12P GAIN WILD-TYPE 122  32  28  32
D22V7, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               19                122
  N1               19                 32
  N2                4                 28
  N3                5                 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
  12P GAIN MUTATED    46   1   1   0   0
  12P GAIN WILD-TYPE 206   3   1   2   5
D22V8, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                46                206
  M1                 1                  3
  M1A                1                  1
  M1B                0                  2
  M1C                0                  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"
D22V9, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   21 11
  12P GAIN WILD-TYPE 83 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     21   11
  12P GAIN WILD-TYPE   83   61
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                21                 83
  YES               11                 61
[1] 2 2
[1] FALSE
D22V10, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     6  43
  12P GAIN WILD-TYPE  28 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6   43
  12P GAIN WILD-TYPE   28  204
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 6                 28
  YES               43                204
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    19  30
  12P GAIN WILD-TYPE  89 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     19   30
  12P GAIN WILD-TYPE   89  143
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               19                 89
  MALE                 30                143
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       3                         0    46
  12P GAIN WILD-TYPE     2                         1   229
D22V13, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   46                229
[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
  12P GAIN MUTATED     0  48
  12P GAIN WILD-TYPE   3 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   48
  12P GAIN WILD-TYPE    3  226
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               48                226
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    14  17
  12Q GAIN WILD-TYPE 123 116
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                31                239 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                17                116 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC 
       70.16        22.55        56.19        64.44        15.25        61.38 
TCGA-D3-A3CF TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-DA-A1HW TCGA-DA-A3F5 
       24.00        52.01         6.97        23.11        35.80        17.56 
TCGA-EB-A44Q TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 TCGA-EE-A2GB 
       13.15        10.55         8.12        11.15         8.94        39.39 
TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A19B 
       47.21         8.84        21.60         0.46        33.60        25.18 
TCGA-ER-A19C TCGA-ER-A19L TCGA-FR-A729 TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-GN-A267 
        3.78        13.45         6.71        12.89        47.38        16.24 
TCGA-GN-A26A 
       12.16 

$`12Q 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-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       45.83        81.24        10.29        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       36.16         6.31        92.42        45.11       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32        82.29        13.32         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         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       17.72         8.84        20.48        13.94        95.38        47.87 
TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        1.55         4.01         2.89         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 
        0.00         0.00        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        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         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        38.63         8.55         4.41         1.08        27.12 
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         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
        9.67        34.29        17.98        34.92        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        30.84         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-A2MG TCGA-EE-A2MH 
        6.18        47.51         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       111.78       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        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         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-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       22.22        27.35        13.94        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-A19M TCGA-ER-A19N TCGA-ER-A19P 
      114.15        34.88         4.21        28.60        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
        9.57        36.07        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-A7U8 
       22.49         1.71        18.41        85.74         4.90         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.36        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-A1ZP 
       19.53        11.08         7.17        30.87        12.92        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         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       12.85        24.85        31.33        84.72        10.13        15.42 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        10.65        11.05         5.79 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.46               0.00 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             70.16             124.31 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             17.56              13.81 
[1] "0.5 - 70.2 (17.6)"  "0.0 - 124.3 (13.8)"
[1] "hr=" "1"  
D23V2, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    15  17
  12Q GAIN WILD-TYPE 127 117
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                32                244 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                17                117 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC 
       71.80        31.59        56.19        66.08        58.06        86.93 
TCGA-D3-A3CF TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-DA-A1HW TCGA-DA-A3F5 
       24.53       135.75         7.43       125.19        36.03       215.44 
TCGA-EB-A44Q TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A29D TCGA-EE-A2A6 
       13.87         3.55        27.22        94.98        13.97        58.75 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A3J5 TCGA-EE-A3JE TCGA-EE-A3JI 
       47.54       208.04        21.67        36.95        33.40       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 
       64.44        32.48 

$`12Q 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-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       90.90        95.74        43.43       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 
       42.08        12.10       171.58        45.11       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32       166.52        60.23        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        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       18.38        10.03        51.68        15.06       110.93       137.92 
TCGA-D3-A5GR TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      166.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        3.25         9.90        25.18        66.25        22.95        48.89 
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-A3F8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       10.49        15.68        10.16        17.85        45.11        35.01 
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       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       39.62        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        37.35        14.47        55.92       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       135.95        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       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        94.82       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       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       144.76       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       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         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-A3JA 
      138.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35       101.79        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        12.59        13.02        26.37       268.93 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
      152.35         6.44        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-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-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
       33.21        92.98       174.21         4.90        15.16         7.00 
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-A1ZP TCGA-FS-A1ZQ 
       15.45         9.70        32.75        47.38        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-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         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
      120.46       117.93        84.72        10.13        62.79        39.58 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              3.55               0.16 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            215.44             357.37 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            57.125             47.460 
[1] "3.5 - 215.4 (57.1)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1"  
D23V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q GAIN MUTATED                    2             0
  12Q GAIN WILD-TYPE                 35             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12Q GAIN MUTATED                                           9
  12Q GAIN WILD-TYPE                                        51
                    vv
clus                 REGIONAL LYMPH NODE
  12Q GAIN MUTATED                    21
  12Q GAIN WILD-TYPE                 158
D23V4, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       2                 35
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                9                 51
  REGIONAL LYMPH NODE                                     21                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
  12Q GAIN MUTATED             0       0       6        1        2        1
  12Q GAIN WILD-TYPE          10       6      17        9       23       16
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12Q GAIN MUTATED           0         0         1         6          2
  12Q GAIN WILD-TYPE        10        14         9        26         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED            5          5        1
  12Q GAIN WILD-TYPE         18         43       11
D23V5, multiclass
             clus
vv            12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    0                  6
  STAGE I                    6                 17
  STAGE IA                   1                  9
  STAGE IB                   2                 23
  STAGE II                   1                 16
  STAGE IIA                  0                 10
  STAGE IIB                  0                 14
  STAGE IIC                  1                  9
  STAGE III                  6                 26
  STAGE IIIA                 2                 12
  STAGE IIIB                 5                 18
  STAGE IIIC                 5                 43
  STAGE IV                   1                 11
[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       8  7  4  8
  12Q GAIN WILD-TYPE    45 53 51 49
D23V6, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                8                 45
  T2                   7                 53
  T3                   4                 51
  T4                   8                 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
  12Q GAIN MUTATED    12  12   2   4
  12Q GAIN WILD-TYPE 129  39  30  33
D23V7, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               12                129
  N1               12                 39
  N2                2                 30
  N3                4                 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
  12Q GAIN MUTATED    30   0   0   0   1
  12Q GAIN WILD-TYPE 222   4   2   2   4
D23V8, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                30                222
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                1                  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"
D23V9, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   13  9
  12Q GAIN WILD-TYPE 91 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     13    9
  12Q GAIN WILD-TYPE   91   63
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                13                 91
  YES                9                 63
[1] 2 2
[1] FALSE
D23V10, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1  31
  12Q GAIN WILD-TYPE  33 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   31
  12Q GAIN WILD-TYPE   33  216
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                 33
  YES               31                216
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    10  22
  12Q GAIN WILD-TYPE  98 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     10   22
  12Q GAIN WILD-TYPE   98  151
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               10                 98
  MALE                 22                151
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         0    30
  12Q GAIN WILD-TYPE     3                         1   245
D23V13, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   30                245
[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
  12Q GAIN MUTATED     0  31
  12Q GAIN WILD-TYPE   3 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   31
  12Q GAIN WILD-TYPE    3  243
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               31                243
[1] 2 2
[1] FALSE

Clustering(24) Variable = 13Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    31  38
  13Q GAIN WILD-TYPE 106  95
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                69                201 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                38                 95 
$`13Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3C6 
       16.47         8.52        70.16        30.87        45.11        15.25 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU TCGA-DA-A1I7 
       61.38        13.32        13.94        47.87        23.11        36.69 
TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20B 
        7.00         0.20         0.00        10.55         8.12        36.07 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29R 
        9.21         7.99         9.90         8.55        12.03         8.84 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
        9.67        39.39        47.21        28.31        33.83         5.42 
TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 
        2.70        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-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
        1.71         4.90         6.71        64.47         3.45        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       14.24        15.52         7.33        19.53         8.65        40.64 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A265 TCGA-GN-A267 
        0.82         3.22         2.27         0.13        84.72        16.24 
TCGA-GN-A268 TCGA-GN-A4U9 TCGA-OD-A75X 
       15.42        10.65        11.05 

$`13Q GAIN WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      111.09        32.42       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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        69.90        11.41         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       92.42        56.19        64.44       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       82.29        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 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
        8.84        20.48        95.38        52.01         1.55         6.97 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01         2.89         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-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH 
       19.36        17.56        14.83        13.15         0.13         0.00 
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-A20C TCGA-EE-A20F TCGA-EE-A20I 
       12.20         5.13         4.31         4.34         5.13         1.18 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15        38.63         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        9.50         8.09         9.99         6.48         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC 
        8.09        11.31        49.22        23.90         8.94        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        30.08        19.43        16.01        35.54 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       30.84         1.15        13.02        34.98        36.33         8.84 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       98.27         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       111.78       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        29.65        27.16        23.05         5.56 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84         3.68        30.15        15.95        12.72 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       22.92        21.60        16.14        27.35         0.46        13.94 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F 
       31.40        18.61        38.40        76.41        25.18        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      114.15        34.88         4.21         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44         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-A7U8 
        9.04         6.58        22.49        18.41        85.74         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
        5.36        11.01         7.30         3.39        20.38         8.22 
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-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       52.08         8.81        49.15         8.68        27.39         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         0.20         0.99         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A 
        7.23        12.85        24.85        31.33        10.13        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       14.70        11.84         5.79 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                  0 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            124.31             122.73 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             13.32              14.70 
[1] "0.0 - 124.3 (13.3)" "0.0 - 122.7 (14.7)"
[1] "hr=" "1.3"
D24V2, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    31  38
  13Q GAIN WILD-TYPE 111  96
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                69                207 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                38                 96 
$`13Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A2JP TCGA-D3-A3C6 
       16.57        16.67        71.80        48.76        45.11        58.06 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU TCGA-DA-A1I7 
       86.93        60.23        15.06       137.92       125.19        61.18 
TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20B 
       10.49        10.16        45.11        27.22        94.98       109.64 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A29R 
      168.26        63.35        80.61        72.07        56.42        14.47 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       39.29        47.54       208.04        75.48        90.97        13.91 
TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AA TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J7 
       28.83       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-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 
       33.21         4.90       210.08       216.92        48.59       202.65 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       20.91        28.08         7.79        40.27       133.55        53.16 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A265 TCGA-GN-A267 
       27.09        50.14        77.88        47.54        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A4U9 TCGA-OD-A75X 
       62.79        12.62       294.77 

$`13Q GAIN WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
      112.04       112.57       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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        69.90        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
      171.58        56.19        66.08       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
      166.52        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 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       10.03        51.68       110.93       135.75       166.19         7.43 
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         3.25 
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-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-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       15.68        13.87        17.85        35.01         3.55        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-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       151.27        78.87        13.55 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       47.84        13.97        39.62        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       18.61        37.35        55.92       345.96        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC 
       17.92        46.82       102.90        24.43        58.75        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95        48.72        89.33        54.74        79.66 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      101.95        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
      129.27        19.76        61.51        47.28       103.27       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       144.76       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       103.56       136.47        41.59        53.26 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84         3.68        54.51        23.47       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        36.95        34.32        27.35        33.40       101.79 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F 
       31.40        35.44        50.76        77.75        98.40        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      268.93       152.35         6.44        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        23.34        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
      247.04        80.32        46.98        92.98       174.21        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
        7.00       228.59        27.72        48.85       357.37        53.52 
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-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       74.73        11.41       148.80        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       49.45         0.20        22.92         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A 
        7.23        14.04       120.46       117.93        10.13        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       39.58        46.36         6.67 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              4.90               0.16 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            294.77             357.37 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             53.19              46.82 
[1] "4.9 - 294.8 (53.2)" "0.2 - 357.4 (46.8)"
[1] "hr=" "1.1"
D24V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q GAIN MUTATED                   15             0
  13Q GAIN WILD-TYPE                 22             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  13Q GAIN MUTATED                                          17
  13Q GAIN WILD-TYPE                                        43
                    vv
clus                 REGIONAL LYMPH NODE
  13Q GAIN MUTATED                    38
  13Q GAIN WILD-TYPE                 141
D24V4, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      15                 22
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               17                 43
  REGIONAL LYMPH NODE                                     38                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
  13Q GAIN MUTATED             2       1       9        2       10        3
  13Q GAIN WILD-TYPE           8       5      14        8       15       14
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  13Q GAIN MUTATED           1         3         6         5          3
  13Q GAIN WILD-TYPE         9        11         4        27         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED            7         10        2
  13Q GAIN WILD-TYPE         16         38       10
D24V5, multiclass
             clus
vv            13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  I OR II NOS                2                  8
  STAGE 0                    1                  5
  STAGE I                    9                 14
  STAGE IA                   2                  8
  STAGE IB                  10                 15
  STAGE II                   3                 14
  STAGE IIA                  1                  9
  STAGE IIB                  3                 11
  STAGE IIC                  6                  4
  STAGE III                  5                 27
  STAGE IIIA                 3                 11
  STAGE IIIB                 7                 16
  STAGE IIIC                10                 38
  STAGE IV                   2                 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
  13Q GAIN MUTATED      13 20  8 17
  13Q GAIN WILD-TYPE    40 40 47 40
D24V6, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               13                 40
  T2                  20                 40
  T3                   8                 47
  T4                  17                 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                  N0  N1  N2  N3
  13Q GAIN MUTATED    40  13   4   7
  13Q GAIN WILD-TYPE 101  38  28  30
D24V7, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               40                101
  N1               13                 38
  N2                4                 28
  N3                7                 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
  13Q GAIN MUTATED    63   1   1   0   0
  13Q GAIN WILD-TYPE 189   3   1   2   5
D24V8, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                63                189
  M1                 1                  3
  M1A                1                  1
  M1B                0                  2
  M1C                0                  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"
D24V9, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   23 20
  13Q GAIN WILD-TYPE 81 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     23   20
  13Q GAIN WILD-TYPE   81   52
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                23                 81
  YES               20                 52
[1] 2 2
[1] FALSE
D24V10, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    10  61
  13Q GAIN WILD-TYPE  24 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     10   61
  13Q GAIN WILD-TYPE   24  186
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                10                 24
  YES               61                186
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    26  45
  13Q GAIN WILD-TYPE  82 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     26   45
  13Q GAIN WILD-TYPE   82  128
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               26                 82
  MALE                 45                128
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       2                         0    69
  13Q GAIN WILD-TYPE     3                         1   206
D24V13, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   69                206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  69
  13Q GAIN WILD-TYPE   3 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   69
  13Q GAIN WILD-TYPE    3  205
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               69                205
[1] 2 2
[1] FALSE

Clustering(25) Variable = 14Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    16  14
  14Q GAIN WILD-TYPE 121 119
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                30                240 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                14                119 
$`14Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D9-A6E9 TCGA-DA-A1I2 
       22.55        88.50        92.42        15.25         9.90        13.68 
TCGA-DA-A1I7 TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29L 
       36.69         0.00         8.12         9.21        11.15         1.08 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MJ TCGA-EE-A2MU 
       47.21        28.31        30.84         8.84        63.42         5.56 
TCGA-EE-A3AE TCGA-EE-A3JH TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A69P 
       30.15        13.94         3.78        13.45        28.60         4.90 
TCGA-FR-A729 TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-GN-A265 TCGA-GN-A26D 
        6.71        52.08        27.39         0.82        84.72        14.70 

$`14Q GAIN 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-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-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        68.22        69.90        11.41        30.87         7.50 
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        45.11       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-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
        6.31         9.34       103.59        26.37         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       13.94        95.38        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       23.11         4.01         2.89        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-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       44.52        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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00        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        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.34         5.13         1.18         7.99         9.90        37.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         8.55         4.41        27.12         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         6.48         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       39.39        34.29        17.98        34.92        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       16.01        35.54        33.83         5.42         1.15        13.02 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       34.98        36.33        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-A2MK 
        9.53        29.46        44.25         7.96        14.56       111.78 
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        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16        23.05       124.31       122.73        25.84         3.68 
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-A3JI 
       21.60        16.14        22.22        27.35         0.46        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-A19W 
        4.21        42.84        34.68         9.57        36.07        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-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       85.74         3.58         5.36        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-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-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       40.64         8.68         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         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        7.23        12.85        24.85        31.33        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       15.42        12.16        11.84        10.65        11.05         5.79 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                  0 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             92.42             124.31 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             14.32              14.07 
[1] "0.0 - 92.4 (14.3)"  "0.0 - 124.3 (14.1)"
[1] "hr=" "1.1"
D25V2, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    16  14
  14Q GAIN WILD-TYPE 126 120
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                30                246 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                14                120 
$`14Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D9-A6E9 TCGA-DA-A1I2 
       31.59       115.53       171.58        58.06         9.90       176.55 
TCGA-DA-A1I7 TCGA-EB-A5SH TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29L 
       61.18        35.01        94.98       168.26        13.97         2.60 
TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MJ TCGA-EE-A2MU 
      208.04        75.48       101.95        21.67        96.23        53.26 
TCGA-EE-A3AE TCGA-EE-A3JH TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A69P 
       54.51       101.79        48.89       131.51        61.05         4.90 
TCGA-FR-A729 TCGA-FS-A1ZP TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-GN-A265 TCGA-GN-A26D 
      210.08        74.73        49.48        27.09        84.72        39.58 

$`14Q GAIN 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-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-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       168.00        69.90        11.87        48.76       113.52 
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        45.11       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-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
       13.87         9.34       103.59        39.75        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       15.06       110.93       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        3.25        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-A1I8 
      117.21        20.38       194.83        35.93       107.34        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        45.11         3.55 
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-A20B 
       33.73        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
      151.27        78.87        13.55        63.35        80.61        47.84 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       39.62        72.07        32.19        44.35        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       345.96        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       47.54        67.43       314.56       135.95        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       54.74        79.66        90.97        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82       129.27        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK 
       47.28       103.27       103.20        16.96       204.66       144.76 
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       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      136.47        41.59       124.31       122.73        25.84         3.68 
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-A3JI 
       64.08        34.32        53.19        27.35        33.40       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-A19W 
        6.44        44.05       162.08        50.89        37.25       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-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
      174.21        15.16         7.00       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-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       53.16        26.56        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         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        7.23        14.04       120.46       117.93        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        32.48        46.36        12.62       294.77         6.67 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              2.60               0.16 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            210.08             357.37 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            61.115             46.980 
[1] "2.6 - 210.1 (61.1)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.3"
D25V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q GAIN MUTATED                    3             1
  14Q GAIN WILD-TYPE                 34             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  14Q GAIN MUTATED                                           6
  14Q GAIN WILD-TYPE                                        54
                    vv
clus                 REGIONAL LYMPH NODE
  14Q GAIN MUTATED                    21
  14Q GAIN WILD-TYPE                 158
D25V4, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       3                 34
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                6                 54
  REGIONAL LYMPH NODE                                     21                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
  14Q GAIN MUTATED             1       1       5        2        3        2
  14Q GAIN WILD-TYPE           9       5      18        8       22       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  14Q GAIN MUTATED           0         1         2         3          2
  14Q GAIN WILD-TYPE        10        13         8        29         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED            3          4        0
  14Q GAIN WILD-TYPE         20         44       12
D25V5, multiclass
             clus
vv            14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  I OR II NOS                1                  9
  STAGE 0                    1                  5
  STAGE I                    5                 18
  STAGE IA                   2                  8
  STAGE IB                   3                 22
  STAGE II                   2                 15
  STAGE IIA                  0                 10
  STAGE IIB                  1                 13
  STAGE IIC                  2                  8
  STAGE III                  3                 29
  STAGE IIIA                 2                 12
  STAGE IIIB                 3                 20
  STAGE IIIC                 4                 44
  STAGE IV                   0                 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
  14Q GAIN MUTATED       4  9  5  8
  14Q GAIN WILD-TYPE    49 51 50 49
D25V6, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                4                 49
  T2                   9                 51
  T3                   5                 50
  T4                   8                 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
  14Q GAIN MUTATED    19   4   3   2
  14Q GAIN WILD-TYPE 122  47  29  35
D25V7, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               19                122
  N1                4                 47
  N2                3                 29
  N3                2                 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
  14Q GAIN MUTATED    27   0   0   0   0
  14Q GAIN WILD-TYPE 225   4   2   2   5
D25V8, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                27                225
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                0                  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"
D25V9, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   12  9
  14Q GAIN WILD-TYPE 92 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     12    9
  14Q GAIN WILD-TYPE   92   63
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                12                 92
  YES                9                 63
[1] 2 2
[1] FALSE
D25V10, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     3  28
  14Q GAIN WILD-TYPE  31 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3   28
  14Q GAIN WILD-TYPE   31  219
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 3                 31
  YES               28                219
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    10  21
  14Q GAIN WILD-TYPE  98 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10   21
  14Q GAIN WILD-TYPE   98  152
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               10                 98
  MALE                 21                152
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0    31
  14Q GAIN WILD-TYPE     5                         1   244
D25V13, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   31                244
[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
  14Q GAIN MUTATED     0  31
  14Q GAIN WILD-TYPE   3 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   31
  14Q GAIN WILD-TYPE    3  243
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               31                243
[1] 2 2
[1] FALSE

Clustering(26) Variable = 15Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    31  28
  15Q GAIN WILD-TYPE 106 105
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                59                211 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                28                105 
$`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        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MV 
       30.87        92.42        56.19        82.29        13.32         5.39 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A183 
       11.31        35.80        36.69        17.56        10.55        12.20 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       36.07         9.21        11.15         6.48         8.68         8.09 
TCGA-EE-A2A1 TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M6 
       49.22        30.08        28.31        30.84         5.42        98.27 
TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
        2.70        63.42        25.08        26.99        29.65        27.16 
TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3JH 
      124.31        30.15        15.95         3.22        21.60        13.94 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S 
       33.60        31.40         3.78        28.60        34.68        36.07 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1Z3 TCGA-FS-A1ZD 
       85.74         4.90         6.71         5.36        14.24         8.22 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 
        0.82         3.22         2.27         7.23        31.33 

$`15Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         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-A2JB 
       45.83        81.24        10.29        85.32         8.38        68.22 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        7.50        36.16         6.31        64.44        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       15.25        46.98        46.32        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        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       41.10        17.72         8.84        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
        2.89         9.90        13.22        14.60        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       10.03        39.19        13.68         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         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        0.20        11.57         6.31         8.12         1.12         1.35 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        5.13         4.31         4.34         5.13         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        38.63         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        2.43        11.31        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        34.92        47.21        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       35.54        33.83         1.15        13.02        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        8.84         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ 
        7.96        14.56       111.78       111.91        56.02        21.60 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       23.05         5.56       122.73        25.84         3.68        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J7 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-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
        0.46        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-A19L TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
        4.21        13.45        42.84         9.57        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-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 
        9.04         6.58        22.49         1.71        18.41         3.58 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       64.47         3.45        11.01        23.80        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.30         3.39        20.38        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-A1ZZ 
        8.81        49.15        40.64         8.68        27.39         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         7.36        28.73        14.20        10.78         5.98 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         0.20         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        9.90        12.85        24.85        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       15.42        12.16        14.70        11.84        10.65        11.05 
TCGA-QB-A6FS 
        5.79 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.82               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            124.31             122.73 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             22.55              13.22 
[1] "0.8 - 124.3 (22.6)" "0.0 - 122.7 (13.2)"
[1] "hr=" "1.2"
D26V2, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    32  28
  15Q GAIN WILD-TYPE 110 106
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                60                216 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                28                106 
$`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        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MV 
       48.76       171.58        56.19       166.52        60.23        21.47 
TCGA-D9-A149 TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A17Y 
       54.67        25.18        36.03        61.18       215.44        27.22 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29W 
       26.89       109.64       168.26        13.97       345.96       171.55 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
       17.92       102.90        48.72        75.48       101.95        13.91 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
      129.27        28.83        96.23        47.54       248.65       103.56 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
      136.47       124.31        54.51        23.47       172.18        36.95 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A19M TCGA-ER-A19P 
      101.79       148.08        31.40        48.89        61.05       162.08 
TCGA-ER-A19S TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1Z3 
       37.25       174.21         4.90       210.08         7.00        20.91 
TCGA-FS-A1ZD TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4FD TCGA-GF-A4EO TCGA-GN-A264 
       53.52        27.09        50.14        77.88         7.23       117.93 

$`15Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        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-A2JB 
       90.90        95.74        43.43       103.10        65.49       168.00 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10        66.08        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
       58.06        46.98        46.32        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       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      131.90        18.38        10.03        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC 
        3.65         6.41        11.34         3.25         9.90        66.25 
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-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       35.93       107.34        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-A5KH 
       28.60        10.49        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 
       45.11        35.01         3.55        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       29.82         8.65        94.98        33.73        14.70        68.15 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.96       151.27        78.87        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        39.62        72.07        32.19         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       18.61        56.42        37.35        14.47        55.92        25.87 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        89.33        54.74        79.66 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       90.97        14.30        55.59        44.88        94.82        21.67 
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-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MT 
      204.66       144.76       203.05       167.90        43.23        41.59 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH 
       53.26       122.73        25.84         3.68        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        64.08        34.32        53.19        27.35        33.40 
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-A19N TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      131.51        44.05        50.89       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-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FS-A1YW 
       80.32        46.98        33.21        92.98        15.16       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
       48.59       228.59       202.65        28.08         7.79        27.72 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       48.85       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-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        49.48        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-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         2.40         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       14.04       120.46        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        39.58        46.36        12.62       294.77         6.67 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              4.90               0.16 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            345.96             357.37 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             58.21              46.34 
[1] "4.9 - 346.0 (58.2)" "0.2 - 357.4 (46.3)"
[1] "hr=" "1.3"
D26V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q GAIN MUTATED                    5             1
  15Q GAIN WILD-TYPE                 32             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  15Q GAIN MUTATED                                          13
  15Q GAIN WILD-TYPE                                        47
                    vv
clus                 REGIONAL LYMPH NODE
  15Q GAIN MUTATED                    43
  15Q GAIN WILD-TYPE                 136
D26V4, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       5                 32
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 47
  REGIONAL LYMPH NODE                                     43                136
[1] 4 2
[1] 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             5       2       8        3        5        5
  15Q GAIN WILD-TYPE           5       4      15        7       20       12
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  15Q GAIN MUTATED           1         2         2         7          1
  15Q GAIN WILD-TYPE         9        12         8        25         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED            6          8        1
  15Q GAIN WILD-TYPE         17         40       11
D26V5, multiclass
             clus
vv            15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  I OR II NOS                5                  5
  STAGE 0                    2                  4
  STAGE I                    8                 15
  STAGE IA                   3                  7
  STAGE IB                   5                 20
  STAGE II                   5                 12
  STAGE IIA                  1                  9
  STAGE IIB                  2                 12
  STAGE IIC                  2                  8
  STAGE III                  7                 25
  STAGE IIIA                 1                 13
  STAGE IIIB                 6                 17
  STAGE IIIC                 8                 40
  STAGE IV                   1                 11
[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      13 17 10  9
  15Q GAIN WILD-TYPE    40 43 45 48
D26V6, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1               13                 40
  T2                  17                 43
  T3                  10                 45
  T4                   9                 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
  15Q GAIN MUTATED    35  11   5   6
  15Q GAIN WILD-TYPE 106  40  27  31
D26V7, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               35                106
  N1               11                 40
  N2                5                 27
  N3                6                 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
  15Q GAIN MUTATED    57   1   0   0   0
  15Q GAIN WILD-TYPE 195   3   2   2   5
D26V8, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                57                195
  M1                 1                  3
  M1A                0                  2
  M1B                0                  2
  M1C                0                  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"
D26V9, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   23 12
  15Q GAIN WILD-TYPE 81 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     23   12
  15Q GAIN WILD-TYPE   81   60
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                23                 81
  YES               12                 60
[1] 2 2
[1] FALSE
D26V10, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    10  52
  15Q GAIN WILD-TYPE  24 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     10   52
  15Q GAIN WILD-TYPE   24  195
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                10                 24
  YES               52                195
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    24  38
  15Q GAIN WILD-TYPE  84 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     24   38
  15Q GAIN WILD-TYPE   84  135
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               24                 84
  MALE                 38                135
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         0    61
  15Q GAIN WILD-TYPE     4                         1   214
D26V13, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   61                214
[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
  15Q GAIN MUTATED     0  61
  15Q GAIN WILD-TYPE   3 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   61
  15Q GAIN WILD-TYPE    3  213
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               61                213
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    20  18
  16P GAIN WILD-TYPE 117 115
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                232 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                18                115 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-EE-A17Y TCGA-EE-A20B 
       70.16        15.25        13.32         1.55        10.55        36.07 
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        39.39 
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         4.90 
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 
        2.27         7.23 

$`16P 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-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-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        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-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       20.48        13.94        95.38        52.01        47.87         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         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-A5UN 
       13.15         0.20         0.13         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        0.20        11.57         6.31         8.12         1.12         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         5.13         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        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S 
        4.41         1.08        27.12         9.50         8.09         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
        6.48         2.43         8.68         8.09        11.31        23.90 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
        8.94        34.29        17.98        34.92        19.43        16.01 
TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       35.54        30.84         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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       56.02        25.08        21.60        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
        5.56       124.31       122.73        25.84         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
       15.95        12.72        22.92        21.60        16.14        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35         0.46        13.94        33.60        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19E TCGA-ER-A19F 
       12.95        38.40         5.72        76.41        11.90        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S 
      114.15        34.88         4.21        13.45         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-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       12.62        11.74         9.04         6.58        22.49        18.41 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
       85.74         3.58         5.36        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-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.89        47.38         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-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       10.78         5.98         6.41         0.20         0.99         0.13 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         0.43         9.90        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        11.05         5.79 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.82               0.00 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             98.27             124.31 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            14.285             14.070 
[1] "0.8 - 98.3 (14.3)"  "0.0 - 124.3 (14.1)"
[1] "hr=" "1"  
D27V2, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    20  18
  16P GAIN WILD-TYPE 122 116
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                238 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                18                116 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-EE-A17Y TCGA-EE-A20B 
       71.80        58.06        60.23       166.19        27.22       109.64 
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        47.54 
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         4.90 
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 
       77.88         7.23 

$`16P 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-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-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        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-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       51.68        15.06       110.93       135.75       137.92         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        3.25         9.90        25.18        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-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        45.11        35.01         3.55        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-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       151.27        78.87        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        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S 
       32.19         2.60        44.35        18.61        37.35        55.92 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
      345.96        25.87       171.55        17.92        46.82        24.43 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       58.75        67.43       314.56       135.95        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66       101.95        13.91        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54        43.23       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       53.26       124.31       122.73        25.84         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
       23.47       138.81       127.20        36.95        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19E TCGA-ER-A19F 
       13.94        50.76         9.17        77.75        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19Q TCGA-ER-A19S 
      268.93       152.35         6.44       131.51        50.89        37.25 
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-FR-A3YN 
       31.27        32.05       247.04        80.32        46.98        92.98 
TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      174.21        15.16         7.00       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-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       23.93       101.26       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-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       12.43        26.73        49.45         0.20        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         2.40         9.90        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              4.90               0.16 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            248.65             357.37 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             60.64              46.59 
[1] "4.9 - 248.7 (60.6)" "0.2 - 357.4 (46.6)"
[1] "hr=" "1.3"
D27V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P GAIN MUTATED                    2             0
  16P GAIN WILD-TYPE                 35             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16P GAIN MUTATED                                          15
  16P GAIN WILD-TYPE                                        45
                    vv
clus                 REGIONAL LYMPH NODE
  16P GAIN MUTATED                    23
  16P GAIN WILD-TYPE                 156
D27V4, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  DISTANT METASTASIS                                       2                 35
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               15                 45
  REGIONAL LYMPH NODE                                     23                156
[1] 4 2
[1] 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             1       1       8        2        7        3
  16P GAIN WILD-TYPE           9       5      15        8       18       14
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16P GAIN MUTATED           2         1         2         3          0
  16P GAIN WILD-TYPE         8        13         8        29         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED            2          3        1
  16P GAIN WILD-TYPE         21         45       11
D27V5, multiclass
             clus
vv            16P GAIN MUTATED 16P GAIN WILD-TYPE
  I OR II NOS                1                  9
  STAGE 0                    1                  5
  STAGE I                    8                 15
  STAGE IA                   2                  8
  STAGE IB                   7                 18
  STAGE II                   3                 14
  STAGE IIA                  2                  8
  STAGE IIB                  1                 13
  STAGE IIC                  2                  8
  STAGE III                  3                 29
  STAGE IIIA                 0                 14
  STAGE IIIB                 2                 21
  STAGE IIIC                 3                 45
  STAGE IV                   1                 11
[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       6 17  7  3
  16P GAIN WILD-TYPE    47 43 48 54
D27V6, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                6                 47
  T2                  17                 43
  T3                   7                 48
  T4                   3                 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
  16P GAIN MUTATED    29   6   0   2
  16P GAIN WILD-TYPE 112  45  32  35
D27V7, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               29                112
  N1                6                 45
  N2                0                 32
  N3                2                 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
  16P GAIN MUTATED    36   0   1   0   0
  16P GAIN WILD-TYPE 216   4   1   2   5
D27V8, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                36                216
  M1                 0                  4
  M1A                1                  1
  M1B                0                  2
  M1C                0                  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"
D27V9, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   12 10
  16P GAIN WILD-TYPE 92 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     12   10
  16P GAIN WILD-TYPE   92   62
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                12                 92
  YES               10                 62
[1] 2 2
[1] FALSE
D27V10, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     4  36
  16P GAIN WILD-TYPE  30 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4   36
  16P GAIN WILD-TYPE   30  211
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                 30
  YES               36                211
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    16  24
  16P GAIN WILD-TYPE  92 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     16   24
  16P GAIN WILD-TYPE   92  149
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               16                 92
  MALE                 24                149
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         0    39
  16P GAIN WILD-TYPE     4                         1   236
D27V13, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   39                236
[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
  16P GAIN MUTATED     0  38
  16P GAIN WILD-TYPE   3 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   38
  16P GAIN WILD-TYPE    3  236
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               38                236
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    15  16
  16Q GAIN WILD-TYPE 122 117
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                31                239 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                117 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-EE-A17Y TCGA-EE-A20B 
       70.16        15.25        13.32         1.55        10.55        36.07 
TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GM 
        9.21         8.84        49.22        39.39        30.08        28.31 
TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-EE-A3J7 
       33.83        98.27         2.70        26.99         3.22        21.60 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A3PL 
        3.78         3.52        11.90        28.60        34.68         1.71 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 
        4.90         6.71         3.45         0.82         7.36        28.73 
TCGA-GF-A4EO 
        7.23 

$`16Q 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-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-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        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-A3MV 
       24.00         6.31         9.34       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       20.48        13.94        95.38        52.01        47.87         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         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-A5UN 
       13.15         0.20         0.13         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        0.20        11.57         6.31         8.12         1.12         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         5.13         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        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         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         6.48         2.43         8.68         8.09        11.31 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        34.29        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP 
       47.21        19.43        16.01        35.54        30.84         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
        1.15        13.02        34.98        36.33         8.84         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       63.42       111.78       111.91        56.02        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
       22.92        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        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-A19W 
        4.21        13.45        42.84         9.57        36.07        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-FR-A3YN TCGA-FR-A44A 
       11.74         9.04         6.58        22.49        18.41        85.74 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.58         5.36        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-GN-A262 
        0.13         0.16         0.43         9.90        12.85        24.85 
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-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        10.65        11.05         5.79 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.82               0.00 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             98.27             124.31 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             11.90              14.24 
[1] "0.8 - 98.3 (11.9)"  "0.0 - 124.3 (14.2)"
[1] "hr=" "1.2"
D28V2, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    15  16
  16Q GAIN WILD-TYPE 127 118
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                31                245 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                118 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A5GR TCGA-EE-A17Y TCGA-EE-A20B 
       71.80        58.06        60.23       166.19        27.22       109.64 
TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GI TCGA-EE-A2GM 
      168.26        14.47       102.90        47.54        48.72        75.48 
TCGA-EE-A2GN TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-EE-A3J7 
       90.97       129.27        28.83       248.65       172.18        64.08 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A3PL 
       48.89        12.59        13.02        61.05       162.08        33.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 
        4.90       210.08        48.59        27.09        66.67        28.73 
TCGA-GF-A4EO 
        7.23 

$`16Q 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-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-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        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-A3MV 
       24.53        13.87         9.34       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       51.68        15.06       110.93       135.75       137.92         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        3.25         9.90        25.18        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-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        45.11        35.01         3.55        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-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       151.27        78.87        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        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        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       345.96        25.87       171.55        17.92        46.82 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        39.29        58.75        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP 
      208.04        89.33        54.74        79.66       101.95        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ 
       96.23       144.76       203.05       167.90        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        54.51        13.81        23.47       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        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       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-A19W 
        6.44       131.51        44.05        50.89        37.25       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-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        92.98       174.21 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       15.16         7.00       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-GN-A262 
       47.54         0.16         2.40         9.90        14.04       120.46 
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-OD-A75X TCGA-QB-A6FS 
       39.58        46.36        12.62       294.77         6.67 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              4.90               0.16 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            248.65             357.37 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             60.23              46.98 
[1] "4.9 - 248.7 (60.2)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.1"
D28V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q GAIN MUTATED                    2             0
  16Q GAIN WILD-TYPE                 35             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16Q GAIN MUTATED                                          13
  16Q GAIN WILD-TYPE                                        47
                    vv
clus                 REGIONAL LYMPH NODE
  16Q GAIN MUTATED                    19
  16Q GAIN WILD-TYPE                 160
D28V4, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       2                 35
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               13                 47
  REGIONAL LYMPH NODE                                     19                160
[1] 4 2
[1] 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             1       1       7        1        7        2
  16Q GAIN WILD-TYPE           9       5      16        9       18       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16Q GAIN MUTATED           2         1         1         3          0
  16Q GAIN WILD-TYPE         8        13         9        29         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED            3          2        1
  16Q GAIN WILD-TYPE         20         46       11
D28V5, multiclass
             clus
vv            16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  I OR II NOS                1                  9
  STAGE 0                    1                  5
  STAGE I                    7                 16
  STAGE IA                   1                  9
  STAGE IB                   7                 18
  STAGE II                   2                 15
  STAGE IIA                  2                  8
  STAGE IIB                  1                 13
  STAGE IIC                  1                  9
  STAGE III                  3                 29
  STAGE IIIA                 0                 14
  STAGE IIIB                 3                 20
  STAGE IIIC                 2                 46
  STAGE IV                   1                 11
[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       5 15  7  2
  16Q GAIN WILD-TYPE    48 45 48 55
D28V6, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                5                 48
  T2                  15                 45
  T3                   7                 48
  T4                   2                 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
  16Q GAIN MUTATED    24   7   0   1
  16Q GAIN WILD-TYPE 117  44  32  36
D28V7, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               24                117
  N1                7                 44
  N2                0                 32
  N3                1                 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
  16Q GAIN MUTATED    31   0   1   0   0
  16Q GAIN WILD-TYPE 221   4   1   2   5
D28V8, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                31                221
  M1                 0                  4
  M1A                1                  1
  M1B                0                  2
  M1C                0                  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"
D28V9, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   11  9
  16Q GAIN WILD-TYPE 93 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     11    9
  16Q GAIN WILD-TYPE   93   63
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                11                 93
  YES                9                 63
[1] 2 2
[1] FALSE
D28V10, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     3  31
  16Q GAIN WILD-TYPE  31 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   31
  16Q GAIN WILD-TYPE   31  216
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 3                 31
  YES               31                216
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    15  19
  16Q GAIN WILD-TYPE  93 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     15   19
  16Q GAIN WILD-TYPE   93  154
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               15                 93
  MALE                 19                154
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         0    33
  16Q GAIN WILD-TYPE     4                         1   242
D28V13, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   33                242
[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
  16Q GAIN MUTATED     0  32
  16Q GAIN WILD-TYPE   3 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   32
  16Q GAIN WILD-TYPE    3  242
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               32                242
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    17  14
  17P GAIN WILD-TYPE 120 119
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                31                239 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                119 
$`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        69.90       114.67        15.25        13.32 
TCGA-D3-A3MV TCGA-D3-A5GU TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-EE-A17Y 
        5.39        23.11        13.22        36.69         4.93        10.55 
TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        1.35         5.13        11.15         9.50        12.03         8.84 
TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 TCGA-EE-A3AE TCGA-EE-A3AG 
        8.94        47.21        28.31         2.70        30.15        15.95 
TCGA-EE-A3JA TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
       22.22         1.87         1.71         8.22        47.38        49.15 
TCGA-GN-A26D 
       14.70 

$`17P GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        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-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        11.41        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
        6.31        92.42        56.19        64.44        45.11        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32        82.29        61.38        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        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       17.72         8.84        20.48        13.94        95.38        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       47.87         1.55         6.97         4.01         2.89         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-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB 
       39.19        13.68         9.99        44.52        25.15        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-A5UN TCGA-EB-A6L9 
        0.20         0.13         0.00         0.00        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        36.07         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        38.63         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       27.12         8.09         9.99         6.48         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.09        11.31        49.22        23.90         9.67        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       34.29        17.98        34.92        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        30.84         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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        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 
      111.78       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 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84         3.68        13.81        12.72         3.22        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        21.60        16.14        27.35         0.46        13.94 
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-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-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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       22.49        18.41        85.74         4.90         6.71         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.36        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-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-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         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        11.84        10.65        11.05         5.79 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.35               0.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            114.67             124.31 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             13.32              14.20 
[1] "1.4 - 114.7 (13.3)" "0.0 - 124.3 (14.2)"
[1] "hr=" "1"  
D29V2, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    17  14
  17P GAIN WILD-TYPE 125 120
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                31                245 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                120 
$`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        69.90       130.72        58.06        60.23 
TCGA-D3-A3MV TCGA-D3-A5GU TCGA-D9-A6EC TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-EE-A17Y 
       21.47       125.19        66.25        61.18        65.92        27.22 
TCGA-EE-A182 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       14.70        78.87        13.97        18.61        56.42        14.47 
TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 TCGA-EE-A3AE TCGA-EE-A3AG 
       58.75       208.04        75.48        28.83        54.51        23.47 
TCGA-EE-A3JA TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
       53.19        23.34        33.21        53.52       101.26       148.80 
TCGA-GN-A26D 
       39.58 

$`17P GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        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-A2JA TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        11.87        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 
       12.10       171.58        56.19        66.08        45.11        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO 
       46.32       166.52        86.93        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       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       18.38        10.03        51.68        15.06       110.93       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      137.92       166.19         7.43       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
        6.41        11.34         3.25         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 
       45.11        35.01         3.55        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       109.64       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        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       44.35        37.35        55.92       345.96        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
       17.92        46.82       102.90        24.43        39.29        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       67.43       314.56       135.95        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       101.95        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       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 
      144.76       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 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84         3.68        13.81       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32        27.35        33.40       101.79 
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-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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       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-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       46.98        92.98       174.21         4.90       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        7.00       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-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-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         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        46.36        12.62       294.77         6.67 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             13.97               0.16 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            208.04             357.37 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             54.51              47.54 
[1] "14.0 - 208.0 (54.5)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1"  
D29V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P GAIN MUTATED                    3             1
  17P GAIN WILD-TYPE                 34             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17P GAIN MUTATED                                           7
  17P GAIN WILD-TYPE                                        53
                    vv
clus                 REGIONAL LYMPH NODE
  17P GAIN MUTATED                    21
  17P GAIN WILD-TYPE                 158
D29V4, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  DISTANT METASTASIS                                       3                 34
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                7                 53
  REGIONAL LYMPH NODE                                     21                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
  17P GAIN MUTATED             2       0       2        2        3        2
  17P GAIN WILD-TYPE           8       6      21        8       22       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17P GAIN MUTATED           1         1         3         4          1
  17P GAIN WILD-TYPE         9        13         7        28         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED            5          5        1
  17P GAIN WILD-TYPE         18         43       11
D29V5, multiclass
             clus
vv            17P GAIN MUTATED 17P GAIN WILD-TYPE
  I OR II NOS                2                  8
  STAGE 0                    0                  6
  STAGE I                    2                 21
  STAGE IA                   2                  8
  STAGE IB                   3                 22
  STAGE II                   2                 15
  STAGE IIA                  1                  9
  STAGE IIB                  1                 13
  STAGE IIC                  3                  7
  STAGE III                  4                 28
  STAGE IIIA                 1                 13
  STAGE IIIB                 5                 18
  STAGE IIIC                 5                 43
  STAGE IV                   1                 11
[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  8  6  6
  17P GAIN WILD-TYPE    43 52 49 51
D29V6, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1               10                 43
  T2                   8                 52
  T3                   6                 49
  T4                   6                 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
  17P GAIN MUTATED    17   7   6   2
  17P GAIN WILD-TYPE 124  44  26  35
D29V7, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               17                124
  N1                7                 44
  N2                6                 26
  N3                2                 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
  17P GAIN MUTATED    30   0   1   0   0
  17P GAIN WILD-TYPE 222   4   1   2   5
D29V8, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                30                222
  M1                 0                  4
  M1A                1                  1
  M1B                0                  2
  M1C                0                  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"
D29V9, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   10 11
  17P GAIN WILD-TYPE 94 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     10   11
  17P GAIN WILD-TYPE   94   61
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                10                 94
  YES               11                 61
[1] 2 2
[1] FALSE
D29V10, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4  28
  17P GAIN WILD-TYPE  30 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4   28
  17P GAIN WILD-TYPE   30  219
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 4                 30
  YES               28                219
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    15  17
  17P GAIN WILD-TYPE  93 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     15   17
  17P GAIN WILD-TYPE   93  156
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               15                 93
  MALE                 17                156
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       1                         0    31
  17P GAIN WILD-TYPE     4                         1   244
D29V13, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   31                244
[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
  17P GAIN MUTATED     1  30
  17P GAIN WILD-TYPE   2 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   30
  17P GAIN WILD-TYPE    2  244
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               30                244
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    28  25
  17Q GAIN WILD-TYPE 109 108
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                53                217 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                25                108 
$`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        69.90 
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         5.39         6.97 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
        9.90        13.22        48.79        36.69         4.93         6.64 
TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F 
       10.55         1.12         1.35         5.13         4.31         5.13 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A6 
       11.15         1.08         9.50        12.03         8.84         8.94 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2MR 
       34.29        47.21        28.31         2.70         9.53        29.65 
TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A2NC 
       27.16        25.84        30.15        21.60        22.22        11.80 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
        1.71        18.41         3.45         8.22        47.38        49.15 
TCGA-FS-A1ZU TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
        8.68        84.72        15.42        14.70         5.79 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
      111.09        32.42        70.16       110.79        28.08        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD 
       10.29        85.32         8.38        21.14        88.50        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87         7.50        36.16         6.31        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       45.11        46.98        46.32        82.29        61.38        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59        26.37        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z1 
       95.38        52.01        47.87         1.55        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.89        11.31        14.60        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB 
       39.19        13.68         9.99        44.52        25.15        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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13         0.00         0.00        13.22         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H 
        6.31         8.12        12.20        36.07         4.34         9.21 
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        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        4.41        27.12         8.09         9.99         6.48         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       39.39        17.98        34.92        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        30.84         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-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       111.78 
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        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
        5.56       124.31       122.73         3.68        13.81        15.95 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD 
       12.72         3.22        22.92        21.60        16.14        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44         1.87         1.51        13.08        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        9.04         6.58        22.49        85.74         4.90         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        3.58         5.36        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-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-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.65         8.81        40.64        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-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       31.33        10.13        16.24        12.16        11.84        10.65 
TCGA-OD-A75X 
       11.05 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1.08               0.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            114.67             124.31 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             13.22              14.24 
[1] "1.1 - 114.7 (13.2)" "0.0 - 124.3 (14.2)"
[1] "hr=" "1"  
D30V2, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    30  25
  17Q GAIN WILD-TYPE 112 109
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                55                221 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                25                109 
$`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        69.90 
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        21.47         7.43 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I7 
      151.53         3.65         9.90        66.25        48.89        61.18 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 
       65.92        68.09        27.22        33.73        14.70        68.15 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
        4.96        78.87        13.97         2.60        18.61        56.42 
TCGA-EE-A29R TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2M7 
       14.47        58.75        67.43       208.04        75.48        28.83 
TCGA-EE-A2MD TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 
       47.28       103.56       136.47        25.84        54.51        36.95 
TCGA-EE-A3JA TCGA-ER-A2NC TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1YX TCGA-FS-A1ZD 
       53.19        43.82        33.21        92.98        48.59        53.52 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
      101.26       148.80        26.56        84.72        62.79        39.58 
TCGA-QB-A6FS 
        6.67 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
      112.04       112.57        71.80       133.25        28.08        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD 
       43.43       103.10        65.49        23.77       115.53        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76       113.52        42.08        12.10        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       45.11        46.98        46.32       166.52        86.93        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        39.75       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A149 
      110.93       135.75       137.92       166.19       125.19        54.67 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW 
        6.41        11.34         3.25        25.18        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        45.11        35.01         3.55 
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       109.64       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        39.62        72.07        32.19        44.35 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       37.35        55.92       345.96        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GD 
       46.82       102.90        24.43        39.29        47.54       314.56 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN 
      135.95        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 
      101.95        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-A2MG 
       21.67       129.27        19.76        61.51       103.27       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       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65        43.23        41.59        53.26       124.31 
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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        64.08        34.32        27.35        33.40       101.79 
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-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-A19W TCGA-ER-A1A1 TCGA-ER-A2ND 
      162.08        50.89        37.25       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-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       46.98       174.21         4.90       210.08        15.16         7.00 
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-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-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       32.75        47.38        23.93        74.73       133.55        11.41 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       53.16        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         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        9.90         7.23        14.04       120.46       117.93        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       64.44        32.48        46.36        12.62       294.77 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              2.60               0.16 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            208.04             357.37 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             53.52              47.38 
[1] "2.6 - 208.0 (53.5)" "0.2 - 357.4 (47.4)"
[1] "hr=" "1"  
D30V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q GAIN MUTATED                    5             2
  17Q GAIN WILD-TYPE                 32             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17Q GAIN MUTATED                                           9
  17Q GAIN WILD-TYPE                                        51
                    vv
clus                 REGIONAL LYMPH NODE
  17Q GAIN MUTATED                    40
  17Q GAIN WILD-TYPE                 139
D30V4, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       5                 32
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                9                 51
  REGIONAL LYMPH NODE                                     40                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
  17Q GAIN MUTATED             3       1       4        2        6        5
  17Q GAIN WILD-TYPE           7       5      19        8       19       12
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17Q GAIN MUTATED           1         3         5         5          2
  17Q GAIN WILD-TYPE         9        11         5        27         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED            7          7        2
  17Q GAIN WILD-TYPE         16         41       10
D30V5, multiclass
             clus
vv            17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    1                  5
  STAGE I                    4                 19
  STAGE IA                   2                  8
  STAGE IB                   6                 19
  STAGE II                   5                 12
  STAGE IIA                  1                  9
  STAGE IIB                  3                 11
  STAGE IIC                  5                  5
  STAGE III                  5                 27
  STAGE IIIA                 2                 12
  STAGE IIIB                 7                 16
  STAGE IIIC                 7                 41
  STAGE IV                   2                 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
  17Q GAIN MUTATED      12 14 12 12
  17Q GAIN WILD-TYPE    41 46 43 45
D30V6, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1               12                 41
  T2                  14                 46
  T3                  12                 43
  T4                  12                 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
  17Q GAIN MUTATED    31  10   9   5
  17Q GAIN WILD-TYPE 110  41  23  32
D30V7, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               31                110
  N1               10                 41
  N2                9                 23
  N3                5                 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
  17Q GAIN MUTATED    51   0   1   1   1
  17Q GAIN WILD-TYPE 201   4   1   1   4
D30V8, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                51                201
  M1                 0                  4
  M1A                1                  1
  M1B                1                  1
  M1C                1                  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"
D30V9, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   22 17
  17Q GAIN WILD-TYPE 82 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     22   17
  17Q GAIN WILD-TYPE   82   55
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                22                 82
  YES               17                 55
[1] 2 2
[1] FALSE
D30V10, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     7  49
  17Q GAIN WILD-TYPE  27 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7   49
  17Q GAIN WILD-TYPE   27  198
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 7                 27
  YES               49                198
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    23  33
  17Q GAIN WILD-TYPE  85 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     23   33
  17Q GAIN WILD-TYPE   85  140
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               23                 85
  MALE                 33                140
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       1                         1    54
  17Q GAIN WILD-TYPE     4                         0   221
D30V13, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   54                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"
D30V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  54
  17Q GAIN WILD-TYPE   2 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   54
  17Q GAIN WILD-TYPE    2  220
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               54                220
[1] 2 2
[1] FALSE

Clustering(31) Variable = 18P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    22  24
  18P GAIN WILD-TYPE 115 109
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                46                224 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                24                109 
$`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-D9-A6EA TCGA-D9-A6EC 
       13.32        80.22        17.72         8.84        11.31        13.22 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A181 
       35.80        10.03        39.19         0.20         8.12         1.12 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM 
       38.63         1.08        12.03        39.39        47.21        28.31 
TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 TCGA-ER-A19W TCGA-ER-A3EV 
        8.84        26.99        21.60        12.95        17.72        22.49 
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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GF-A4EO 
       12.92        12.89        40.64         8.68         3.22         7.23 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        16.24        12.16        14.70 

$`18P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        70.16       110.79        28.08 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       81.24        10.29        85.32         8.38        88.50        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       92.42        64.44        45.11       114.67        15.25        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32        82.29        24.00         6.31         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R 
       26.37         5.39        42.71        15.09        41.10        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       13.94        95.38        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV 
       23.11         4.01         2.89         9.90        14.60        48.79 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       51.12        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         0.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       13.22        11.57        10.55         6.31         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        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        4.41        27.12         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 
        6.48         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        34.29        17.98        34.92 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       30.08        19.43        16.01        35.54        33.83        30.84 
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-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       111.78       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        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       18.61        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-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-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       11.74         9.04         6.58        85.74         4.90         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        5.36        64.47        11.01        14.24        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
        7.30         3.39         8.22        19.53        11.08         7.17 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       30.87        47.38        52.08         8.65         8.81        49.15 
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-A6C8 
        0.99         0.13         0.16         0.43         9.90        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 
       24.85        31.33        10.13        15.42        11.84        10.65 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               0.2                0.0 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             84.72             124.31 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            16.980             13.875 
[1] "0.2 - 84.7 (17.0)"  "0.0 - 124.3 (13.9)"
[1] "hr=" "1.1"
D31V2, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    23  24
  18P GAIN WILD-TYPE 119 110
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                47                229 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                24                110 
$`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-D9-A6EA TCGA-D9-A6EC 
       60.23       161.85        18.38        10.03        25.18        66.25 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A180 
       36.03        20.38       194.83         3.55        12.20        94.98 
TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH 
       33.73        39.62         2.60        56.42        47.54       208.04 
TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 TCGA-ER-A19W 
       75.48        21.67       248.65        36.95        13.94       148.18 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 
       46.98        33.21        92.98       210.08        48.59       202.65 
TCGA-FS-A1ZC TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F2 
      357.37        47.38        23.93        53.16        26.56        50.14 
TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        7.23        84.72        64.44        32.48        39.58 

$`18P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04        71.80       133.25        28.08 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49       115.53       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
      171.58        66.08        45.11       130.72        58.06        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR 
       46.32       166.52        24.53        13.87         9.34       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51R 
       39.75        21.47        43.69        40.14       131.90        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       15.06       110.93       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 
        3.25         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        45.11        35.01        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       109.64       151.27        78.87       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        32.19 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       44.35        18.61        37.35        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       39.29        58.75        67.43       314.56       135.95        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       101.95        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-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       144.76       203.05       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         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-A3JA 
      138.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 
       61.05        44.05       162.08        50.89        37.25        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-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 
      247.04        80.32       174.21         4.90        15.16         7.00 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
      216.92       228.59        20.91        28.08         7.79        27.72 
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-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-GN-A262 
       47.54         0.16         2.40         9.90        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
      117.93        10.13        62.79        46.36        12.62       294.77 
TCGA-QB-A6FS 
        6.67 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              2.60               0.16 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            357.37             345.96 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             47.54              47.84 
[1] "2.6 - 357.4 (47.5)" "0.2 - 346.0 (47.8)"
[1] "hr=" "1.1"
D31V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P GAIN MUTATED                    7             2
  18P GAIN WILD-TYPE                 30             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18P GAIN MUTATED                                          11
  18P GAIN WILD-TYPE                                        49
                    vv
clus                 REGIONAL LYMPH NODE
  18P GAIN MUTATED                    27
  18P GAIN WILD-TYPE                 152
D31V4, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  DISTANT METASTASIS                                       7                 30
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               11                 49
  REGIONAL LYMPH NODE                                     27                152
[1] 4 2
[1] 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           6       6      17        9       23       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18P GAIN MUTATED           0         0         6         7          3
  18P GAIN WILD-TYPE        10        14         4        25         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED            6          5        3
  18P GAIN WILD-TYPE         17         43        9
D31V5, multiclass
             clus
vv            18P GAIN MUTATED 18P GAIN WILD-TYPE
  I OR II NOS                4                  6
  STAGE 0                    0                  6
  STAGE I                    6                 17
  STAGE IA                   1                  9
  STAGE IB                   2                 23
  STAGE II                   2                 15
  STAGE IIA                  0                 10
  STAGE IIB                  0                 14
  STAGE IIC                  6                  4
  STAGE III                  7                 25
  STAGE IIIA                 3                 11
  STAGE IIIB                 6                 17
  STAGE IIIC                 5                 43
  STAGE IV                   3                  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
  18P GAIN MUTATED       7 10  5 17
  18P GAIN WILD-TYPE    46 50 50 40
D31V6, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                7                 46
  T2                  10                 50
  T3                   5                 50
  T4                  17                 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                  N0  N1  N2  N3
  18P GAIN MUTATED    24  12   2   7
  18P GAIN WILD-TYPE 117  39  30  30
D31V7, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               24                117
  N1               12                 39
  N2                2                 30
  N3                7                 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
  18P GAIN MUTATED    41   0   2   0   1
  18P GAIN WILD-TYPE 211   4   0   2   4
D31V8, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                41                211
  M1                 0                  4
  M1A                2                  0
  M1B                0                  2
  M1C                1                  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"
D31V9, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   16 14
  18P GAIN WILD-TYPE 88 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     16   14
  18P GAIN WILD-TYPE   88   58
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                16                 88
  YES               14                 58
[1] 2 2
[1] FALSE
D31V10, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     6  42
  18P GAIN WILD-TYPE  28 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6   42
  18P GAIN WILD-TYPE   28  205
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 6                 28
  YES               42                205
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    22  26
  18P GAIN WILD-TYPE  86 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     22   26
  18P GAIN WILD-TYPE   86  147
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               22                 86
  MALE                 26                147
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       1                         0    47
  18P GAIN WILD-TYPE     4                         1   228
D31V13, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   47                228
[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
  18P GAIN MUTATED     1  47
  18P GAIN WILD-TYPE   2 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   47
  18P GAIN WILD-TYPE    2  227
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               47                227
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    20  16
  18Q GAIN WILD-TYPE 117 117
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                36                234 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                117 
$`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        45.11        61.38 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I1 
       80.22        17.72         8.84        11.31        35.80        39.19 
TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GM 
        8.12         1.08        12.03        39.39        47.21        28.31 
TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 TCGA-ER-A3PL TCGA-FR-A3YN 
        8.84        26.99        21.60        12.95         1.71        18.41 
TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZT TCGA-FS-A1ZU 
        6.71         3.45        23.80        20.38        40.64         8.68 
TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        3.22         7.23        84.72        16.24        12.16        14.70 

$`18Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       22.55        81.24        10.29        85.32         8.38        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       68.22        69.90        11.41        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
        6.31        92.42        64.44       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         5.39        42.71        15.09        41.10 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       20.48        13.94        95.38        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC 
        6.97        23.11         4.01         2.89         9.90        13.22 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       14.60        48.79        51.12        10.03        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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13         0.00         0.00        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        36.07         4.34         5.13         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        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        4.41        27.12         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 
        6.48         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         9.67         8.94        34.29        17.98        34.92 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       30.08        19.43        16.01        35.54        33.83        30.84 
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-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       111.78       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        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       18.61        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-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-FR-A44A 
       12.62        11.74         9.04         6.58        22.49        85.74 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        4.90         3.58         5.36        64.47        11.01        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         7.30         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-A1ZW TCGA-FS-A1ZY 
       52.08         8.65         8.81        49.15        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-GN-A262 TCGA-GN-A264 
        0.16         0.43         9.90        12.85        24.85        31.33 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       10.13        15.42        11.84        10.65        11.05         5.79 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.08               0.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             84.72             124.31 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            19.395             13.565 
[1] "1.1 - 84.7 (19.4)"  "0.0 - 124.3 (13.6)"
[1] "hr=" "1.2"
D32V2, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    21  16
  18Q GAIN WILD-TYPE 121 118
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                37                239 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                118 
$`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        45.11        86.93 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51N TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I1 
      161.85        18.38        10.03        25.18        36.03       194.83 
TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH 
        3.55        94.98         2.60        56.42        47.54       208.04 
TCGA-EE-A2GM TCGA-EE-A2M5 TCGA-EE-A2MP TCGA-EE-A3J5 TCGA-ER-A197 TCGA-ER-A3PL 
       75.48        21.67       248.65        36.95        13.94        33.21 
TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZC TCGA-FS-A1ZT 
       92.98       210.08        48.59       202.65       357.37        53.16 
TCGA-FS-A1ZU TCGA-FS-A4F2 TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       26.56        50.14         7.23        84.72        64.44        32.48 
TCGA-GN-A26D 
       39.58 

$`18Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
       31.59        95.74        43.43       103.10        65.49       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      168.00        69.90        11.87        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       12.10       171.58        66.08       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        21.47        43.69        40.14       131.90 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       51.68        15.06       110.93       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       11.34         3.25         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        45.11 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       35.01        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 
      109.64       151.27        78.87       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        39.62        72.07        32.19 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       44.35        18.61        37.35        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       39.29        58.75        67.43       314.56       135.95        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       101.95        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-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       144.76       203.05       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         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-A3JA 
      138.81       172.18       127.20        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       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-FR-A44A TCGA-FR-A69P 
       32.05       247.04        80.32        46.98       174.21         4.90 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.16         7.00       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-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-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      133.55        11.41       148.80        49.48        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-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        2.40         9.90        14.04       120.46       117.93        10.13 
TCGA-GN-A268 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        46.36        12.62       294.77         6.67 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              2.60               0.16 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            357.37             345.96 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             50.14              47.54 
[1] "2.6 - 357.4 (50.1)" "0.2 - 346.0 (47.5)"
[1] "hr=" "1.5"
D32V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q GAIN MUTATED                    5             1
  18Q GAIN WILD-TYPE                 32             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18Q GAIN MUTATED                                          10
  18Q GAIN WILD-TYPE                                        50
                    vv
clus                 REGIONAL LYMPH NODE
  18Q GAIN MUTATED                    22
  18Q GAIN WILD-TYPE                 157
D32V4, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       5                 32
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               10                 50
  REGIONAL LYMPH NODE                                     22                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
  18Q GAIN MUTATED             4       1       5        1        2        0
  18Q GAIN WILD-TYPE           6       5      18        9       23       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18Q GAIN MUTATED           0         0         6         5          2
  18Q GAIN WILD-TYPE        10        14         4        27         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED            4          5        2
  18Q GAIN WILD-TYPE         19         43       10
D32V5, multiclass
             clus
vv            18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  I OR II NOS                4                  6
  STAGE 0                    1                  5
  STAGE I                    5                 18
  STAGE IA                   1                  9
  STAGE IB                   2                 23
  STAGE II                   0                 17
  STAGE IIA                  0                 10
  STAGE IIB                  0                 14
  STAGE IIC                  6                  4
  STAGE III                  5                 27
  STAGE IIIA                 2                 12
  STAGE IIIB                 4                 19
  STAGE IIIC                 5                 43
  STAGE IV                   2                 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
  18Q GAIN MUTATED       7  9  2 13
  18Q GAIN WILD-TYPE    46 51 53 44
D32V6, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                7                 46
  T2                   9                 51
  T3                   2                 53
  T4                  13                 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                  N0  N1  N2  N3
  18Q GAIN MUTATED    21   9   1   6
  18Q GAIN WILD-TYPE 120  42  31  31
D32V7, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               21                120
  N1                9                 42
  N2                1                 31
  N3                6                 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
  18Q GAIN MUTATED    34   0   1   0   1
  18Q GAIN WILD-TYPE 218   4   1   2   4
D32V8, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                34                218
  M1                 0                  4
  M1A                1                  1
  M1B                0                  2
  M1C                1                  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"
D32V9, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED   12 11
  18Q GAIN WILD-TYPE 92 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     12   11
  18Q GAIN WILD-TYPE   92   61
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                12                 92
  YES               11                 61
[1] 2 2
[1] FALSE
D32V10, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     6  33
  18Q GAIN WILD-TYPE  28 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6   33
  18Q GAIN WILD-TYPE   28  214
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 6                 28
  YES               33                214
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    17  22
  18Q GAIN WILD-TYPE  91 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     17   22
  18Q GAIN WILD-TYPE   91  151
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               17                 91
  MALE                 22                151
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0    39
  18Q GAIN WILD-TYPE     5                         1   236
D32V13, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   39                236
[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
  18Q GAIN MUTATED     1  38
  18Q GAIN WILD-TYPE   2 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   38
  18Q GAIN WILD-TYPE    2  236
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               38                236
[1] 2 2
[1] FALSE

Clustering(33) Variable = 19P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    22  20
  19P GAIN WILD-TYPE 115 113
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                42                228 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                113 
$`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        69.90        64.44 
TCGA-D3-A2JP TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EE-A17Y TCGA-EE-A180 
       45.11        23.11         9.90        13.22        10.55         8.12 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2GH TCGA-EE-A2GO 
       38.63         1.08        12.03         8.84        47.21        30.84 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MM TCGA-EE-A3JI TCGA-ER-A199 
       13.02        98.27         2.70        56.02        33.60         5.72 
TCGA-ER-A19E TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1YX 
       11.90         1.87        12.62         1.71         6.71         3.45 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU 
       14.24        20.38         8.22        47.38        49.15         8.68 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GN-A266 TCGA-GN-A267 
        0.82         3.22        28.73         0.20        10.13        16.24 

$`19P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47         8.52       111.09       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       45.83        10.29        85.32         8.38        21.14        68.22 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        30.87         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19       114.67        15.25        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         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       17.72         8.84        20.48        13.94        95.38        52.01 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA 
       47.87         1.55         6.97         4.01         2.89        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-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         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.20        11.57         6.31         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        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
        4.41        27.12         9.50         8.09         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
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-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
        5.42         1.15        34.98        36.33         8.84         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        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       111.78       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 
       29.65        27.16        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         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         0.46        13.94        31.40        18.61        12.95 
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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       34.68         9.57        36.07        17.72        78.44        11.80 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
        1.51        13.08        11.74         9.04         6.58        22.49 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       18.41        85.74         4.90         3.58         5.36        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       11.01        23.80        15.52         7.33         7.30         3.39 
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-A1ZZ 
       52.08         8.65         8.81        40.64        27.39         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       53.85         7.36        14.20        10.78         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        7.23        12.85        24.85        31.33        84.72        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        14.70        11.84        10.65        11.05         5.79 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               0.2                0.0 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             98.27             124.31 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             13.12              14.38 
[1] "0.2 - 98.3 (13.1)"  "0.0 - 124.3 (14.4)"
[1] "hr=" "1.1"
D33V2, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    22  20
  19P GAIN WILD-TYPE 120 114
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                42                234 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                114 
$`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        69.90        66.08 
TCGA-D3-A2JP TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EE-A17Y TCGA-EE-A180 
       45.11       125.19         9.90        66.25        27.22        94.98 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2GH TCGA-EE-A2GO 
       39.62         2.60        56.42        14.47       208.04       101.95 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MM TCGA-EE-A3JI TCGA-ER-A199 
       55.59       129.27        28.83       167.90       148.08         9.17 
TCGA-ER-A19E TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A729 TCGA-FS-A1YX 
       13.02        23.34        31.27        33.21       210.08        48.59 
TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZU 
       20.91       357.37        53.52       101.26       148.80        26.56 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GN-A266 TCGA-GN-A267 
       27.09        50.14        28.73         0.20        10.13        64.44 

$`19P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.57        16.67       112.04       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        48.76       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19       130.72        58.06        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        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       18.38        10.03        51.68        15.06       110.93       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      137.92       166.19         7.43       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
        6.41        11.34         3.25        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        45.11        35.01         3.55        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       12.20        29.82         8.65        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       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        80.61        47.84        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       32.19        44.35        18.61        37.35        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
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-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
       13.91        14.30        44.88        94.82        21.67        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       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       144.76       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 
      103.56       136.47        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         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        33.40       101.79        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-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       148.18        79.99        43.82 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV 
       20.15        16.37        32.05       247.04        80.32        46.98 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       92.98       174.21         4.90        15.16         7.00       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        28.08         7.79        27.72        48.85 
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-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       74.73       133.55        11.41        53.16        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        66.67       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         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        7.23        14.04       120.46       117.93        84.72        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        39.58        46.36        12.62       294.77         6.67 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.20               0.16 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            357.37             345.96 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            54.555             47.460 
[1] "0.2 - 357.4 (54.6)" "0.2 - 346.0 (47.5)"
[1] "hr=" "1.1"
D33V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P GAIN MUTATED                    7             2
  19P GAIN WILD-TYPE                 30             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19P GAIN MUTATED                                          11
  19P GAIN WILD-TYPE                                        49
                    vv
clus                 REGIONAL LYMPH NODE
  19P GAIN MUTATED                    22
  19P GAIN WILD-TYPE                 157
D33V4, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  DISTANT METASTASIS                                       7                 30
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               11                 49
  REGIONAL LYMPH NODE                                     22                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
  19P GAIN MUTATED             2       0       6        0        4        3
  19P GAIN WILD-TYPE           8       6      17       10       21       14
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19P GAIN MUTATED           1         1         3         5          4
  19P GAIN WILD-TYPE         9        13         7        27         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED            2          7        3
  19P GAIN WILD-TYPE         21         41        9
D33V5, multiclass
             clus
vv            19P GAIN MUTATED 19P GAIN WILD-TYPE
  I OR II NOS                2                  8
  STAGE 0                    0                  6
  STAGE I                    6                 17
  STAGE IA                   0                 10
  STAGE IB                   4                 21
  STAGE II                   3                 14
  STAGE IIA                  1                  9
  STAGE IIB                  1                 13
  STAGE IIC                  3                  7
  STAGE III                  5                 27
  STAGE IIIA                 4                 10
  STAGE IIIB                 2                 21
  STAGE IIIC                 7                 41
  STAGE IV                   3                  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
  19P GAIN MUTATED       7 11 10  9
  19P GAIN WILD-TYPE    46 49 45 48
D33V6, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                7                 46
  T2                  11                 49
  T3                  10                 45
  T4                   9                 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
  19P GAIN MUTATED    24   8   3   6
  19P GAIN WILD-TYPE 117  43  29  31
D33V7, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               24                117
  N1                8                 43
  N2                3                 29
  N3                6                 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
  19P GAIN MUTATED    38   2   1   0   0
  19P GAIN WILD-TYPE 214   2   1   2   5
D33V8, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                38                214
  M1                 2                  2
  M1A                1                  1
  M1B                0                  2
  M1C                0                  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"
D33V9, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   16 12
  19P GAIN WILD-TYPE 88 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16   12
  19P GAIN WILD-TYPE   88   60
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                16                 88
  YES               12                 60
[1] 2 2
[1] FALSE
D33V10, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6  36
  19P GAIN WILD-TYPE  28 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6   36
  19P GAIN WILD-TYPE   28  211
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 6                 28
  YES               36                211
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    21  21
  19P GAIN WILD-TYPE  87 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     21   21
  19P GAIN WILD-TYPE   87  152
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               21                 87
  MALE                 21                152
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         0    41
  19P GAIN WILD-TYPE     4                         1   234
D33V13, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   41                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"
D33V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  41
  19P GAIN WILD-TYPE   3 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   41
  19P GAIN WILD-TYPE    3  233
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               41                233
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    22  21
  19Q GAIN WILD-TYPE 115 112
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                43                227 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                21                112 
$`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        69.90        64.44 
TCGA-D3-A2JP TCGA-D3-A3CE TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EE-A17Y TCGA-EE-A180 
       45.11        13.32         9.90        13.22        10.55         8.12 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2GD 
       38.63         1.08        12.03         8.84         6.48        17.98 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A3JI 
       47.21        30.84        13.02        98.27         2.70        33.60 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3PL 
       12.95         5.72        11.90        12.62         6.58         1.71 
TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        3.45        14.24        20.38         8.22        47.38         8.65 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GN-A266 
       49.15         8.68         0.82        28.73         0.20        10.13 
TCGA-GN-A267 
       16.24 

$`19Q GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
        8.52       111.09       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-A2JB 
       81.24        10.29        85.32         8.38        21.14        68.22 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.41        30.87         7.50        36.16         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19       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-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 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
        8.84        20.48        13.94        95.38        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA 
        1.55         6.97        23.11         4.01         2.89        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-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         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.20        11.57         6.31         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        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
        1.18         7.99         9.90        37.97        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
        4.41        27.12         9.50         8.09         9.99         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
        8.94        39.39        34.29        34.92        30.08        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-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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
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        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
       27.16        23.05         5.56       124.31       122.73        25.84 
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-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
        0.46        13.94        31.40        18.61        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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       13.08        11.74         9.04        22.49        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY 
        4.90         6.71         3.58         5.36        64.47        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE 
       23.80        15.52         7.33         7.30         3.39        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-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
        8.81        40.64        27.39         5.23        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        7.36        14.20        10.78         5.98         6.41         2.27 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.99         0.13         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A 
       12.85        24.85        31.33        84.72        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        10.65        11.05         5.79 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               0.2                0.0 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             98.27             124.31 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             13.02              14.60 
[1] "0.2 - 98.3 (13.0)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1"  
D34V2, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    22  21
  19Q GAIN WILD-TYPE 120 113
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                43                233 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                21                113 
$`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        69.90        66.08 
TCGA-D3-A2JP TCGA-D3-A3CE TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-EE-A17Y TCGA-EE-A180 
       45.11        60.23         9.90        66.25        27.22        94.98 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2GD 
       39.62         2.60        56.42        14.47       345.96       314.56 
TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A3JI 
      208.04       101.95        55.59       129.27        28.83       148.08 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3PL 
       13.94         9.17        13.02        31.27        80.32        33.21 
TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       48.59        20.91       357.37        53.52       101.26       133.55 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F5 TCGA-FW-A3I3 TCGA-GN-A266 
      148.80        26.56        27.09        28.73         0.20        10.13 
TCGA-GN-A267 
       64.44 

$`19Q GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.67       112.04       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-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL 
       11.87        48.76       113.52        42.08        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19       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-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 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       10.03        51.68        15.06       110.93       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
        6.41        11.34         3.25        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        45.11        35.01         3.55        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       12.20        29.82         8.65        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       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G 
       13.55        63.35        80.61        47.84        13.97        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       32.19        44.35        18.61        37.35        55.92        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       58.75        47.54        67.43       135.95        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48        90.97        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
      103.27       103.20        16.96       204.66        96.23       144.76 
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       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      136.47        41.59        53.26       124.31       122.73        25.84 
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-A3JD 
      127.20        36.95        64.08        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       33.40       101.79        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-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-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       16.37        32.05       247.04        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY 
        4.90       210.08        15.16         7.00       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZE 
      202.65        28.08         7.79        27.72        48.85        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-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       11.41        53.16        49.48        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-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A 
       14.04       120.46       117.93        84.72        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       39.58        46.36        12.62       294.77         6.67 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.20               0.16 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            357.37             294.77 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             55.59              47.54 
[1] "0.2 - 357.4 (55.6)" "0.2 - 294.8 (47.5)"
[1] "hr=" "1.2"
D34V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q GAIN MUTATED                    7             2
  19Q GAIN WILD-TYPE                 30             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19Q GAIN MUTATED                                          12
  19Q GAIN WILD-TYPE                                        48
                    vv
clus                 REGIONAL LYMPH NODE
  19Q GAIN MUTATED                    21
  19Q GAIN WILD-TYPE                 158
D34V4, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       7                 30
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               12                 48
  REGIONAL LYMPH NODE                                     21                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
  19Q GAIN MUTATED             3       0       4        0        3        3
  19Q GAIN WILD-TYPE           7       6      19       10       22       14
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19Q GAIN MUTATED           1         2         2         5          5
  19Q GAIN WILD-TYPE         9        12         8        27          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED            3          7        3
  19Q GAIN WILD-TYPE         20         41        9
D34V5, multiclass
             clus
vv            19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    0                  6
  STAGE I                    4                 19
  STAGE IA                   0                 10
  STAGE IB                   3                 22
  STAGE II                   3                 14
  STAGE IIA                  1                  9
  STAGE IIB                  2                 12
  STAGE IIC                  2                  8
  STAGE III                  5                 27
  STAGE IIIA                 5                  9
  STAGE IIIB                 3                 20
  STAGE IIIC                 7                 41
  STAGE IV                   3                  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
  19Q GAIN MUTATED       5 10 11 10
  19Q GAIN WILD-TYPE    48 50 44 47
D34V6, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                5                 48
  T2                  10                 50
  T3                  11                 44
  T4                  10                 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                  N0  N1  N2  N3
  19Q GAIN MUTATED    22  11   2   6
  19Q GAIN WILD-TYPE 119  40  30  31
D34V7, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               22                119
  N1               11                 40
  N2                2                 30
  N3                6                 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
  19Q GAIN MUTATED    39   2   1   0   0
  19Q GAIN WILD-TYPE 213   2   1   2   5
D34V8, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                39                213
  M1                 2                  2
  M1A                1                  1
  M1B                0                  2
  M1C                0                  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"
D34V9, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   14 13
  19Q GAIN WILD-TYPE 90 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     14   13
  19Q GAIN WILD-TYPE   90   59
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                14                 90
  YES               13                 59
[1] 2 2
[1] FALSE
D34V10, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     6  37
  19Q GAIN WILD-TYPE  28 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6   37
  19Q GAIN WILD-TYPE   28  210
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 6                 28
  YES               37                210
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    22  21
  19Q GAIN WILD-TYPE  86 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     22   21
  19Q GAIN WILD-TYPE   86  152
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               22                 86
  MALE                 21                152
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         0    42
  19Q GAIN WILD-TYPE     4                         1   233
D34V13, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   42                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"
D34V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0  42
  19Q GAIN WILD-TYPE   3 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   42
  19Q GAIN WILD-TYPE    3  232
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               42                232
[1] 2 2
[1] FALSE

Clustering(35) Variable = 20P GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   57 56
  20P GAIN WILD-TYPE 80 77
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               113                157 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                56                 77 
$`20P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JF 
       16.47        32.42        22.55        88.50        11.41        30.87 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR 
       36.16        56.19        15.25        82.29        13.32       103.59 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
        5.39        41.10        17.72        20.48        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        1.55        23.11         2.89         9.90        11.31        13.22 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A6L9 
       35.80        10.03        13.68        36.69        17.56         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        36.07         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         6.48         8.68         8.09        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        9.67         8.94        39.39        34.92        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        30.84         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        25.84        30.15         3.22        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19B 
       21.60        22.22        13.94        33.60         5.72        25.18 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
      114.15         4.21        13.45        28.60        34.68         9.57 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       11.80         1.87        22.49        18.41        85.74         4.90 
TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        6.71         3.45        23.80        15.52         7.33         7.30 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
       20.38         8.22         7.17        12.92        12.89        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 
        8.65        49.15         8.68         0.82         3.22        28.73 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       14.20         2.27         0.20        31.33        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        14.70        10.65        11.05         5.79 

$`20P GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.52       111.09        70.16       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       81.24        10.29        85.32         8.38        21.14        68.22 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
       69.90         7.50         6.31        92.42        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
      114.67        46.98        46.32        61.38        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N 
        9.34        26.37        80.22        42.71        15.09         8.84 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6EG TCGA-DA-A1HV 
       13.94        95.38         6.97         4.01        14.60        48.79 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
       51.12        39.19         9.99        44.52        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-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X 
        0.20         0.13         0.00         0.00        13.22        11.57 
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-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        5.13         1.18         9.90        37.97        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD 
        9.99         2.43        11.31        23.90        34.29        17.98 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       19.43        16.01        35.54         1.15        13.02        34.98 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51         9.53        29.46        44.25        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.78       111.91        56.02        25.08        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       27.16        23.05         3.68        13.81        15.95        12.72 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 
       22.92        16.14        27.35         0.46        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       12.95        38.40        76.41         3.78         3.52        11.90 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       11.11        34.88        42.84        36.07        17.72        78.44 
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-A3PL TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        1.71         3.58         5.36        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-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 
       40.64        27.39         5.23        53.85         7.36        10.78 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        5.98         6.41         0.99         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         7.23        12.85        24.85        84.72        10.13 
TCGA-GN-A4U8 
       11.84 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               0.2                0.0 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            124.31             114.67 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             14.20              13.94 
[1] "0.2 - 124.3 (14.2)" "0.0 - 114.7 (13.9)"
[1] "hr=" "1"  
D35V2, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   58 57
  20P GAIN WILD-TYPE 84 77
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               115                161 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                57                 77 
$`20P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JF 
       16.57       112.57        31.59       115.53        11.87        48.76 
TCGA-D3-A2JH TCGA-D3-A2JN TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR 
       42.08        56.19        58.06       166.52        60.23       103.59 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO 
       21.47       131.90        18.38        51.68       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
      166.19       125.19         6.41         3.25         9.90        25.18 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 
       66.25        36.03        20.38       176.55        61.18       215.44 
TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B 
        3.55        12.20        27.22        94.98        33.73       109.64 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W 
      168.26        63.35        13.97        14.47       345.96       171.55 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       17.92       102.90        39.29        58.75        47.54       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
      208.04        48.72        75.48        90.97       101.95        13.91 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH 
       94.82        21.67       129.27        28.83        19.76        16.96 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE 
      248.65        53.26       124.31       122.73        25.84        54.51 
TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
      172.18        36.95        64.08        53.19       101.79       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-A2NC TCGA-ER-A2ND TCGA-ER-A3EV TCGA-FR-A3YN 
      162.08        50.89        43.82        23.34        46.98        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 
      174.21         4.90       210.08        48.59       202.65        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        7.79        27.72       357.37        53.52         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY 
       23.93       101.26       133.55       148.80        26.56        27.09 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A264 
       50.14        28.73       174.84        77.88         0.20       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X 
       64.44        62.79        32.48        39.58        12.62       294.77 
TCGA-QB-A6FS 
        6.67 

$`20P GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP 
       69.90       113.52        12.10       171.58        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML 
      130.72        46.98        46.32        86.93        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N 
        9.34        39.75       161.85        43.69        40.14        10.03 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
       15.06       110.93         7.43       151.53        54.67         3.65 
TCGA-D9-A3Z1 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
       11.34        22.95        48.89       117.21       194.83        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
      107.34        53.92        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-A5SG 
       10.49        15.68        13.87        10.16        17.85        45.11 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       35.01        52.01         6.35        29.82         8.65        14.70 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       26.89        68.15         4.96       151.27        78.87        13.55 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       44.35        18.61        56.42        37.35        55.92        25.87 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK 
       46.82        24.43        67.43       314.56        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MC TCGA-EE-A2MD 
       79.66        14.30        55.59        44.88        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54        43.23       103.56       136.47        41.59 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 
        3.68        13.81        23.47       138.81       127.20        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       27.35        33.40        31.40        35.44        13.94        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-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF 
       44.05        37.25       148.18        79.99        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A7U8 
       31.27        32.05       247.04        80.32        33.21        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE 
        7.00       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         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 
       14.04       120.46        84.72        10.13        46.36 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.20               0.16 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            357.37             314.56 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             54.51              44.88 
[1] "0.2 - 357.4 (54.5)" "0.2 - 314.6 (44.9)"
[1] "hr=" "1.3"
D35V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P GAIN MUTATED                   18             3
  20P GAIN WILD-TYPE                 19             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20P GAIN MUTATED                                          25
  20P GAIN WILD-TYPE                                        35
                    vv
clus                 REGIONAL LYMPH NODE
  20P GAIN MUTATED                    73
  20P GAIN WILD-TYPE                 106
D35V4, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  DISTANT METASTASIS                                      18                 19
  PRIMARY TUMOR                                            3                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               25                 35
  REGIONAL LYMPH NODE                                     73                106
[1] 4 2
[1] 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             7       2      14        7       13        8
  20P GAIN WILD-TYPE           3       4       9        3       12        9
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20P GAIN MUTATED           3         2         4        15          6
  20P GAIN WILD-TYPE         7        12         6        17          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           10         16        3
  20P GAIN WILD-TYPE         13         32        9
D35V5, multiclass
             clus
vv            20P GAIN MUTATED 20P GAIN WILD-TYPE
  I OR II NOS                7                  3
  STAGE 0                    2                  4
  STAGE I                   14                  9
  STAGE IA                   7                  3
  STAGE IB                  13                 12
  STAGE II                   8                  9
  STAGE IIA                  3                  7
  STAGE IIB                  2                 12
  STAGE IIC                  4                  6
  STAGE III                 15                 17
  STAGE IIIA                 6                  8
  STAGE IIIB                10                 13
  STAGE IIIC                16                 32
  STAGE IV                   3                  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
  20P GAIN MUTATED      28 31 16 23
  20P GAIN WILD-TYPE    25 29 39 34
D35V6, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               28                 25
  T2                  31                 29
  T3                  16                 39
  T4                  23                 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
  20P GAIN MUTATED   68 24 10 12
  20P GAIN WILD-TYPE 73 27 22 25
D35V7, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               68                 73
  N1               24                 27
  N2               10                 22
  N3               12                 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
  20P GAIN MUTATED   112   2   1   0   0
  20P GAIN WILD-TYPE 140   2   1   2   5
D35V8, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               112                140
  M1                 2                  2
  M1A                1                  1
  M1B                0                  2
  M1C                0                  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"
D35V9, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   49 24
  20P GAIN WILD-TYPE 55 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     49   24
  20P GAIN WILD-TYPE   55   48
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                49                 55
  YES               24                 48
[1] 2 2
[1] FALSE
D35V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    12 107
  20P GAIN WILD-TYPE  22 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12  107
  20P GAIN WILD-TYPE   22  140
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                12                 22
  YES              107                140
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   45 74
  20P GAIN WILD-TYPE 63 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     45   74
  20P GAIN WILD-TYPE   63   99
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               45                 63
  MALE                 74                 99
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       2                         0   117
  20P GAIN WILD-TYPE     3                         1   158
D35V13, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  117                158
[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
  20P GAIN MUTATED     1 116
  20P GAIN WILD-TYPE   2 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1  116
  20P GAIN WILD-TYPE    2  158
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO              116                158
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   71 64
  20Q GAIN WILD-TYPE 66 69
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               135                135 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                64                 69 
$`20Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       16.47        32.42        22.55        88.50        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
       30.87        36.16        92.42        56.19        45.11        15.25 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J 
       82.29        13.32       103.59        26.37         5.39        41.10 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       17.72        20.48        52.01        47.87         1.55        23.11 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        2.89         9.90        11.31        13.22        48.79        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-EB-A5SH 
       10.03        13.68        36.69         4.93        17.56         0.00 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B 
        0.20        10.55         8.12        12.20         5.13        36.07 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P 
        9.21         7.99        11.15        38.63         1.08        12.03 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 
        8.84         6.48         8.68         8.09        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM 
        8.94        39.39        34.92        47.21        30.08        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       33.83        30.84         5.42        36.33         8.84        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MS 
        2.70         6.18        44.25         7.96        26.99        27.16 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH 
       15.95         3.22        21.60        21.60        22.22        13.94 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J 
       33.60        12.95         5.72        25.18       114.15         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NC 
       13.45        28.60        34.68         9.57        17.72        11.80 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        1.87        12.62        22.49         1.71        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        4.90         6.71         3.45        23.80        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        7.30        20.38         8.22         7.17        12.92        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
       47.38         8.65        49.15        40.64         8.68         0.82 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO 
        3.22        28.73        14.20         2.27         0.20         7.23 
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-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       10.65        11.05         5.79 

$`20Q GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.52       111.09        70.16       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       81.24        10.29        85.32         8.38        21.14        68.22 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
        7.50         6.31        64.44       114.67        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F 
       61.38        24.00         6.31         9.34        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D9-A3Z1 
       15.09         8.84        13.94        95.38         6.97         4.01 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       14.60        51.12        39.19         9.99        44.52        25.15 
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-A5SG TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z 
        0.20         0.13         0.00        13.22        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
        1.12         1.35         4.31         4.34         5.13         1.18 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
        9.90        37.97         8.55         4.41        27.12         9.50 
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        23.90        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-A2MI TCGA-EE-A2MJ 
       34.98        47.51         9.53        29.46        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.78       111.91        56.02        25.08        21.60        29.65 
TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD 
       23.05        13.81        12.72        22.92        16.14        27.35 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C 
        0.46        31.40        18.61        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-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       78.44         1.51        13.08        11.74         9.04         6.58 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB 
        3.58         5.36        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-A1ZW 
       19.53        11.08        30.87        52.08         8.81        27.39 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
        5.23        53.85         7.36        10.78         5.98         6.41 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 
        0.99         0.13         0.16         0.43         9.90        12.85 
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U8 
       24.85        10.13        11.84 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  0 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            124.31             114.67 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             14.70              13.81 
[1] "0.0 - 124.3 (14.7)" "0.0 - 114.7 (13.8)"
[1] "hr=" "1.1"
D36V2, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   73 65
  20Q GAIN WILD-TYPE 69 69
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               138                138 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                65                 69 
$`20Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       16.57       112.57        31.59       115.53        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 
       48.76        42.08       171.58        56.19        45.11        58.06 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J 
      166.52        60.23       103.59        39.75        21.47       131.90 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GU 
       18.38        51.68       135.75       137.92       166.19       125.19 
TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
      151.53         6.41         3.25         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA 
       48.89        36.03        20.38       176.55        61.18        65.92 
TCGA-DA-A3F5 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
      215.44        35.01         3.55        12.20        27.22        94.98 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D 
       26.89        68.15       109.64       168.26        63.35        13.97 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W 
       39.62         2.60        56.42        14.47       345.96       171.55 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       17.92       102.90        39.29        58.75        47.54       135.95 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
      208.04        48.72        75.48        90.97       101.95        13.91 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG 
       94.82        21.67       129.27        28.83        19.76       103.20 
TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       16.96       248.65       136.47        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J5 
       25.84         3.68        54.51        23.47       172.18        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 
       64.08        53.19       101.79       148.08        13.94         9.17 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       98.40       268.93         6.44       131.51        61.05       162.08 
TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3EV 
       50.89       148.18        43.82        23.34        31.27        46.98 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YX 
       33.21        92.98       174.21         4.90       210.08        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
      202.65        28.08         7.79        27.72       357.37        53.52 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        9.70        47.38        23.93       101.26       133.55       148.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 
       53.16        26.56        27.09        50.14        28.73       174.84 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       77.88         0.20         7.23       117.93        84.72        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        32.48        39.58        12.62       294.77         6.67 

$`20Q GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
      113.52        12.10        66.08       130.72        46.98        46.32 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F 
       86.93        24.53        13.87         9.34       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS TCGA-D9-A149 
       40.14        10.03        15.06       110.93         7.43        54.67 
TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
        3.65        11.34        22.95       117.21       194.83        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
      107.34        53.92        23.44        68.09        28.60        10.49 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5UN 
       15.68        13.87        10.16        17.85        45.11        52.01 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
        6.35        29.82         8.65        33.73        14.70         4.96 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29G 
      151.27        78.87        13.55        80.61        47.84        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       32.19        44.35        18.61        37.35        55.92        25.87 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GK 
       46.82        24.43        67.43       314.56        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2MC TCGA-EE-A2MD 
       79.66        14.30        55.59        44.88        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
      103.27       204.66        96.23       144.76       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AF TCGA-EE-A3AH 
       47.54        43.23       103.56        41.59        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 
      127.20        34.32        27.35        33.40        31.40        35.44 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       50.76        77.75        48.89        12.59        13.02        26.37 
TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF 
      152.35        44.05        37.25        79.99        20.15        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       32.05       247.04        80.32        15.16         7.00       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH 
      228.59        20.91        48.85        40.27        15.45        32.75 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       74.73        11.41        49.48        27.02        77.82        66.67 
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-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U8 
        2.40         9.90        14.04       120.46        10.13        46.36 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.20               0.16 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            357.37             314.56 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             53.39              44.20 
[1] "0.2 - 357.4 (53.4)" "0.2 - 314.6 (44.2)"
[1] "hr=" "1.3"
D36V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20Q GAIN MUTATED                   21             3
  20Q GAIN WILD-TYPE                 16             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20Q GAIN MUTATED                                          28
  20Q GAIN WILD-TYPE                                        32
                    vv
clus                 REGIONAL LYMPH NODE
  20Q GAIN MUTATED                    89
  20Q GAIN WILD-TYPE                  90
D36V4, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      21                 16
  PRIMARY TUMOR                                            3                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               28                 32
  REGIONAL LYMPH NODE                                     89                 90
[1] 4 2
[1] 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             8       3      15        7       14        8
  20Q GAIN WILD-TYPE           2       3       8        3       11        9
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20Q GAIN MUTATED           3         2         5        20          7
  20Q GAIN WILD-TYPE         7        12         5        12          7
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           14         19        4
  20Q GAIN WILD-TYPE          9         29        8
D36V5, multiclass
             clus
vv            20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  I OR II NOS                8                  2
  STAGE 0                    3                  3
  STAGE I                   15                  8
  STAGE IA                   7                  3
  STAGE IB                  14                 11
  STAGE II                   8                  9
  STAGE IIA                  3                  7
  STAGE IIB                  2                 12
  STAGE IIC                  5                  5
  STAGE III                 20                 12
  STAGE IIIA                 7                  7
  STAGE IIIB                14                  9
  STAGE IIIC                19                 29
  STAGE IV                   4                  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
  20Q GAIN MUTATED      33 35 20 27
  20Q GAIN WILD-TYPE    20 25 35 30
D36V6, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               33                 20
  T2                  35                 25
  T3                  20                 35
  T4                  27                 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                 N0 N1 N2 N3
  20Q GAIN MUTATED   75 29 14 16
  20Q GAIN WILD-TYPE 66 22 18 21
D36V7, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               75                 66
  N1               29                 22
  N2               14                 18
  N3               16                 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
  20Q GAIN MUTATED   130   2   2   1   0
  20Q GAIN WILD-TYPE 122   2   0   1   5
D36V8, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               130                122
  M1                 2                  2
  M1A                2                  0
  M1B                1                  1
  M1C                0                  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"
D36V9, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   56 30
  20Q GAIN WILD-TYPE 48 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     56   30
  20Q GAIN WILD-TYPE   48   42
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                56                 48
  YES               30                 42
[1] 2 2
[1] FALSE
D36V10, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    19 123
  20Q GAIN WILD-TYPE  15 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     19  123
  20Q GAIN WILD-TYPE   15  124
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                19                 15
  YES              123                124
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   54 88
  20Q GAIN WILD-TYPE 54 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     54   88
  20Q GAIN WILD-TYPE   54   85
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               54                 54
  MALE                 88                 85
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         0   140
  20Q GAIN WILD-TYPE     3                         1   135
D36V13, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  140                135
[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
  20Q GAIN MUTATED     1 139
  20Q GAIN WILD-TYPE   2 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1  139
  20Q GAIN WILD-TYPE    2  135
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO              139                135
[1] 2 2
[1] FALSE

Clustering(37) Variable = 21Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    29  21
  21Q GAIN WILD-TYPE 108 112
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                50                220 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                112 
$`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        30.87        45.11        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         5.39        52.01        23.11 
TCGA-D9-A6EC TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D 
       13.22         0.20         5.13         9.21         7.99        11.15 
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GH 
        1.08         8.84        11.31        49.22         9.67        47.21 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3J3 
       28.31        33.83        26.99        21.60       124.31         3.22 
TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A2NF 
       21.60        25.18         3.52        13.45        34.68        13.08 
TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       12.62         1.71        18.41        85.74         6.71         3.58 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-FW-A3I3 
       15.52         8.22        12.92        49.15         3.22         0.20 
TCGA-GF-A4EO TCGA-GN-A26D 
        7.23        14.70 

$`21Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       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-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        69.90        11.41         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       92.42        56.19        64.44       114.67        46.98        46.32 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       13.32        24.00         6.31         9.34        26.37        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 
       13.94        95.38        47.87         1.55         6.97         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        2.89         9.90        11.31        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-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00        13.22        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        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        4.34         5.13         1.18         9.90        37.97        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55         4.41        27.12         9.50        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 
        9.99         6.48         2.43         8.68         8.09        23.90 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
        8.94        39.39        34.29        17.98        34.92        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        30.84         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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       111.91        56.02        25.08 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
       29.65        27.16        23.05         5.56       122.73        25.84 
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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       21.60        16.14        22.22        27.35         0.46        13.94 
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-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       76.41         3.78        11.90        11.11       114.15        34.88 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
        4.21        28.60        42.84         9.57        36.07        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-FS-A1YW TCGA-FS-A1YX 
        6.58        22.49         4.90         5.36        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       11.01        23.80        14.24         7.33         7.30         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
       20.38        19.53        11.08         7.17        30.87        12.89 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
       47.38        52.08         8.65         8.81        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-A3R5 
       14.20        10.78         5.98         6.41         2.27         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
        0.13         0.16         0.43         9.90        12.85        24.85 
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-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        11.05         5.79 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               0.2                0.0 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            124.31             122.73 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            14.075             14.070 
[1] "0.2 - 124.3 (14.1)" "0.0 - 122.7 (14.1)"
[1] "hr=" "1.2"
D37V2, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    29  21
  21Q GAIN WILD-TYPE 113 113
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                50                226 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                113 
$`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        48.76        45.11        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        21.47       135.75       125.19 
TCGA-D9-A6EC TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D 
       66.25        12.20        68.15       168.26        63.35        13.97 
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GH 
        2.60        14.47        46.82       102.90        39.29       208.04 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3J3 
       75.48        90.97       248.65        43.23       124.31       172.18 
TCGA-EE-A3J7 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A2NF 
       64.08        98.40        12.59       131.51       162.08        16.37 
TCGA-ER-A2NG TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       31.27        33.21        92.98       174.21       210.08        15.16 
TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZJ TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-FW-A3I3 
       28.08        53.52        47.38       148.80        50.14         0.20 
TCGA-GF-A4EO TCGA-GN-A26D 
        7.23        39.58 

$`21Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       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-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        69.90        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
      171.58        56.19        66.08       130.72        46.98        46.32 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       60.23        24.53        13.87         9.34        39.75       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 
       15.06       110.93       137.92       166.19         7.43       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        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-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       15.68        13.87        10.16        17.85        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        3.55        52.01         6.35        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       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
      151.27        78.87        13.55        80.61        47.84        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19        44.35        18.61        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 
       55.92       345.96        25.87       171.55        17.92        24.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       58.75        47.54        67.43       314.56       135.95        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       89.33        54.74        79.66       101.95        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       203.05       167.90        47.54 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC 
      103.56       136.47        41.59        53.26       122.73        25.84 
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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        34.32        53.19        27.35        33.40       101.79 
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-A19C TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H 
       77.75        48.89        13.02        26.37       268.93       152.35 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
        6.44        61.05        44.05        50.89        37.25       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-FS-A1YW TCGA-FS-A1YX 
       80.32        46.98         4.90         7.00       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        20.91         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK 
      357.37        40.27        15.45         9.70        32.75        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26        74.73       133.55        11.41        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-A3R5 
      174.84        12.43        26.73        49.45        77.88        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
       47.54         0.16         2.40         9.90        14.04       120.46 
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-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.20               0.16 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            248.65             357.37 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            60.705             47.130 
[1] "0.2 - 248.7 (60.7)" "0.2 - 357.4 (47.1)"
[1] "hr=" "1.4"
D37V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q GAIN MUTATED                    7             2
  21Q GAIN WILD-TYPE                 30             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  21Q GAIN MUTATED                                          12
  21Q GAIN WILD-TYPE                                        48
                    vv
clus                 REGIONAL LYMPH NODE
  21Q GAIN MUTATED                    31
  21Q GAIN WILD-TYPE                 148
D37V4, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  DISTANT METASTASIS                                       7                 30
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               12                 48
  REGIONAL LYMPH NODE                                     31                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
  21Q GAIN MUTATED             3       0       8        1        8        2
  21Q GAIN WILD-TYPE           7       6      15        9       17       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  21Q GAIN MUTATED           3         0         5         2          3
  21Q GAIN WILD-TYPE         7        14         5        30         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED            2          9        2
  21Q GAIN WILD-TYPE         21         39       10
D37V5, multiclass
             clus
vv            21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    0                  6
  STAGE I                    8                 15
  STAGE IA                   1                  9
  STAGE IB                   8                 17
  STAGE II                   2                 15
  STAGE IIA                  3                  7
  STAGE IIB                  0                 14
  STAGE IIC                  5                  5
  STAGE III                  2                 30
  STAGE IIIA                 3                 11
  STAGE IIIB                 2                 21
  STAGE IIIC                 9                 39
  STAGE IV                   2                 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
  21Q GAIN MUTATED       8 18 10  9
  21Q GAIN WILD-TYPE    45 42 45 48
D37V6, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                8                 45
  T2                  18                 42
  T3                  10                 45
  T4                   9                 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
  21Q GAIN MUTATED    34   7   3   6
  21Q GAIN WILD-TYPE 107  44  29  31
D37V7, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               34                107
  N1                7                 44
  N2                3                 29
  N3                6                 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
  21Q GAIN MUTATED    47   1   1   0   0
  21Q GAIN WILD-TYPE 205   3   1   2   5
D37V8, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                47                205
  M1                 1                  3
  M1A                1                  1
  M1B                0                  2
  M1C                0                  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"
D37V9, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   16 18
  21Q GAIN WILD-TYPE 88 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     16   18
  21Q GAIN WILD-TYPE   88   54
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                16                 88
  YES               18                 54
[1] 2 2
[1] FALSE
D37V10, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     6  46
  21Q GAIN WILD-TYPE  28 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      6   46
  21Q GAIN WILD-TYPE   28  201
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 6                 28
  YES               46                201
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    21  31
  21Q GAIN WILD-TYPE  87 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     21   31
  21Q GAIN WILD-TYPE   87  142
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               21                 87
  MALE                 31                142
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       1                         0    51
  21Q GAIN WILD-TYPE     4                         1   224
D37V13, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   51                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"
D37V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  51
  21Q GAIN WILD-TYPE   3 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   51
  21Q GAIN WILD-TYPE    3  223
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               51                223
[1] 2 2
[1] FALSE

Clustering(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   55 44
  22Q GAIN WILD-TYPE 82 89
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                99                171 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                44                 89 
$`22Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JO TCGA-D3-A2JP 
       16.47        22.55        85.32        88.50        64.44        45.11 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV 
       15.25        61.38        13.32         9.34        26.37         5.39 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
       52.01         1.55         6.97         4.01         9.90        11.31 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 
       13.22        48.79        35.80        10.03        39.19        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5SG 
       25.15         4.93        22.36        17.56         0.13         0.00 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29L 
        0.00         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 
       27.12         9.50         8.09         8.84         8.68         8.09 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GN 
        9.67        39.39        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 
       30.84        98.27         2.70        63.42        21.60        29.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       27.16         5.56       124.31       122.73         3.68        30.15 
TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A19C TCGA-ER-A19G 
       15.95        21.60        21.60        27.35         3.78       114.15 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ET 
       13.45        28.60        17.72        13.08        12.62         6.58 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YY TCGA-FS-A1Z7 
       18.41        85.74         4.90         6.71        11.01         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS 
        7.30         8.22        30.87        47.38         8.65        49.15 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FD 
       40.64         8.68        27.39         3.22        28.73         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        0.20         0.13        31.33        84.72        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       12.16        14.70         5.79 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       45.83        81.24        10.29         8.38        21.14        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       92.42        56.19       114.67        46.98        46.32        82.29 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       24.00         6.31       103.59        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       41.10        17.72         8.84        20.48        13.94        95.38 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 
       47.87        23.11         2.89        14.60        51.12        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
        9.99        44.52         6.64        19.36         7.00        14.83 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       13.15         0.20        13.22        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        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        5.13         1.18         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T 
       38.63         8.55         4.41        12.03         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC 
        2.43        11.31        49.22        23.90         8.94        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP 
       17.98        34.92        19.43        16.01        35.54         5.42 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M8 
        1.15        13.02        34.98        36.33         8.84         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT 
      111.78       111.91        56.02        25.08        26.99        23.05 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       25.84        13.81        12.72         3.22        22.92        16.14 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       22.22         0.46        13.94        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-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P 
       11.90        11.11        34.88         4.21        42.84        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
        9.57        36.07        78.44        11.80         1.87         1.51 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7U9 
       11.74         9.04        22.49         1.71         3.58         5.36 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB 
       64.47         3.45        23.80        14.24        15.52         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       20.38        19.53        11.08         7.17        12.92        12.89 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       52.08         8.81         0.82         5.23        53.85         7.36 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV 
       14.20        10.78         5.98         6.41         0.99         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
        0.43         9.90         7.23        12.85        24.85        10.13 
TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       11.84        10.65        11.05 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.00               0.16 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            124.31             114.67 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             15.42              13.81 
[1] "0.0 - 124.3 (15.4)" "0.2 - 114.7 (13.8)"
[1] "hr=" "1.2"
D38V2, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   57 44
  22Q GAIN WILD-TYPE 85 90
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               101                175 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                44                 90 
$`22Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JO TCGA-D3-A2JP 
       16.57        31.59       103.10       115.53        66.08        45.11 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV 
       58.06        86.93        60.23         9.34        39.75        21.47 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A3Z1 TCGA-D9-A6E9 
      135.75       166.19         7.43       151.53        11.34         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 
       25.18        66.25        48.89        36.03        20.38       194.83 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EB-A5KH 
       61.18        53.92        65.92        23.44       215.44        17.85 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A180 
       45.11        35.01         3.55        12.20        27.22        94.98 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
      168.26         2.60        44.35        18.61        37.35        14.47 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GI 
      171.55        17.92        39.29        47.54       208.04        48.72 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MJ 
       75.48        90.97       101.95       129.27        28.83        96.23 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       103.56       136.47        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD 
        3.68        54.51        23.47        36.95        64.08        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         4.90       210.08 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM 
      228.59         7.79        27.72        53.52        32.75       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 
      133.55       148.80        53.16        26.56        49.48        50.14 
TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A265 
       28.73        77.88         0.20        47.54       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-QB-A6FS 
       64.44        62.79        32.48        39.58         6.67 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        95.74        43.43        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
      171.58        56.19       130.72        46.98        46.32       166.52 
TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       24.53        13.87       103.59       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      131.90        18.38        10.03        51.68        15.06       110.93 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 
      137.92       125.19        54.67         3.65         6.41         3.25 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC 
       22.95       117.21       176.55        35.93       107.34        68.09 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5UN 
       28.60        10.49        15.68        13.87        10.16        52.01 
TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        6.35        29.82         8.65        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       68.15         4.96       109.64       151.27        78.87        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        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 
       32.19        56.42        55.92       345.96        25.87        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
      102.90        24.43        58.75        67.43       314.56       135.95 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       89.33        54.74        79.66        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF 
      167.90        47.54       248.65        41.59        25.84        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE 
      138.81       172.18       127.20        34.32        53.19        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        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-A19H TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
      152.35         6.44        44.05       162.08        50.89        37.25 
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-A3EV TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
       46.98        33.21        15.16         7.00       216.92        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZE 
      202.65        20.91        28.08        48.85       357.37        40.27 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR 
       15.45         9.70        47.38        23.93        74.73        11.41 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        27.02        77.82        66.67       174.84        12.43 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       26.73        49.45        22.92         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A4U8 TCGA-GN-A4U9 
        7.23        14.04       120.46        10.13        46.36        12.62 
TCGA-OD-A75X 
      294.77 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.20               0.16 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            268.93             357.37 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             50.14              46.98 
[1] "0.2 - 268.9 (50.1)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.2"
D38V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q GAIN MUTATED                   11             4
  22Q GAIN WILD-TYPE                 26             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  22Q GAIN MUTATED                                          26
  22Q GAIN WILD-TYPE                                        34
                    vv
clus                 REGIONAL LYMPH NODE
  22Q GAIN MUTATED                    62
  22Q GAIN WILD-TYPE                 117
D38V4, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  DISTANT METASTASIS                                      11                 26
  PRIMARY TUMOR                                            4                  0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               26                 34
  REGIONAL LYMPH NODE                                     62                117
[1] 4 2
[1] 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       8        3        7        5
  22Q GAIN WILD-TYPE           7       4      15        7       18       12
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  22Q GAIN MUTATED           3         2         5        16          8
  22Q GAIN WILD-TYPE         7        12         5        16          6
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           10         19        4
  22Q GAIN WILD-TYPE         13         29        8
D38V5, multiclass
             clus
vv            22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    2                  4
  STAGE I                    8                 15
  STAGE IA                   3                  7
  STAGE IB                   7                 18
  STAGE II                   5                 12
  STAGE IIA                  3                  7
  STAGE IIB                  2                 12
  STAGE IIC                  5                  5
  STAGE III                 16                 16
  STAGE IIIA                 8                  6
  STAGE IIIB                10                 13
  STAGE IIIC                19                 29
  STAGE IV                   4                  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
  22Q GAIN MUTATED      22 26 17 20
  22Q GAIN WILD-TYPE    31 34 38 37
D38V6, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1               22                 31
  T2                  26                 34
  T3                  17                 38
  T4                  20                 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
  22Q GAIN MUTATED   42 23 14 17
  22Q GAIN WILD-TYPE 99 28 18 20
D38V7, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               42                 99
  N1               23                 28
  N2               14                 18
  N3               17                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B M1C
  22Q GAIN MUTATED    90   1   1   1   2
  22Q GAIN WILD-TYPE 162   3   1   1   3
D38V8, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                90                162
  M1                 1                  3
  M1A                1                  1
  M1B                1                  1
  M1C                2                  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"
D38V9, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   39 28
  22Q GAIN WILD-TYPE 65 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     39   28
  22Q GAIN WILD-TYPE   65   44
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                39                 65
  YES               28                 44
[1] 2 2
[1] FALSE
D38V10, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    14  89
  22Q GAIN WILD-TYPE  20 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     14   89
  22Q GAIN WILD-TYPE   20  158
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                14                 20
  YES               89                158
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    44  59
  22Q GAIN WILD-TYPE  64 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     44   59
  22Q GAIN WILD-TYPE   64  114
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               44                 64
  MALE                 59                114
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       3                         0   100
  22Q GAIN WILD-TYPE     2                         1   175
D38V13, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  100                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"
D38V14, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0 102
  22Q GAIN WILD-TYPE   3 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0  102
  22Q GAIN WILD-TYPE    3  172
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO              102                172
[1] 2 2
[1] FALSE

Clustering(39) Variable = XQ GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    13  17
  XQ GAIN WILD-TYPE 124 116
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               30               240 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               17               116 
$`XQ GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A3MV 
        8.52        88.50        69.90        13.32        26.37         5.39 
TCGA-DA-A3F3 TCGA-EB-A5KH TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A2GN 
        7.00         0.13         5.13         7.99         8.84        33.83 
TCGA-EE-A2MU TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2ND 
        5.56        15.95        21.60        28.60        11.80         1.87 
TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU 
       18.41         6.71         7.17        12.89        52.08         8.68 
TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
        0.82         2.27         0.16        31.33        15.42        14.70 

$`XQ GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       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-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        68.22        11.41        30.87         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        45.11       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       15.25        46.98        46.32        82.29        61.38        24.00 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        6.31         9.34       103.59        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       41.10        17.72         8.84        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        2.89         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-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       19.36        17.56        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00        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        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
        4.34         5.13         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        38.63         8.55         4.41         1.08        27.12 
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         6.48         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        8.94        39.39        34.29        17.98        34.92        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        30.84 
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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       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        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.05       124.31       122.73        25.84         3.68        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-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        13.45        42.84        34.68         9.57        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-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P 
        9.04         6.58        22.49         1.71        85.74         4.90 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        3.58         5.36        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         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         7.23        12.85        24.85        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       16.24        12.16        11.84        10.65        11.05         5.79 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.13              0.00 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            88.50            124.31 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            10.32             14.58 
[1] "0.1 - 88.5 (10.3)"  "0.0 - 124.3 (14.6)"
[1] "hr=" "1.6"
D39V2, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    13  17
  XQ GAIN WILD-TYPE 129 117
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               30               246 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               17               117 
$`XQ GAIN MUTATED`
TCGA-D3-A1Q3 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A3CE TCGA-D3-A3MU TCGA-D3-A3MV 
       16.67       115.53        69.90        60.23        39.75        21.47 
TCGA-DA-A3F3 TCGA-EB-A5KH TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A2GN 
       10.49        17.85        68.15        63.35        14.47        90.97 
TCGA-EE-A2MU TCGA-EE-A3AG TCGA-EE-A3J7 TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2ND 
       53.26        23.47        64.08        61.05        43.82        23.34 
TCGA-FR-A3YN TCGA-FR-A729 TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZU 
       92.98       210.08         9.70        23.93        74.73        26.56 
TCGA-FS-A1ZY TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
       27.09        77.88         0.16       117.93        62.79        39.58 

$`XQ GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       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-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       168.00        11.87        48.76       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        45.11       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF 
       58.06        46.98        46.32       166.52        86.93        24.53 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.87         9.34       103.59       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      131.90        18.38        10.03        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         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        45.11        35.01         3.55 
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       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
      151.27        78.87       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        39.62        72.07        32.19         2.60        44.35 
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       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       58.75        47.54        67.43       314.56       135.95       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       101.95 
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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       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       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       41.59       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       13.81       138.81       172.18       127.20        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       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-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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
        6.44       131.51        44.05       162.08        50.89        37.25 
TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
      148.18        79.99        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P 
      247.04        80.32        46.98        33.21       174.21         4.90 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       15.16         7.00       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         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         7.23        14.04       120.46        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       64.44        32.48        46.36        12.62       294.77         6.67 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.16              0.20 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           210.08            357.37 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            48.54             47.69 
[1] "0.2 - 210.1 (48.5)" "0.2 - 357.4 (47.7)"
[1] "hr=" "1.5"
D39V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ GAIN MUTATED                    7             0
  XQ GAIN WILD-TYPE                 30             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  XQ GAIN MUTATED                                           7
  XQ GAIN WILD-TYPE                                        53
                   vv
clus                REGIONAL LYMPH NODE
  XQ GAIN MUTATED                    17
  XQ GAIN WILD-TYPE                 162
D39V4, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  DISTANT METASTASIS                                      7                30
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               7                53
  REGIONAL LYMPH NODE                                    17               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
  XQ GAIN MUTATED             0       1       2        1        4        2
  XQ GAIN WILD-TYPE          10       5      21        9       21       15
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XQ GAIN MUTATED           1         2         3         5          3
  XQ GAIN WILD-TYPE         9        12         7        27         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED            2          4        0
  XQ GAIN WILD-TYPE         21         44       12
D39V5, multiclass
             clus
vv            XQ GAIN MUTATED XQ GAIN WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   1                 5
  STAGE I                   2                21
  STAGE IA                  1                 9
  STAGE IB                  4                21
  STAGE II                  2                15
  STAGE IIA                 1                 9
  STAGE IIB                 2                12
  STAGE IIC                 3                 7
  STAGE III                 5                27
  STAGE IIIA                3                11
  STAGE IIIB                2                21
  STAGE IIIC                4                44
  STAGE IV                  0                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
  XQ GAIN MUTATED       9  9  5  6
  XQ GAIN WILD-TYPE    44 51 50 51
D39V6, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1               9                44
  T2                  9                51
  T3                  5                50
  T4                  6                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
  XQ GAIN MUTATED    16   5   7   2
  XQ GAIN WILD-TYPE 125  46  25  35
D39V7, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              16               125
  N1               5                46
  N2               7                25
  N3               2                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
  XQ GAIN MUTATED    29   0   0   0   0
  XQ GAIN WILD-TYPE 223   4   2   2   5
D39V8, multiclass
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               29               223
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 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
  XQ GAIN MUTATED   12  9
  XQ GAIN WILD-TYPE 92 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     12    9
  XQ GAIN WILD-TYPE   92   63
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               12                92
  YES               9                63
[1] 2 2
[1] FALSE
D39V10, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     4  27
  XQ GAIN WILD-TYPE  30 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4   27
  XQ GAIN WILD-TYPE   30  220
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                4                30
  YES              27               220
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    11  20
  XQ GAIN WILD-TYPE  97 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     11   20
  XQ GAIN WILD-TYPE   97  153
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              11                97
  MALE                20               153
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       1                         0    30
  XQ GAIN WILD-TYPE     4                         1   245
D39V13, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  30               245
[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
  XQ GAIN MUTATED     0  30
  XQ GAIN WILD-TYPE   3 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   30
  XQ GAIN WILD-TYPE    3  244
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              30               244
[1] 2 2
[1] FALSE

Clustering(40) Variable = 1P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    24  12
  1P LOSS WILD-TYPE 113 121
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               36               234 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12               121 
$`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         5.39        52.01         1.55 
TCGA-D3-A5GS TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R 
        6.97        13.68        36.69        17.56        14.83         0.20 
TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GR 
        9.21         8.84        34.92        47.21        30.84         1.15 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-ER-A19C 
      111.78        26.99        27.16         3.68         3.22         3.78 
TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A69P 
       13.45         1.87        12.62        11.74        22.49         4.90 
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 

$`1P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52        32.42        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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
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-A51E 
       24.00         6.31         9.34       103.59        26.37        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.94        95.38        47.87        23.11         4.01         2.89 
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-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-EB-A44Q 
        4.93        22.36         6.64        19.36         7.00        13.15 
TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13         0.00         0.00        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-A20I 
        5.13         4.31        36.07         4.34         5.13         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        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         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         6.48         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       17.98        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       33.83         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-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        29.65        23.05         5.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84        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-A3JD 
       22.92        21.60        21.60        16.14        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        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-A19M TCGA-ER-A19N 
       11.11       114.15        34.88         4.21        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-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
        1.51        13.08         9.04         6.58         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
       85.74         6.71         3.58         5.36        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
       11.01        23.80        14.24        15.52         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-A1ZQ TCGA-FS-A1ZR 
       12.92        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       49.15         8.68         0.82         5.23        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
        7.36        28.73        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.99         0.13         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       15.42        12.16        11.84        10.65        11.05         5.79 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.16              0.00 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           111.78            124.31 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            13.94             14.09 
[1] "0.2 - 111.8 (13.9)" "0.0 - 124.3 (14.1)"
[1] "hr=" "1.4"
D40V2, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    24  12
  1P LOSS WILD-TYPE 118 122
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               36               240 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12               122 
$`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        21.47       135.75       166.19 
TCGA-D3-A5GS TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R 
        7.43       176.55        61.18       215.44        15.68        10.16 
TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GR 
      168.26        14.47       135.95       208.04       101.95        14.30 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-ER-A19C 
      144.76       248.65       136.47         3.68       172.18        48.89 
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         4.90 
TCGA-FS-A1Z7 TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-GN-A26D 
        7.79        53.16        49.48       174.84         0.16        39.58 

$`1P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.57        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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
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-A51E 
       24.53        13.87         9.34       103.59        39.75       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
       15.06       110.93       137.92       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        3.65         6.41        11.34         3.25         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-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-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       68.09        28.60        10.49        13.87        17.85        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       35.01         3.55        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-A20I 
       68.15         4.96       109.64       151.27        78.87        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        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       32.19         2.60        44.35        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       345.96        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      314.56        48.72        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       90.97        13.91        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      103.20        16.96       204.66        96.23       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54        43.23       103.56        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      122.73        25.84        54.51        13.81        23.47       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
      127.20        36.95        64.08        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       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-A19M TCGA-ER-A19N 
       26.37       268.93       152.35         6.44        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-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       20.15        16.37       247.04        80.32        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
      174.21       210.08        15.16         7.00       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        20.91        28.08        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-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-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
      148.80        26.56        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-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        22.92        47.54         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       14.04       120.46       117.93        84.72        10.13        64.44 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        32.48        46.36        12.62       294.77         6.67 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.16              0.20 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           248.65            357.37 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            51.32             47.54 
[1] "0.2 - 248.7 (51.3)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.9"
D40V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P LOSS MUTATED                    4             0
  1P LOSS WILD-TYPE                 33             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1P LOSS MUTATED                                           6
  1P LOSS WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  1P LOSS MUTATED                    26
  1P LOSS WILD-TYPE                 153
D40V4, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  DISTANT METASTASIS                                      4                33
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               6                54
  REGIONAL LYMPH NODE                                    26               153
[1] 4 2
[1] 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        1        3
  1P LOSS WILD-TYPE          10       6      16       10       24       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1P LOSS MUTATED           0         0         2         6          0
  1P LOSS WILD-TYPE        10        14         8        26         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED            6          9        1
  1P LOSS WILD-TYPE         17         39       11
D40V5, multiclass
             clus
vv            1P LOSS MUTATED 1P LOSS WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   7                16
  STAGE IA                  0                10
  STAGE IB                  1                24
  STAGE II                  3                14
  STAGE IIA                 0                10
  STAGE IIB                 0                14
  STAGE IIC                 2                 8
  STAGE III                 6                26
  STAGE IIIA                0                14
  STAGE IIIB                6                17
  STAGE IIIC                9                39
  STAGE IV                  1                11
[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 11  4  9
  1P LOSS WILD-TYPE    44 49 51 48
D40V6, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               9                44
  T2                 11                49
  T3                  4                51
  T4                  9                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
  1P LOSS MUTATED    14   8   7   5
  1P LOSS WILD-TYPE 127  43  25  32
D40V7, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              14               127
  N1               8                43
  N2               7                25
  N3               5                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
  1P LOSS MUTATED    32   0   0   0   1
  1P LOSS WILD-TYPE 220   4   2   2   4
D40V8, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               32               220
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               1                 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"
D40V9, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    9 10
  1P LOSS WILD-TYPE 95 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      9   10
  1P LOSS WILD-TYPE   95   62
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                9                95
  YES              10                62
[1] 2 2
[1] FALSE
D40V10, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3  33
  1P LOSS WILD-TYPE  31 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3   33
  1P LOSS WILD-TYPE   31  214
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3                31
  YES              33               214
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    14  22
  1P LOSS WILD-TYPE  94 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     14   22
  1P LOSS WILD-TYPE   94  151
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              14                94
  MALE                22               151
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         0    35
  1P LOSS WILD-TYPE     4                         1   240
D40V13, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  35               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"
D40V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  36
  1P LOSS WILD-TYPE   3 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   36
  1P LOSS WILD-TYPE    3  238
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              36               238
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    10  10
  1Q LOSS WILD-TYPE 127 123
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               250 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               123 
$`1Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A5GR TCGA-D3-A5GS TCGA-DA-A1I2 TCGA-DA-A1I8 
       22.55        61.38         1.55         6.97        13.68        25.15 
TCGA-DA-A3F8 TCGA-EE-A20H TCGA-EE-A29X TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2MP 
       14.83         9.21         8.09        30.84        98.27        26.99 
TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A69P 
        3.22        31.40         3.78        12.62        22.49         4.90 
TCGA-FR-A7U9 TCGA-FS-A4F8 
        5.36        14.20 

$`1Q 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-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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       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 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
        8.84        20.48        13.94        95.38        52.01        47.87 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         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-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-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       19.36         7.00        17.56        13.15         0.20         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.00         0.00        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        36.07         4.34         5.13         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        38.63         8.55         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.50        12.03         8.09         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         6.48         2.43         8.68        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       23.90         9.67         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83         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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
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        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 
       30.15        13.81        15.95        12.72        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         0.46        13.94 
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-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-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-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        17.72        78.44        11.80         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       13.08        11.74         9.04         6.58         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       85.74         6.71         3.58        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-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-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 
        0.43         9.90         7.23        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        11.05         5.79 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.55              0.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            98.27            124.31 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            13.94             14.09 
[1] "1.6 - 98.3 (13.9)"  "0.0 - 124.3 (14.1)"
[1] "hr=" "1.2"
D41V2, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    10  10
  1Q LOSS WILD-TYPE 132 124
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               256 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               124 
$`1Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A5GR TCGA-D3-A5GS TCGA-DA-A1I2 TCGA-DA-A1I8 
       31.59        86.93       166.19         7.43       176.55        53.92 
TCGA-DA-A3F8 TCGA-EE-A20H TCGA-EE-A29X TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2MP 
       15.68       168.26        17.92       101.95       129.27       248.65 
TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A19C TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A69P 
      172.18        31.40        48.89        31.27        46.98         4.90 
TCGA-FR-A7U9 TCGA-FS-A4F8 
        7.00       174.84 

$`1Q 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-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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       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 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       10.03        51.68        15.06       110.93       135.75       137.92 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        3.25         9.90        25.18        66.25        22.95        48.89 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.21        20.38       194.83        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-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
      215.44        13.87        10.16        17.85        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.55        52.01         6.35        12.20        29.82        27.22 
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-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A 
        4.96       109.64       151.27        78.87        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        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92       345.96        25.87       171.55        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       75.48        90.97        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82        21.67        28.83        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       144.76 
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       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       64.08        34.32        53.19        27.35        33.40       101.79 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      148.08        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-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-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       16.37        32.05       247.04        80.32        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
      174.21       210.08        15.16       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-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-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-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             4.90              0.16 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           248.65            357.37 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           51.405            47.540 
[1] "4.9 - 248.7 (51.4)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.2"
D41V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q LOSS MUTATED                    2             0
  1Q LOSS WILD-TYPE                 35             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  1Q LOSS MUTATED                                           4
  1Q LOSS WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  1Q LOSS MUTATED                    14
  1Q LOSS WILD-TYPE                 165
D41V4, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      2                35
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                56
  REGIONAL LYMPH NODE                                    14               165
[1] 4 2
[1] 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          10       6      18       10       23       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  1Q LOSS MUTATED           0         1         1         2          0
  1Q LOSS WILD-TYPE        10        13         9        30         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED            2          5        1
  1Q LOSS WILD-TYPE         21         43       11
D41V5, multiclass
             clus
vv            1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   5                18
  STAGE IA                  0                10
  STAGE IB                  2                23
  STAGE II                  1                16
  STAGE IIA                 0                10
  STAGE IIB                 1                13
  STAGE IIC                 1                 9
  STAGE III                 2                30
  STAGE IIIA                0                14
  STAGE IIIB                2                21
  STAGE IIIC                5                43
  STAGE IV                  1                11
[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       4  6  4  5
  1Q LOSS WILD-TYPE    49 54 51 52
D41V6, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               4                49
  T2                  6                54
  T3                  4                51
  T4                  5                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
  1Q LOSS MUTATED    10   2   3   4
  1Q LOSS WILD-TYPE 131  49  29  33
D41V7, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              10               131
  N1               2                49
  N2               3                29
  N3               4                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
  1Q LOSS MUTATED    18   0   0   0   1
  1Q LOSS WILD-TYPE 234   4   2   2   4
D41V8, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               18               234
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               1                 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"
D41V9, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    7  6
  1Q LOSS WILD-TYPE 97 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      7    6
  1Q LOSS WILD-TYPE   97   66
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                7                97
  YES               6                66
[1] 2 2
[1] FALSE
D41V10, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  19
  1Q LOSS WILD-TYPE  33 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   19
  1Q LOSS WILD-TYPE   33  228
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                1                33
  YES              19               228
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9  11
  1Q LOSS WILD-TYPE  99 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   11
  1Q LOSS WILD-TYPE   99  162
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               9                99
  MALE                11               162
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0    20
  1Q LOSS WILD-TYPE     5                         1   255
D41V13, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  20               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"
D41V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  20
  1Q LOSS WILD-TYPE   3 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   20
  1Q LOSS WILD-TYPE    3  254
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              20               254
[1] 2 2
[1] FALSE

Clustering(42) Variable = 2P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    18  17
  2P LOSS WILD-TYPE 119 116
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               35               235 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               116 
$`2P LOSS MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
       69.90         7.50        15.25        24.00       103.59        26.37 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1I2 TCGA-EE-A180 
       13.94        47.87         2.89        11.31        13.68         8.12 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH 
       36.07         5.13         1.18        12.03        34.29        47.21 
TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3J3 
        1.15        63.42       111.78        27.16         3.68         3.22 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A3PL TCGA-FS-A1YW 
       22.22         0.46         3.78        34.68         1.71        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D 
       11.01        23.80        31.33        16.24        14.70 

$`2P 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-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-A2JD TCGA-D3-A2JF 
        8.38        21.14        88.50        68.22        11.41        30.87 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       36.16         6.31        92.42        56.19        64.44        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
        6.31         9.34         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
       41.10        17.72         8.84        20.48        95.38        52.01 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC 
        1.55         6.97        23.11         4.01         9.90        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-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-A5UN TCGA-EB-A6L9 
        0.20         0.13         0.00         0.00        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-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
        5.13         4.31         4.34         9.21         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        38.63         8.55         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       27.12         9.50         8.09         8.84         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
        9.67         8.94        39.39        17.98        34.92        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        30.84 
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-A2MG 
        2.70         6.18        47.51         9.53        29.46        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        29.65        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       25.84        30.15        13.81        15.95        12.72        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        21.60        16.14        27.35        13.94        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-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A19S 
        4.21        13.45        28.60        42.84         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-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       12.62        11.74         9.04         6.58        22.49        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YX 
       85.74         4.90         6.71         3.58         5.36         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-GN-A262 TCGA-GN-A265 
        0.43         9.90         7.23        12.85        24.85        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       10.13        15.42        12.16        11.84        10.65        11.05 
TCGA-QB-A6FS 
        5.79 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.46              0.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           111.78            124.31 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            15.25             13.81 
[1] "0.5 - 111.8 (15.2)" "0.0 - 124.3 (13.8)"
[1] "hr=" "1"  
D42V2, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    19  17
  2P LOSS WILD-TYPE 123 117
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               36               240 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               117 
$`2P LOSS MUTATED`
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A3MU 
       69.90       113.52        58.06        24.53       103.59        39.75 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1I2 
       15.06       137.92        54.67         3.25        25.18       176.55 
TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29P TCGA-EE-A2GC 
       94.98       109.64        78.87        13.55        56.42        67.43 
TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AD 
      208.04        14.30        96.23       144.76       136.47         3.68 
TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A3PL 
      172.18        53.19        33.40        48.89       162.08        33.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D 
      216.92       228.59       202.65       117.93        64.44        39.58 

$`2P 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-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-A2JD TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        11.87        48.76 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        56.19        66.08        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       13.87         9.34        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN 
      131.90        18.38        10.03        51.68       110.93       135.75 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
      166.19         7.43       125.19       151.53         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       11.34         9.90        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-A1I7 
      117.21        20.38       194.83        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        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       35.01         3.55        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-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        4.96       151.27       168.26        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        39.62        72.07        32.19         2.60        44.35 
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       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ 
       58.75        47.54       314.56       135.95        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       101.95        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-A2MG TCGA-EE-A2MH 
       19.76        61.51        47.28       103.27       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 
      103.56        41.59        53.26       124.31       122.73        25.84 
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-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       64.08        34.32        27.35       101.79       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-A19W 
      131.51        61.05        44.05        50.89        37.25       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-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z3 
        4.90       210.08        15.16         7.00        48.59        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-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-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         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        9.90         7.23        14.04       120.46        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        32.48        46.36        12.62       294.77         6.67 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             3.25              0.16 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           228.59            357.37 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           68.665            46.900 
[1] "3.2 - 228.6 (68.7)" "0.2 - 357.4 (46.9)"
[1] "hr=" "1.4"
D42V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P LOSS MUTATED                    4             1
  2P LOSS WILD-TYPE                 33             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2P LOSS MUTATED                                           8
  2P LOSS WILD-TYPE                                        52
                   vv
clus                REGIONAL LYMPH NODE
  2P LOSS MUTATED                    23
  2P LOSS WILD-TYPE                 156
D42V4, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  DISTANT METASTASIS                                      4                33
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               8                52
  REGIONAL LYMPH NODE                                    23               156
[1] 4 2
[1] 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             0       0       3        1        4        4
  2P LOSS WILD-TYPE          10       6      20        9       21       13
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2P LOSS MUTATED           1         1         2         6          3
  2P LOSS WILD-TYPE         9        13         8        26         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED            2          4        2
  2P LOSS WILD-TYPE         21         44       10
D42V5, multiclass
             clus
vv            2P LOSS MUTATED 2P LOSS WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   3                20
  STAGE IA                  1                 9
  STAGE IB                  4                21
  STAGE II                  4                13
  STAGE IIA                 1                 9
  STAGE IIB                 1                13
  STAGE IIC                 2                 8
  STAGE III                 6                26
  STAGE IIIA                3                11
  STAGE IIIB                2                21
  STAGE IIIC                4                44
  STAGE IV                  2                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
  2P LOSS MUTATED       6  5  9 12
  2P LOSS WILD-TYPE    47 55 46 45
D42V6, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               6                47
  T2                  5                55
  T3                  9                46
  T4                 12                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
  2P LOSS MUTATED    21   8   3   2
  2P LOSS WILD-TYPE 120  43  29  35
D42V7, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              21               120
  N1               8                43
  N2               3                29
  N3               2                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
  2P LOSS MUTATED    32   0   1   0   1
  2P LOSS WILD-TYPE 220   4   1   2   4
D42V8, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               32               220
  M1                0                 4
  M1A               1                 1
  M1B               0                 2
  M1C               1                 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"
D42V9, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   17  9
  2P LOSS WILD-TYPE 87 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     17    9
  2P LOSS WILD-TYPE   87   63
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               17                87
  YES               9                63
[1] 2 2
[1] FALSE
D42V10, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3  33
  2P LOSS WILD-TYPE  31 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   33
  2P LOSS WILD-TYPE   31  214
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                3                31
  YES              33               214
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    14  22
  2P LOSS WILD-TYPE  94 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     14   22
  2P LOSS WILD-TYPE   94  151
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              14                94
  MALE                22               151
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0    36
  2P LOSS WILD-TYPE     5                         1   239
D42V13, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  36               239
[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
  2P LOSS MUTATED     0  36
  2P LOSS WILD-TYPE   3 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   36
  2P LOSS WILD-TYPE    3  238
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              36               238
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    15  19
  2Q LOSS WILD-TYPE 122 114
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               34               236 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               19               114 
$`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        13.94 
TCGA-D9-A6EA TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I 
       11.31         8.12        36.07         4.34         5.13         1.18 
TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GR TCGA-EE-A2MJ 
       11.15        12.03        34.29        47.21         1.15        63.42 
TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3JA TCGA-EE-A3JE 
      111.78        27.16        13.81         3.22        22.22         0.46 
TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1YY 
        3.78        34.68         1.87         1.71        64.47        11.01 
TCGA-FS-A1Z0 TCGA-FS-A1ZQ TCGA-GN-A267 TCGA-GN-A26D 
       23.80         8.65        16.24        14.70 

$`2Q 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-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        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87        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 
       45.11       114.67        46.98        46.32        82.29        61.38 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       13.32         6.31         9.34         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL 
       15.09        41.10        17.72         8.84        20.48        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
        2.89         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-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 
        0.00         0.00        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-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        9.21         7.99         9.90        37.97        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
        4.41         1.08        27.12         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         6.48         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        23.90         9.67         8.94        39.39        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83        30.84         5.42        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM 
       29.46        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        29.65        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG 
      124.31       122.73        25.84         3.68        30.15        15.95 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD 
       12.72        22.92        21.60        21.60        16.14        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        33.60        31.40        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-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE 
        9.57        36.07        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-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74         4.90         6.71         3.58         5.36 
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-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
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-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.46              0.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           111.78            124.31 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           13.875            14.220 
[1] "0.5 - 111.8 (13.9)" "0.0 - 124.3 (14.2)"
[1] "hr=" "1.3"
D43V2, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    17  19
  2Q LOSS WILD-TYPE 125 115
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               36               240 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               19               115 
$`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        15.06 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A6EA TCGA-EE-A180 TCGA-EE-A20B TCGA-EE-A20C 
      151.53        54.67        25.18        94.98       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH 
       78.87        13.55        13.97        56.42        67.43       208.04 
TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MS TCGA-EE-A3AF TCGA-EE-A3J3 
       14.30        96.23       144.76       136.47        13.81       172.18 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A2ND TCGA-ER-A3PL 
       53.19        33.40        48.89       162.08        23.34        33.21 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZQ TCGA-GN-A267 TCGA-GN-A26D 
      216.92       228.59       202.65       133.55        64.44        39.58 

$`2Q 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-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        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76        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 
       45.11       130.72        46.98        46.32       166.52        86.93 
TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F 
       60.23        13.87         9.34        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL 
       40.14       131.90        18.38        10.03        51.68       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A1JW 
      135.75       137.92       166.19         7.43       125.19         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        6.41        11.34         3.25         9.90        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        45.11        35.01         3.55        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-A20H TCGA-EE-A29A 
       14.70        26.89        68.15         4.96       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       80.61        47.84        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       44.35        18.61        37.35        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       39.29        58.75        47.54       314.56       135.95        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       101.95 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       13.91        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-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       16.96       204.66       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       43.23       103.56        41.59        53.26       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       25.84         3.68        54.51        23.47       138.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI 
       36.95        64.08        34.32        27.35       101.79       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-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-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z3 
        4.90       210.08        15.16         7.00        48.59        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-A1ZK 
       40.27        15.45         9.70        32.75        47.38        23.93 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      101.26        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-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         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       117.93        84.72        10.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        32.48        46.36        12.62       294.77         6.67 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            13.55              0.16 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           228.59            357.37 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           65.935            46.980 
[1] "13.6 - 228.6 (65.9)" "0.2 - 357.4 (47.0)" 
[1] "hr=" "1.2"
D43V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q LOSS MUTATED                    6             1
  2Q LOSS WILD-TYPE                 31             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  2Q LOSS MUTATED                                           8
  2Q LOSS WILD-TYPE                                        52
                   vv
clus                REGIONAL LYMPH NODE
  2Q LOSS MUTATED                    21
  2Q LOSS WILD-TYPE                 158
D43V4, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      6                31
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               8                52
  REGIONAL LYMPH NODE                                    21               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
  2Q LOSS MUTATED             1       1       3        1        4        3
  2Q LOSS WILD-TYPE           9       5      20        9       21       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  2Q LOSS MUTATED           1         1         2         4          3
  2Q LOSS WILD-TYPE         9        13         8        28         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED            1          6        2
  2Q LOSS WILD-TYPE         22         42       10
D43V5, multiclass
             clus
vv            2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   1                 5
  STAGE I                   3                20
  STAGE IA                  1                 9
  STAGE IB                  4                21
  STAGE II                  3                14
  STAGE IIA                 1                 9
  STAGE IIB                 1                13
  STAGE IIC                 2                 8
  STAGE III                 4                28
  STAGE IIIA                3                11
  STAGE IIIB                1                22
  STAGE IIIC                6                42
  STAGE IV                  2                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
  2Q LOSS MUTATED       6  5  9 10
  2Q LOSS WILD-TYPE    47 55 46 47
D43V6, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               6                47
  T2                  5                55
  T3                  9                46
  T4                 10                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                 N0  N1  N2  N3
  2Q LOSS MUTATED    22   7   1   5
  2Q LOSS WILD-TYPE 119  44  31  32
D43V7, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              22               119
  N1               7                44
  N2               1                31
  N3               5                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
  2Q LOSS MUTATED    32   0   1   1   1
  2Q LOSS WILD-TYPE 220   4   1   1   4
D43V8, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               32               220
  M1                0                 4
  M1A               1                 1
  M1B               1                 1
  M1C               1                 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"
D43V9, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   17  9
  2Q LOSS WILD-TYPE 87 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     17    9
  2Q LOSS WILD-TYPE   87   63
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               17                87
  YES               9                63
[1] 2 2
[1] FALSE
D43V10, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  34
  2Q LOSS WILD-TYPE  32 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   34
  2Q LOSS WILD-TYPE   32  213
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2                32
  YES              34               213
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    14  22
  2Q LOSS WILD-TYPE  94 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     14   22
  2Q LOSS WILD-TYPE   94  151
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              14                94
  MALE                22               151
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0    36
  2Q LOSS WILD-TYPE     5                         1   239
D43V13, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  36               239
[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
  2Q LOSS MUTATED     0  36
  2Q LOSS WILD-TYPE   3 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   36
  2Q LOSS WILD-TYPE    3  238
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              36               238
[1] 2 2
[1] FALSE

Clustering(44) Variable = 3P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    23  22
  3P LOSS WILD-TYPE 114 111
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               45               225 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22               111 
$`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-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       56.19        15.25        23.11         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-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A3AA 
        8.55        12.03        34.29        47.21        98.27       124.31 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19H 
       15.95         3.22        21.60        18.61        12.95        34.88 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        1.87        12.62         5.36         3.45        47.38         8.65 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
       14.20         2.27         0.13        12.85        24.85        31.33 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
       16.24        15.42        10.65 

$`3P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.47         8.52        70.16        28.08        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       81.24        10.29         8.38        21.14        68.22        69.90 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       11.41        30.87        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-A3CC 
       45.11       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 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
        8.84        20.48        13.94        95.38        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG 
        1.55         6.97         4.01         2.89        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-A5UN 
       13.15         0.20         0.13         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        0.20        11.57         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        36.07         5.13         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        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
        4.41         1.08        27.12         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         6.48         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        23.90         9.67         8.94        39.39        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        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        30.84         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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK 
       29.46        44.25         7.96        14.56        63.42       111.78 
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        29.65 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       27.16        23.05         5.56       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       30.15        13.81        12.72        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
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-A19J TCGA-ER-A19L TCGA-ER-A19M 
       11.90        11.11       114.15         4.21        13.45        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       11.80         1.51        13.08        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         4.90         6.71 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
        3.58        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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       11.08         7.17        30.87        12.92        12.89        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-A4F5 TCGA-FS-A4F9 
        5.23        53.85         3.22         7.36        28.73        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         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
        9.90         7.23        84.72        10.13        12.16        14.70 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        11.05         5.79 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.13              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           124.31            122.73 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            15.95             13.45 
[1] "0.1 - 124.3 (15.9)" "0.0 - 122.7 (13.4)"
[1] "hr=" "1.2"
D44V2, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    23  22
  3P LOSS WILD-TYPE 119 112
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               45               231 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22               112 
$`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-D9-A6E9 TCGA-D9-A6EA TCGA-DA-A1HV 
       56.19        58.06       125.19         9.90        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17Y TCGA-EE-A20C 
       36.03       176.55       107.34        61.18        27.22       151.27 
TCGA-EE-A29G TCGA-EE-A29P TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A3AA 
       72.07        56.42        67.43       208.04       129.27       124.31 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A19H 
       23.47       172.18        64.08        35.44        13.94       152.35 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       23.34        31.27         7.00        48.59       101.26       133.55 
TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
      174.84        77.88        47.54        14.04       120.46       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
       64.44        62.79        12.62 

$`3P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.57        16.67        71.80        28.08        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       95.74        43.43        65.49        23.77       168.00        69.90 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JO 
       11.87        48.76        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-A3CC 
       45.11       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 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       10.03        51.68        15.06       110.93       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      166.19         7.43       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         3.25        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        45.11        35.01         3.55        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       109.64        78.87       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        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       32.19         2.60        44.35        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       345.96        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      102.90        24.43        39.29        58.75        47.54       314.56 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      135.95        48.72        89.33        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       101.95        13.91        14.30        55.59        44.88 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       94.82        21.67        28.83        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       144.76 
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       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      136.47        41.59        53.26       122.73        25.84         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J8 
       54.51        13.81       138.81       127.20        36.95        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
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-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-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       43.82        20.15        16.37        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         4.90       210.08 
TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.16       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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       15.45         9.70        32.75        47.38        23.93        74.73 
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-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY 
       26.73        49.45         0.20        22.92         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
        9.90         7.23        84.72        10.13        32.48        39.58 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       46.36       294.77         6.67 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             7.00              0.16 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           208.04            357.37 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            67.43             45.11 
[1] "7.0 - 208.0 (67.4)" "0.2 - 357.4 (45.1)"
[1] "hr=" "1.2"
D44V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P LOSS MUTATED                    5             2
  3P LOSS WILD-TYPE                 32             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3P LOSS MUTATED                                          11
  3P LOSS WILD-TYPE                                        49
                   vv
clus                REGIONAL LYMPH NODE
  3P LOSS MUTATED                    26
  3P LOSS WILD-TYPE                 153
D44V4, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  DISTANT METASTASIS                                      5                32
  PRIMARY TUMOR                                           2                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              11                49
  REGIONAL LYMPH NODE                                    26               153
[1] 4 2
[1] 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       5        0        4        0
  3P LOSS WILD-TYPE           8       5      18       10       21       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3P LOSS MUTATED           0         3         1         4          5
  3P LOSS WILD-TYPE        10        11         9        28          9
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED            5          9        1
  3P LOSS WILD-TYPE         18         39       11
D44V5, multiclass
             clus
vv            3P LOSS MUTATED 3P LOSS WILD-TYPE
  I OR II NOS               2                 8
  STAGE 0                   1                 5
  STAGE I                   5                18
  STAGE IA                  0                10
  STAGE IB                  4                21
  STAGE II                  0                17
  STAGE IIA                 0                10
  STAGE IIB                 3                11
  STAGE IIC                 1                 9
  STAGE III                 4                28
  STAGE IIIA                5                 9
  STAGE IIIB                5                18
  STAGE IIIC                9                39
  STAGE IV                  1                11
[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      12 10  8  7
  3P LOSS WILD-TYPE    41 50 47 50
D44V6, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              12                41
  T2                 10                50
  T3                  8                47
  T4                  7                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
  3P LOSS MUTATED    18  11   6   6
  3P LOSS WILD-TYPE 123  40  26  31
D44V7, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              18               123
  N1              11                40
  N2               6                26
  N3               6                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
  3P LOSS MUTATED    41   0   0   0   1
  3P LOSS WILD-TYPE 211   4   2   2   4
D44V8, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               41               211
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               1                 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"
D44V9, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   16 12
  3P LOSS WILD-TYPE 88 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     16   12
  3P LOSS WILD-TYPE   88   60
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               16                88
  YES              12                60
[1] 2 2
[1] FALSE
D44V10, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     5  40
  3P LOSS WILD-TYPE  29 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5   40
  3P LOSS WILD-TYPE   29  207
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                5                29
  YES              40               207
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    19  26
  3P LOSS WILD-TYPE  89 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     19   26
  3P LOSS WILD-TYPE   89  147
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              19                89
  MALE                26               147
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       1                         0    44
  3P LOSS WILD-TYPE     4                         1   231
D44V13, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  44               231
[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
  3P LOSS MUTATED     0  44
  3P LOSS WILD-TYPE   3 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   44
  3P LOSS WILD-TYPE    3  230
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              44               230
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    19  17
  3Q LOSS WILD-TYPE 118 116
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               36               234 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               17               116 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A5GU TCGA-D9-A6E9 
      111.09        32.42       110.79         7.50        23.11         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       11.31        48.79        35.80        13.68        44.52        36.69 
TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GC 
       10.55         4.34         8.55         4.41        12.03        34.29 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-ER-A195 TCGA-ER-A197 
       47.21        19.43        15.95         3.22        18.61        12.95 
TCGA-ER-A19H TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A4F8 TCGA-FS-A4FD 
       34.88         5.36         3.45        47.38        14.20         2.27 
TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
        0.13        24.85        31.33        16.24        15.42        10.65 

$`3Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.47         8.52        70.16        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        69.90        11.41        30.87        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        45.11       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         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       13.94        95.38        52.01        47.87         1.55         6.97 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
        4.01         2.89        13.22        14.60        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       39.19         9.99        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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
        0.13         0.00         0.00        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        36.07         5.13         9.21         1.18         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        38.63         1.08        27.12 
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         6.48         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.68         8.09        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK 
        8.94        39.39        17.98        34.92        30.08        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        30.84         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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       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        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        30.15        13.81 
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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 
       27.35         0.46        13.94        33.60        31.40        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-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-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-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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        6.71         3.58        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-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-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-A6C8 TCGA-GN-A265 
        0.16         0.43         9.90         7.23        12.85        84.72 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       10.13        12.16        14.70        11.84        11.05         5.79 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.13              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           111.09            124.31 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           15.685            13.875 
[1] "0.1 - 111.1 (15.7)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1.1"
D45V2, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    19  17
  3Q LOSS WILD-TYPE 123 117
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               36               240 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               17               117 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2JG TCGA-D3-A5GU TCGA-D9-A6E9 
      112.04       112.57       133.25       113.52       125.19         9.90 
TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       25.18        48.89        36.03       176.55       107.34        61.18 
TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GC 
       27.22       151.27        72.07        32.19        56.42        67.43 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-ER-A195 TCGA-ER-A197 
      208.04        89.33        23.47       172.18        35.44        13.94 
TCGA-ER-A19H TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-FS-A4F8 TCGA-FS-A4FD 
      152.35         7.00        48.59       101.26       174.84        77.88 
TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
       47.54       120.46       117.93        64.44        62.79        12.62 

$`3Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.57        16.67        71.80        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        69.90        11.87        48.76        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        45.11       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        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       15.06       110.93       135.75       137.92       166.19         7.43 
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         3.25 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       66.25        22.95       117.21        20.38       194.83        35.93 
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        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       35.01         3.55        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-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.96       109.64        78.87       168.26        13.55        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M 
       80.61        47.84        13.97        39.62         2.60        44.35 
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       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GK 
       58.75        47.54       314.56       135.95        48.72        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       101.95        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       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       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 
       27.35        33.40       101.79       148.08        31.40        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-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93         6.44       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-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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       80.32        46.98        33.21        92.98       174.21         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
      210.08        15.16       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-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-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-GN-A265 
        0.16         2.40         9.90         7.23        14.04        84.72 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       10.13        32.48        39.58        46.36       294.77         6.67 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             7.00              0.16 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           208.04            357.37 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            69.75             46.59 
[1] "7.0 - 208.0 (69.8)" "0.2 - 357.4 (46.6)"
[1] "hr=" "1.3"
D45V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q LOSS MUTATED                    3             2
  3Q LOSS WILD-TYPE                 34             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  3Q LOSS MUTATED                                           9
  3Q LOSS WILD-TYPE                                        51
                   vv
clus                REGIONAL LYMPH NODE
  3Q LOSS MUTATED                    21
  3Q LOSS WILD-TYPE                 158
D45V4, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      3                34
  PRIMARY TUMOR                                           2                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               9                51
  REGIONAL LYMPH NODE                                    21               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
  3Q LOSS MUTATED             1       1       3        2        3        0
  3Q LOSS WILD-TYPE           9       5      20        8       22       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  3Q LOSS MUTATED           0         2         1         2          4
  3Q LOSS WILD-TYPE        10        12         9        30         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED            5          6        1
  3Q LOSS WILD-TYPE         18         42       11
D45V5, multiclass
             clus
vv            3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   1                 5
  STAGE I                   3                20
  STAGE IA                  2                 8
  STAGE IB                  3                22
  STAGE II                  0                17
  STAGE IIA                 0                10
  STAGE IIB                 2                12
  STAGE IIC                 1                 9
  STAGE III                 2                30
  STAGE IIIA                4                10
  STAGE IIIB                5                18
  STAGE IIIC                6                42
  STAGE IV                  1                11
[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      10  7  5  7
  3Q LOSS WILD-TYPE    43 53 50 50
D45V6, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1              10                43
  T2                  7                53
  T3                  5                50
  T4                  7                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
  3Q LOSS MUTATED    16   7   6   4
  3Q LOSS WILD-TYPE 125  44  26  33
D45V7, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              16               125
  N1               7                44
  N2               6                26
  N3               4                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
  3Q LOSS MUTATED    32   0   0   0   1
  3Q LOSS WILD-TYPE 220   4   2   2   4
D45V8, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               32               220
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               1                 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"
D45V9, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   14  8
  3Q LOSS WILD-TYPE 90 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     14    8
  3Q LOSS WILD-TYPE   90   64
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               14                90
  YES               8                64
[1] 2 2
[1] FALSE
D45V10, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3  33
  3Q LOSS WILD-TYPE  31 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3   33
  3Q LOSS WILD-TYPE   31  214
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                3                31
  YES              33               214
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    15  21
  3Q LOSS WILD-TYPE  93 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     15   21
  3Q LOSS WILD-TYPE   93  152
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              15                93
  MALE                21               152
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         0    35
  3Q LOSS WILD-TYPE     4                         1   240
D45V13, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  35               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"
D45V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  35
  3Q LOSS WILD-TYPE   3 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   35
  3Q LOSS WILD-TYPE    3  239
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              35               239
[1] 2 2
[1] FALSE

Clustering(46) Variable = 4P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    28  27
  4P LOSS WILD-TYPE 109 106
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               55               215 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               27               106 
$`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-D9-A3Z3 TCGA-D9-A6EC 
       61.38       103.59         5.39        42.71         2.89        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        36.07 
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        27.12         6.48 
TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 
        8.68         9.67        47.21        28.31        30.84         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        27.16        15.95        16.14 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E 
        0.46        31.40        12.95        25.18         3.52        11.90 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A7U8 
       36.07         1.87        12.62        11.74        22.49         3.58 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 
       23.80        15.52         7.30        14.20         0.13        12.85 
TCGA-GN-A266 
       10.13 

$`4P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
        8.52        32.42        70.16       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       45.83        81.24        85.32         8.38        21.14        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       92.42        45.11       114.67        15.25        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
       82.29        13.32        24.00         6.31         9.34        26.37 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       80.22        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       13.94        95.38        52.01        47.87         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
       23.11         4.01         9.90        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-A5UN 
        7.00        17.56        13.15         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.20        11.57        10.55         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       12.20         5.13         4.31         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        7.99        38.63         8.55         4.41         1.08         9.50 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       12.03         8.09         8.84         9.99         2.43         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        49.22        23.90         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        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-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-A2MN 
        7.96        14.56        63.42       111.78       111.91        25.08 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       26.99        29.65        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 
       25.84         3.68        30.15        13.81        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JH 
       22.92        21.60        21.60        22.22        27.35        13.94 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C 
       33.60        18.61        38.40         5.72        76.41         3.78 
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-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
        1.51        13.08         9.04         6.58         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
       85.74         4.90         6.71         5.36        64.47         3.45 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
       11.01        14.24         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-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-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-FS-A4FD 
        7.36        28.73        10.78         5.98         6.41         2.27 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.99         0.16         0.43         9.90         7.23 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        31.33        84.72        16.24        15.42        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        10.65        11.05         5.79 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.00 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           111.09            124.31 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            14.83             13.94 
[1] "0.1 - 111.1 (14.8)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1"  
D46V2, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    30  27
  4P LOSS WILD-TYPE 112 107
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               57               219 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               27               107 
$`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-D9-A148 TCGA-D9-A149 
       86.93       103.59        21.47        43.69       151.53        54.67 
TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH 
        3.25        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       109.64       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 
       44.35       345.96       171.55        39.29       208.04        75.48 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS 
      101.95        21.67       129.27       167.90        43.23       136.47 
TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B 
       23.47        34.32        33.40        31.40        13.94        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
       12.59        13.02        37.25        23.34        31.27        32.05 
TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A4F8 
       46.98        15.16       202.65        28.08        27.72       174.84 
TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A266 
       47.54        14.04        10.13 

$`4P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       90.90        95.74       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
      171.58        45.11       130.72        58.06        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU 
      166.52        60.23        24.53        13.87         9.34        39.75 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
      161.85        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS 
       15.06       110.93       135.75       137.92       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA 
      125.19         3.65         6.41        11.34         9.90        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-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-A5SG 
       68.09        28.60        10.49       215.44        13.87        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       35.01         3.55        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-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29E 
        4.96        78.87       168.26        13.55        63.35        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         2.60        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-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP 
       48.72        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
       96.23       144.76       203.05        47.54       248.65       103.56 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         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-A3J7 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       64.08        53.19        27.35       101.79       148.08        35.44 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G 
       50.76         9.17        77.75        48.89        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-A2NE TCGA-ER-A2NF 
       50.89       148.18        79.99        43.82        20.15        16.37 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
      247.04        80.32        33.21        92.98       174.21         4.90 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
      210.08         7.00       216.92        48.59       228.59        20.91 
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-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-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-GN-A262 TCGA-GN-A264 
        0.16         2.40         9.90         7.23       120.46       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-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             3.25              0.16 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           345.96            357.37 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            43.69             48.85 
[1] "3.2 - 346.0 (43.7)" "0.2 - 357.4 (48.9)"
[1] "hr=" "1"  
D46V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P LOSS MUTATED                   10             1
  4P LOSS WILD-TYPE                 27             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4P LOSS MUTATED                                          16
  4P LOSS WILD-TYPE                                        44
                   vv
clus                REGIONAL LYMPH NODE
  4P LOSS MUTATED                    30
  4P LOSS WILD-TYPE                 149
D46V4, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  DISTANT METASTASIS                                     10                27
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              16                44
  REGIONAL LYMPH NODE                                    30               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
  4P LOSS MUTATED             1       2       6        1        5        3
  4P LOSS WILD-TYPE           9       4      17        9       20       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4P LOSS MUTATED           0         4         2         6          4
  4P LOSS WILD-TYPE        10        10         8        26         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED            8          9        0
  4P LOSS WILD-TYPE         15         39       12
D46V5, multiclass
             clus
vv            4P LOSS MUTATED 4P LOSS WILD-TYPE
  I OR II NOS               1                 9
  STAGE 0                   2                 4
  STAGE I                   6                17
  STAGE IA                  1                 9
  STAGE IB                  5                20
  STAGE II                  3                14
  STAGE IIA                 0                10
  STAGE IIB                 4                10
  STAGE IIC                 2                 8
  STAGE III                 6                26
  STAGE IIIA                4                10
  STAGE IIIB                8                15
  STAGE IIIC                9                39
  STAGE IV                  0                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
  4P LOSS MUTATED      11 13 13  9
  4P LOSS WILD-TYPE    42 47 42 48
D46V6, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              11                42
  T2                 13                47
  T3                 13                42
  T4                  9                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
  4P LOSS MUTATED    26  14   6   7
  4P LOSS WILD-TYPE 115  37  26  30
D46V7, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              26               115
  N1              14                37
  N2               6                26
  N3               7                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
  4P LOSS MUTATED    54   0   0   1   0
  4P LOSS WILD-TYPE 198   4   2   1   5
D46V8, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               54               198
  M1                0                 4
  M1A               0                 2
  M1B               1                 1
  M1C               0                 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"
D46V9, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   25 14
  4P LOSS WILD-TYPE 79 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     25   14
  4P LOSS WILD-TYPE   79   58
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               25                79
  YES              14                58
[1] 2 2
[1] FALSE
D46V10, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     6  52
  4P LOSS WILD-TYPE  28 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6   52
  4P LOSS WILD-TYPE   28  195
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                6                28
  YES              52               195
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    28  30
  4P LOSS WILD-TYPE  80 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     28   30
  4P LOSS WILD-TYPE   80  143
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              28                80
  MALE                30               143
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       2                         0    56
  4P LOSS WILD-TYPE     3                         1   219
D46V13, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  56               219
[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
  4P LOSS MUTATED     0  58
  4P LOSS WILD-TYPE   3 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0   58
  4P LOSS WILD-TYPE    3  216
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              58               216
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    30  28
  4Q LOSS WILD-TYPE 107 105
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               58               212 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               28               105 
$`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         5.39        42.71         8.84 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5KH 
        2.89         9.90        35.80        14.83         0.20         0.13 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29C 
       10.55         8.12         1.12        36.07         4.34        37.97 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2GI 
       27.12         6.48         8.68         9.67        47.21        30.08 
TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MM TCGA-EE-A2MQ 
       28.31        30.84         8.84        98.27        56.02        21.60 
TCGA-EE-A2MS TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A197 
       27.16        15.95        16.14         0.46        31.40        12.95 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG 
       25.18         3.52        11.90        36.07         1.87        12.62 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA 
       11.74        22.49         3.58        23.80        15.52         7.30 
TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A266 
       14.20         0.13        12.85        10.13 

$`4Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
        8.52        32.42        70.16       110.79        22.55        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       81.24        10.29        85.32         8.38        21.14        68.22 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.41        30.87         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB 
       92.42        45.11       114.67        15.25        46.32        82.29 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       13.32        24.00         6.31         9.34        26.37        80.22 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       15.09        41.10        17.72        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        13.22        14.60        48.79        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-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X 
       13.15         0.00         0.00        13.22         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F 
        6.31         1.35        12.20         5.13         4.31         5.13 
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        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55         4.41         1.08         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-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         8.94        39.39        34.29        17.98        34.92 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       19.43        16.01        35.54        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        9.53        29.46        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-A2MT 
      111.78       111.91        25.08        26.99        29.65        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
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-A3JA TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       22.22        27.35        13.94        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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
        6.58         1.71        18.41        85.74         4.90         6.71 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 
        5.36        64.47         3.45        11.01        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-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-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-A3TV 
        5.98         6.41         2.27         0.20         0.99         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        0.43         9.90         7.23        24.85        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-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.13              0.00 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           111.09            124.31 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           15.735            13.745 
[1] "0.1 - 111.1 (15.7)" "0.0 - 124.3 (13.7)"
[1] "hr=" "1.1"
D47V2, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    32  28
  4Q LOSS WILD-TYPE 110 106
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               60               216 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               28               106 
$`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        21.47        43.69        10.03 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A3F8 
      151.53        54.67         3.25         9.90        36.03        15.68 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B 
       10.16        17.85        27.22        94.98        33.73       109.64 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 
      151.27        47.84        44.35       345.96       171.55        39.29 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 
      208.04        48.72        75.48       101.95        21.67       129.27 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE 
      167.90        43.23       136.47        23.47        34.32        33.40 
TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19S 
       31.40        13.94        98.40        12.59        13.02        37.25 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1Z0 
       23.34        31.27        32.05        46.98        15.16       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A266 
       28.08        27.72       174.84        47.54        14.04        10.13 

$`4Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.67       112.57        71.80       133.25        31.59        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       95.74        43.43       103.10        65.49        23.77       168.00 
TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       69.90        11.87        48.76       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB 
      171.58        45.11       130.72        58.06        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E 
       60.23        24.53        13.87         9.34        39.75       161.85 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       40.14       131.90        18.38        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A1JW 
      135.75       137.92       166.19         7.43       125.19         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        6.41        11.34        25.18        66.25        22.95        48.89 
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-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL 
       10.49       215.44        13.87        45.11        35.01         3.55 
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-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       26.89        68.15         4.96        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H 
       63.35        80.61        13.97        39.62        72.07        32.19 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        2.60        18.61        56.42        37.35        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       25.87        17.92        46.82       102.90        24.43        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GJ TCGA-EE-A2GK 
       47.54        67.43       314.56       135.95        89.33        54.74 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       79.66        90.97        13.91        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       47.54       248.65       103.56        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      122.73        25.84         3.68        54.51        13.81       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JD 
      172.18       127.20        36.95        64.08        53.19        27.35 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      101.79       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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YW 
       92.98       174.21         4.90       210.08         7.00       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
       48.59       228.59        20.91         7.79        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-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-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       50.14        66.67        28.73        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        22.92         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        7.23       120.46       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        39.58        46.36        12.62       294.77         6.67 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             3.25              0.16 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           345.96            357.37 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           41.260            49.465 
[1] "3.2 - 346.0 (41.3)" "0.2 - 357.4 (49.5)"
[1] "hr=" "1"  
D47V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q LOSS MUTATED                    8             1
  4Q LOSS WILD-TYPE                 29             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  4Q LOSS MUTATED                                          17
  4Q LOSS WILD-TYPE                                        43
                   vv
clus                REGIONAL LYMPH NODE
  4Q LOSS MUTATED                    33
  4Q LOSS WILD-TYPE                 146
D47V4, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      8                29
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              17                43
  REGIONAL LYMPH NODE                                    33               146
[1] 4 2
[1] 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        2        5        4
  4Q LOSS WILD-TYPE          10       4      17        8       20       13
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  4Q LOSS MUTATED           0         2         2         7          4
  4Q LOSS WILD-TYPE        10        12         8        25         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED            9          8        2
  4Q LOSS WILD-TYPE         14         40       10
D47V5, multiclass
             clus
vv            4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   2                 4
  STAGE I                   6                17
  STAGE IA                  2                 8
  STAGE IB                  5                20
  STAGE II                  4                13
  STAGE IIA                 0                10
  STAGE IIB                 2                12
  STAGE IIC                 2                 8
  STAGE III                 7                25
  STAGE IIIA                4                10
  STAGE IIIB                9                14
  STAGE IIIC                8                40
  STAGE IV                  2                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
  4Q LOSS MUTATED      15 12 12  9
  4Q LOSS WILD-TYPE    38 48 43 48
D47V6, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              15                38
  T2                 12                48
  T3                 12                43
  T4                  9                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
  4Q LOSS MUTATED    25  15   6   9
  4Q LOSS WILD-TYPE 116  36  26  28
D47V7, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              25               116
  N1              15                36
  N2               6                26
  N3               9                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
  4Q LOSS MUTATED    54   0   0   2   1
  4Q LOSS WILD-TYPE 198   4   2   0   4
D47V8, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               54               198
  M1                0                 4
  M1A               0                 2
  M1B               2                 0
  M1C               1                 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"
D47V9, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   26 12
  4Q LOSS WILD-TYPE 78 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     26   12
  4Q LOSS WILD-TYPE   78   60
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               26                78
  YES              12                60
[1] 2 2
[1] FALSE
D47V10, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     9  51
  4Q LOSS WILD-TYPE  25 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9   51
  4Q LOSS WILD-TYPE   25  196
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                9                25
  YES              51               196
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    30  30
  4Q LOSS WILD-TYPE  78 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     30   30
  4Q LOSS WILD-TYPE   78  143
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              30                78
  MALE                30               143
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       3                         0    57
  4Q LOSS WILD-TYPE     2                         1   218
D47V13, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  57               218
[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
  4Q LOSS MUTATED     0  59
  4Q LOSS WILD-TYPE   3 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      0   59
  4Q LOSS WILD-TYPE    3  215
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              59               215
[1] 2 2
[1] FALSE

Clustering(48) Variable = 5P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    31  29
  5P LOSS WILD-TYPE 106 104
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               60               210 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               29               104 
$`5P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO 
       16.47        68.22        11.41         7.50        92.42        64.44 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GO TCGA-DA-A1HV TCGA-DA-A1HW 
       61.38        24.00         5.39        47.87        48.79        35.80 
TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 TCGA-EE-A185 
       17.56         0.13        11.57        10.55         5.13         4.31 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GB 
       37.97        38.63        27.12        12.03        23.90        39.39 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GR 
       17.98        34.92        47.21        30.08        19.43         1.15 
TCGA-EE-A2GT TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AH 
       34.98        56.02        21.60         5.56         3.68        12.72 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
       21.60        21.60         5.72         1.87         1.51        12.62 
TCGA-ER-A2NH TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT 
       11.74         4.90         8.22         7.17        47.38        40.64 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB 
       27.39         0.82         3.22         7.36        14.20         5.98 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-OD-A75X 
       12.85        24.85        10.13        16.24        15.42        11.05 

$`5P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       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-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       21.14        88.50        69.90        30.87        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        45.11       114.67        15.25        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 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       20.48        13.94        95.38        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       23.11         4.01         2.89         9.90        11.31        13.22 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       14.60        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-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
       19.36         7.00        14.83        13.15         0.20         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        0.00        13.22         0.20         6.31         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        1.35        12.20        36.07         4.34         5.13         9.21 
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         4.41 
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         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        2.43         8.68         8.09        11.31        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
        8.94        34.29        16.01        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       30.84         5.42        13.02        36.33         8.84        98.27 
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-A2MN 
        7.96        14.56        63.42       111.78       111.91        25.08 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
       26.99        29.65        27.16        23.05       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84        30.15        13.81        15.95         3.22        22.92 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        33.60 
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-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-A2NC TCGA-ER-A2NF TCGA-ER-A3ES 
       36.07        17.72        78.44        11.80        13.08         9.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
        6.58        22.49         1.71        18.41        85.74         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        3.58         5.36        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-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       19.53        11.08        30.87        12.92        12.89        52.08 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
        8.65         8.81        49.15         8.68         5.23        53.85 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       28.73        10.78         6.41         2.27         0.20         0.99 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 
        0.13         0.16         0.43         9.90         7.23        31.33 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       84.72        12.16        14.70        11.84        10.65         5.79 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.13              0.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            92.42            124.31 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           15.830            13.875 
[1] "0.1 - 92.4 (15.8)"  "0.0 - 124.3 (13.9)"
[1] "hr=" "1"  
D48V2, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    32  29
  5P LOSS WILD-TYPE 110 105
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               61               215 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               29               105 
$`5P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A2JO 
       16.57       168.00        11.87       113.52       171.58        66.08 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GO TCGA-DA-A1HV TCGA-DA-A1HW 
       86.93        24.53        21.47       137.92        48.89        36.03 
TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A184 
      215.44        17.85         3.55        29.82        27.22        68.15 
TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A2 
        4.96        47.84        39.62        44.35        56.42        24.43 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       47.54       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AD 
       14.30        44.88       167.90        43.23        53.26         3.68 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A2ND TCGA-ER-A2NE 
      138.81        36.95        64.08         9.17        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A69P TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZM 
       31.27        32.05         4.90        53.52         9.70       101.26 
TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 
       53.16        49.48        27.09        50.14        66.67       174.84 
TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       26.73        14.04       120.46        10.13        64.44        62.79 
TCGA-OD-A75X 
      294.77 

$`5P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       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-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       115.53        69.90        48.76        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        45.11       130.72        58.06        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 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS 
       51.68        15.06       110.93       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      125.19       151.53        54.67         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
        3.25         9.90        25.18        66.25        22.95       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-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN 
       15.68        13.87        10.16        45.11        35.01        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        6.35        12.20         8.65        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       26.89       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
       63.35        80.61        13.97        72.07        32.19         2.60 
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       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
      171.55        17.92        46.82       102.90        39.29        58.75 
TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
       67.43        54.74        79.66        75.48        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        55.59        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66        96.23       144.76       203.05        47.54       248.65 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      103.56       136.47        41.59       124.31       122.73        25.84 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       54.51        13.81        23.47       172.18       127.20        34.32 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       53.19        27.35        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       35.44        13.94        50.76        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-A2NF TCGA-ER-A3ES TCGA-ER-A3ET 
      148.18        79.99        43.82        16.37       247.04        80.32 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 
       46.98        33.21        92.98       174.21       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        7.00       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-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
       15.45        32.75        47.38        23.93        74.73       133.55 
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-GN-A264 TCGA-GN-A265 
        0.16         2.40         9.90         7.23       117.93        84.72 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       32.48        39.58        46.36        12.62         6.67 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.55              0.16 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           314.56            357.37 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            47.84             47.54 
[1] "3.5 - 314.6 (47.8)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1"  
D48V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P LOSS MUTATED                    8             0
  5P LOSS WILD-TYPE                 29             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5P LOSS MUTATED                                          15
  5P LOSS WILD-TYPE                                        45
                   vv
clus                REGIONAL LYMPH NODE
  5P LOSS MUTATED                    41
  5P LOSS WILD-TYPE                 138
D48V4, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  DISTANT METASTASIS                                      8                29
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              15                45
  REGIONAL LYMPH NODE                                    41               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
  5P LOSS MUTATED             3       3       5        4        3        3
  5P LOSS WILD-TYPE           7       3      18        6       22       14
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5P LOSS MUTATED           3         4         3         7          3
  5P LOSS WILD-TYPE         7        10         7        25         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED            7         13        0
  5P LOSS WILD-TYPE         16         35       12
D48V5, multiclass
             clus
vv            5P LOSS MUTATED 5P LOSS WILD-TYPE
  I OR II NOS               3                 7
  STAGE 0                   3                 3
  STAGE I                   5                18
  STAGE IA                  4                 6
  STAGE IB                  3                22
  STAGE II                  3                14
  STAGE IIA                 3                 7
  STAGE IIB                 4                10
  STAGE IIC                 3                 7
  STAGE III                 7                25
  STAGE IIIA                3                11
  STAGE IIIB                7                16
  STAGE IIIC               13                35
  STAGE IV                  0                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
  5P LOSS MUTATED      12 16  9 16
  5P LOSS WILD-TYPE    41 44 46 41
D48V6, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              12                41
  T2                 16                44
  T3                  9                46
  T4                 16                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
  5P LOSS MUTATED    30  15   5  10
  5P LOSS WILD-TYPE 111  36  27  27
D48V7, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              30               111
  N1              15                36
  N2               5                27
  N3              10                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
  5P LOSS MUTATED    61   0   0   0   0
  5P LOSS WILD-TYPE 191   4   2   2   5
D48V8, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               61               191
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 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"
D48V9, binary
                   cls
clus                 0  1
  5P LOSS MUTATED   20 21
  5P LOSS WILD-TYPE 84 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     20   21
  5P LOSS WILD-TYPE   84   51
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               20                84
  YES              21                51
[1] 2 2
[1] FALSE
D48V10, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     4  60
  5P LOSS WILD-TYPE  30 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4   60
  5P LOSS WILD-TYPE   30  187
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                4                30
  YES              60               187
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    27  37
  5P LOSS WILD-TYPE  81 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     27   37
  5P LOSS WILD-TYPE   81  136
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              27                81
  MALE                37               136
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       2                         1    61
  5P LOSS WILD-TYPE     3                         0   214
D48V13, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  61               214
[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
  5P LOSS MUTATED     0  61
  5P LOSS WILD-TYPE   3 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   61
  5P LOSS WILD-TYPE    3  213
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              61               213
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   38 38
  5Q LOSS WILD-TYPE 99 95
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               76               194 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               38                95 
$`5Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
       28.08        68.22        11.41         7.50         6.31        92.42 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GL 
       64.44        15.25        61.38        24.00         5.39        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       52.01        47.87         4.01        13.22        48.79        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EE-A17X 
       10.03        44.52        36.69        17.56         0.13        11.57 
TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M 
       10.55         4.31         9.21        37.97        38.63        27.12 
TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       12.03         2.43        23.90        39.39        17.98        34.92 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GT 
       47.21        30.08        19.43        28.31         1.15        34.98 
TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A3AB TCGA-EE-A3AD 
       98.27        63.42        56.02        21.60       122.73         3.68 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A2ND 
       12.72        21.60        21.60         5.72        25.18         1.87 
TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZB 
        1.51        11.74        85.74         4.90         3.45         3.39 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY 
        7.17        47.38         8.65        40.64        27.39         0.82 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-GF-A6C8 TCGA-GN-A262 
        3.22         7.36        14.20         5.98        12.85        24.85 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-OD-A75X 
       10.13        16.24        15.42        11.05 

$`5Q 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-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-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN 
       21.14        88.50        69.90        30.87        36.16        56.19 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       45.11       114.67        46.98        46.32        82.29        13.32 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
        6.31         9.34       103.59        26.37        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       15.09        41.10        17.72         8.84        20.48        13.94 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        1.55         6.97        23.11         2.89         9.90        11.31 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 
       14.60        51.12        39.19        13.68         9.99        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-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       13.15         0.20         0.00         0.00        13.22         0.20 
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-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       36.07         4.34         5.13         1.18         7.99         9.90 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29Q 
       11.15         8.55         4.41         1.08         9.50         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         6.48         8.68         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         8.94        34.29        16.01        35.54 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 
       33.83        30.84         5.42        13.02        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-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
        7.96        14.56       111.78       111.91        25.08        26.99 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC 
       29.65        27.16        23.05         5.56       124.31        25.84 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 
       30.15        13.81        15.95         3.22        22.92        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       22.22        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D 
       18.61        12.95        38.40        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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       78.44        11.80        13.08        12.62         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       22.49         1.71        18.41         6.71         3.58         5.36 
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-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.30        20.38         8.22        19.53        11.08        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU 
       12.92        12.89        52.08         8.81        49.15         8.68 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
        5.23        53.85        28.73        10.78         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         0.43         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
        7.23        31.33        84.72        12.16        14.70        11.84 
TCGA-GN-A4U9 TCGA-QB-A6FS 
       10.65         5.79 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.13              0.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           122.73            124.31 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           17.770            13.385 
[1] "0.1 - 122.7 (17.8)" "0.0 - 124.3 (13.4)"
[1] "hr=" "1.1"
D49V2, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    39  39
  5Q LOSS WILD-TYPE 103  95
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               78               198 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               39                95 
$`5Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
       28.08       168.00        11.87       113.52        12.10       171.58 
TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D3-A5GL 
       66.08        58.06        86.93        24.53        21.47       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV 
      135.75       137.92         6.41        11.34        66.25        48.89 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EB-A5KH 
       36.03        20.38       107.34        61.18       215.44        17.85 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29C 
        3.55        29.82        27.22         4.96       168.26        47.84 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GB 
       39.62        44.35        56.42        25.87        24.43        47.54 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM 
      314.56       135.95       208.04        48.72        89.33        75.48 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MQ 
       14.30        44.88       129.27        96.23       167.90        43.23 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-ER-A199 
      122.73         3.68       138.81        36.95        64.08         9.17 
TCGA-ER-A19B TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A69P 
       98.40        23.34        20.15        32.05       174.21         4.90 
TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       48.59        48.85         9.70       101.26       133.55        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-OD-A75X 
       14.04       120.46        10.13        64.44        62.79       294.77 

$`5Q 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-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-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JN 
       23.77       115.53        69.90        48.76        42.08        56.19 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       45.11       130.72        46.98        46.32       166.52        60.23 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       13.87         9.34       103.59        39.75       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       40.14       131.90        18.38        10.03        51.68        15.06 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
        3.25         9.90        25.18        22.95       117.21       194.83 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
      176.55        35.93        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        45.11 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A180 
       35.01        52.01         6.35        12.20         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20C 
       33.73        14.70        26.89        68.15       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
       78.87        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 
       32.19         2.60        18.61        37.35        14.47        55.92 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
      345.96       171.55        17.92        46.82       102.90        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       58.75        67.43        54.74        79.66        90.97       101.95 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.91        55.59        94.82        21.67        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
      144.76       203.05        47.54       248.65       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
       41.59        53.26       124.31        25.84        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD 
       23.47       172.18       127.20        34.32        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       33.40       101.79       148.08        31.40        35.44        13.94 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       50.76        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-A19N 
      268.93       152.35         6.44       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-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-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY 
       92.98       210.08        15.16         7.00       216.92       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      202.65        20.91        28.08         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        40.27        15.45        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 
       74.73        11.41       148.80        26.56        27.02        77.82 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       28.73        12.43        49.45        77.88         0.20        22.92 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A264 
       47.54         0.16         2.40         9.90         7.23       117.93 
TCGA-GN-A265 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       84.72        32.48        39.58        46.36        12.62         6.67 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             3.55              0.16 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           314.56            357.37 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           49.185            46.980 
[1] "3.5 - 314.6 (49.2)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1"  
D49V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q LOSS MUTATED                   12             1
  5Q LOSS WILD-TYPE                 25             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  5Q LOSS MUTATED                                          19
  5Q LOSS WILD-TYPE                                        41
                   vv
clus                REGIONAL LYMPH NODE
  5Q LOSS MUTATED                    49
  5Q LOSS WILD-TYPE                 130
D49V4, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     12                25
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              19                41
  REGIONAL LYMPH NODE                                    49               130
[1] 4 2
[1] 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        3        4        5
  5Q LOSS WILD-TYPE           6       3      14        7       21       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  5Q LOSS MUTATED           2         4         4         9          4
  5Q LOSS WILD-TYPE         8        10         6        23         10
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED            8         14        3
  5Q LOSS WILD-TYPE         15         34        9
D49V5, multiclass
             clus
vv            5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  I OR II NOS               4                 6
  STAGE 0                   3                 3
  STAGE I                   9                14
  STAGE IA                  3                 7
  STAGE IB                  4                21
  STAGE II                  5                12
  STAGE IIA                 2                 8
  STAGE IIB                 4                10
  STAGE IIC                 4                 6
  STAGE III                 9                23
  STAGE IIIA                4                10
  STAGE IIIB                8                15
  STAGE IIIC               14                34
  STAGE IV                  3                 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
  5Q LOSS MUTATED      16 19 12 20
  5Q LOSS WILD-TYPE    37 41 43 37
D49V6, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              16                37
  T2                 19                41
  T3                 12                43
  T4                 20                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
  5Q LOSS MUTATED    40  17   8  11
  5Q LOSS WILD-TYPE 101  34  24  26
D49V7, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              40               101
  N1              17                34
  N2               8                24
  N3              11                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  5Q LOSS MUTATED    75   0   1   1   1
  5Q LOSS WILD-TYPE 177   4   1   1   4
D49V8, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               75               177
  M1                0                 4
  M1A               1                 1
  M1B               1                 1
  M1C               1                 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"
D49V9, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   27 23
  5Q LOSS WILD-TYPE 77 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     27   23
  5Q LOSS WILD-TYPE   77   49
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               27                77
  YES              23                49
[1] 2 2
[1] FALSE
D49V10, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     7  74
  5Q LOSS WILD-TYPE  27 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7   74
  5Q LOSS WILD-TYPE   27  173
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                7                27
  YES              74               173
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    33  48
  5Q LOSS WILD-TYPE  75 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     33   48
  5Q LOSS WILD-TYPE   75  125
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              33                75
  MALE                48               125
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       2                         1    78
  5Q LOSS WILD-TYPE     3                         0   197
D49V13, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  78               197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0  78
  5Q LOSS WILD-TYPE   3 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   78
  5Q LOSS WILD-TYPE    3  196
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              78               196
[1] 2 2
[1] FALSE

Clustering(50) Variable = 6P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    21  30
  6P LOSS WILD-TYPE 116 103
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               51               219 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               30               103 
$`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        69.90        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         5.39         8.84 
TCGA-D3-A5GR TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
        1.55        11.31        13.22        14.60        51.12        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A180 
        9.99        25.15         6.64        17.56        10.55         8.12 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A0 
        7.99        11.15         8.55         8.09         8.68        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-A2MT TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A2NE 
       23.05        22.92        25.18         3.52        11.11         1.51 
TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        4.90         3.45         3.39         7.17        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
        8.81        49.15        40.64 

$`6P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52        32.42        70.16       110.79        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       45.83        81.24         8.38        21.14        88.50        68.22 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       30.87         7.50         6.31        64.44        45.11       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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.00         9.34       103.59        26.37        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       15.09        41.10        17.72        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01        47.87         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 
        9.90        48.79        35.80        10.03        13.68        44.52 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       36.69         4.93        22.36        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         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.20        11.57         6.31         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        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        1.18         9.90        37.97        38.63         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       27.12         9.50        12.03         8.84         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
        2.43         8.09        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       16.01        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       13.02        34.98        36.33         6.18         9.53        29.46 
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       111.78       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        29.65        27.16 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        15.95        12.72         3.22        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        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-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.78        11.90       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       78.44        11.80         1.87        13.08        12.62        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-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        6.71         3.58         5.36        64.47        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD 
       14.24        15.52         7.33         7.30        20.38         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       19.53        11.08        30.87        12.92        12.89        52.08 
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         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       10.65        11.05         5.79 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             1.51              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           111.09            124.31 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            11.31             14.70 
[1] "1.5 - 111.1 (11.3)" "0.0 - 124.3 (14.7)"
[1] "hr=" "1.3"
D50V2, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    21  30
  6P LOSS WILD-TYPE 121 104
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               51               225 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               30               104 
$`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        69.90        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        21.47        10.03 
TCGA-D3-A5GR TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
      166.19        25.18        66.25        22.95       117.21       194.83 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A180 
       35.93        53.92        68.09       215.44        27.22        94.98 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29W TCGA-EE-A2A0 
       63.35        13.97        72.07        37.35       171.55        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-A2MT TCGA-EE-A3J4 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A2NE 
       41.59       127.20        98.40        12.59        26.37        20.15 
TCGA-FR-A69P TCGA-FS-A1YX TCGA-FS-A1ZB TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ 
        4.90        48.59        48.85         9.70       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       11.41       148.80        53.16 

$`6P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.57        71.80       133.25        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       90.90        95.74        65.49        23.77       115.53       168.00 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       48.76       113.52        12.10        66.08        45.11       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-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F 
       24.53         9.34       103.59        39.75       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       40.14       131.90        18.38        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
      135.75       137.92         7.43       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV 
        3.65         6.41        11.34         3.25         9.90        48.89 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       36.03        20.38       176.55       107.34        61.18        65.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R 
       23.44        28.60        10.49        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        45.11        35.01         3.55        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       12.20        29.82         8.65        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       109.64       151.27        78.87       168.26 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       13.55        80.61        47.84        39.62        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       44.35        18.61        56.42        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       25.87        17.92        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
       55.59        44.88        94.82        19.76        47.28       103.27 
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       144.76       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       103.56       136.47 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         3.68        54.51 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        23.47       138.81       172.18        36.95        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       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-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
       48.89        13.02       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-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        43.82        23.34        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      210.08        15.16         7.00       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-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         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             4.90              0.16 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           215.44            357.37 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            53.16             47.54 
[1] "4.9 - 215.4 (53.2)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.3"
D50V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P LOSS MUTATED                    6             2
  6P LOSS WILD-TYPE                 31             2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6P LOSS MUTATED                                          16
  6P LOSS WILD-TYPE                                        44
                   vv
clus                REGIONAL LYMPH NODE
  6P LOSS MUTATED                    29
  6P LOSS WILD-TYPE                 150
D50V4, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  DISTANT METASTASIS                                      6                31
  PRIMARY TUMOR                                           2                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              16                44
  REGIONAL LYMPH NODE                                    29               150
[1] 4 2
[1] 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             4       2       4        0        4        5
  6P LOSS WILD-TYPE           6       4      19       10       21       12
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6P LOSS MUTATED           2         2         0         6          5
  6P LOSS WILD-TYPE         8        12        10        26          9
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED            4         12        1
  6P LOSS WILD-TYPE         19         36       11
D50V5, multiclass
             clus
vv            6P LOSS MUTATED 6P LOSS WILD-TYPE
  I OR II NOS               4                 6
  STAGE 0                   2                 4
  STAGE I                   4                19
  STAGE IA                  0                10
  STAGE IB                  4                21
  STAGE II                  5                12
  STAGE IIA                 2                 8
  STAGE IIB                 2                12
  STAGE IIC                 0                10
  STAGE III                 6                26
  STAGE IIIA                5                 9
  STAGE IIIB                4                19
  STAGE IIIC               12                36
  STAGE IV                  1                11
[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       8 13 15  8
  6P LOSS WILD-TYPE    45 47 40 49
D50V6, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               8                45
  T2                 13                47
  T3                 15                40
  T4                  8                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
  6P LOSS MUTATED    26  11   9   7
  6P LOSS WILD-TYPE 115  40  23  30
D50V7, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              26               115
  N1              11                40
  N2               9                23
  N3               7                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
  6P LOSS MUTATED    51   0   0   0   1
  6P LOSS WILD-TYPE 201   4   2   2   4
D50V8, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               51               201
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               1                 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"
D50V9, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   18 15
  6P LOSS WILD-TYPE 86 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     18   15
  6P LOSS WILD-TYPE   86   57
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               18                86
  YES              15                57
[1] 2 2
[1] FALSE
D50V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  48
  6P LOSS WILD-TYPE  29 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   48
  6P LOSS WILD-TYPE   29  199
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                5                29
  YES              48               199
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    17  36
  6P LOSS WILD-TYPE  91 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     17   36
  6P LOSS WILD-TYPE   91  137
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              17                91
  MALE                36               137
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         0    52
  6P LOSS WILD-TYPE     4                         1   223
D50V13, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  52               223
[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
  6P LOSS MUTATED     0  51
  6P LOSS WILD-TYPE   3 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   51
  6P LOSS WILD-TYPE    3  223
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              51               223
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   63 66
  6Q LOSS WILD-TYPE 74 67
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              129               141 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               66                67 
$`6Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 
       16.47       111.09        32.42        22.55        10.29        85.32 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
       68.22        69.90        11.41        30.87        36.16        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU 
       56.19        64.44        15.25         6.31       103.59        26.37 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
        5.39        41.10         8.84        13.94        95.38        52.01 
TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        1.55         2.89        11.31        13.22        14.60        48.79 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       51.12        39.19         9.99        36.69        25.15         4.93 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
        6.64        17.56        13.22        10.55         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H 
        1.35        12.20         5.13         4.31        36.07         9.21 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H 
        1.18         7.99        37.97        11.15         8.55         4.41 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       27.12         8.09         9.99         6.48         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       39.39        17.98        34.92        35.54        33.83        30.84 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC 
        5.42        36.33         8.84        98.27         2.70        47.51 
TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF 
       26.99        23.05         5.56        25.84         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 
       15.95        22.92        21.60        13.94        18.61         5.72 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P 
       25.18         3.52        11.11         4.21        42.84        34.68 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YX 
        1.51        13.08         1.71         4.90         3.58         3.45 
TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
       23.80         3.39        20.38        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
       12.92        47.38         8.65         8.81        49.15        40.64 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3R5 
        8.68        27.39         5.23        28.73         5.98         0.99 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 
        7.23        31.33        16.24        15.42        12.16        11.84 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       10.65        11.05         5.79 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
        8.52        70.16       110.79        28.08        45.83        81.24 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JP 
        8.38        21.14        88.50         7.50         6.31        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      114.67        46.98        46.32        82.29        61.38        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
       24.00         9.34        80.22        42.71        15.09        17.72 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 
       20.48        47.87         6.97        23.11         4.01         9.90 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 
       35.80        10.03        13.68        44.52        22.36        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         0.00 
TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A20C TCGA-EE-A20F 
        0.00         0.20        11.57         6.31         4.34         5.13 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        9.90        38.63         1.08         9.50        12.03         8.84 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GM 
       34.29        47.21        30.08        19.43        16.01        28.31 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME 
        1.15        13.02        34.98         6.18         9.53        29.46 
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       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
       56.02        25.08        21.60        29.65        27.16       124.31 
TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J8 
      122.73        30.15        12.72         3.22        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
       22.22        27.35         0.46        33.60        31.40        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H 
       38.40        76.41         3.78        11.90       114.15        34.88 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       13.45        28.60         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       11.80         1.87        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YW 
       22.49        18.41        85.74         6.71         5.36        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD 
       11.01        14.24        15.52         7.33         7.30         8.22 
TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 
       19.53        12.89        52.08         0.82        53.85         3.22 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 
        7.36        14.20        10.78         6.41         2.27         0.20 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 
        0.13         0.16         0.43         9.90        12.85        24.85 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D 
       84.72        10.13        14.70 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.99              0.00 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           111.09            124.31 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            13.22             14.83 
[1] "1.0 - 111.1 (13.2)" "0.0 - 124.3 (14.8)"
[1] "hr=" "1.2"
D51V2, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   66 67
  6Q LOSS WILD-TYPE 76 67
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              133               143 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               67                67 
$`6Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J7 
       16.57       112.04       112.57        31.59        43.43       103.10 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL 
      168.00        69.90        11.87        48.76        42.08       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU 
       56.19        66.08        58.06        13.87       103.59        39.75 
TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       21.47       131.90        10.03        15.06       110.93       135.75 
TCGA-D3-A5GR TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA 
      166.19       151.53         3.65         6.41         3.25        25.18 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
       66.25        22.95        48.89       117.21       194.83        35.93 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A5UL 
       61.18        53.92        65.92        68.09       215.44         3.55 
TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       52.01        27.22        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       68.15         4.96       109.64       168.26        13.55        63.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
       47.84        13.97        72.07        32.19        44.35        37.35 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       55.92       345.96        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      102.90        24.43        39.29        58.75        47.54       314.56 
TCGA-EE-A2GE TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GU 
      135.95        79.66        90.97       101.95        13.91        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MP TCGA-EE-A2MT 
       21.67       129.27        28.83        61.51       248.65        41.59 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 
       53.26        25.84         3.68        13.81        23.47       127.20 
TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
       64.08       101.79        35.44         9.17        98.40        12.59 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A2NE TCGA-ER-A2NF 
       26.37         6.44        44.05       162.08        20.15        16.37 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1ZB 
       33.21         4.90        15.16        48.59       202.65        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM 
      357.37        15.45         9.70        32.75        47.38       101.26 
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-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3R5 TCGA-GF-A4EO TCGA-GN-A264 
       27.02        28.73        26.73        22.92         7.23       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       64.44        62.79        32.48        46.36        12.62       294.77 
TCGA-QB-A6FS 
        6.67 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB 
       16.67        71.80       133.25        28.08        90.90        95.74 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JP 
       65.49        23.77       115.53       113.52        12.10        45.11 
TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE 
      130.72        46.98        46.32       166.52        86.93        60.23 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
       24.53         9.34       161.85        43.69        40.14        18.38 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A3Z1 
       51.68       137.92         7.43       125.19        54.67        11.34 
TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB 
        9.90        36.03        20.38       176.55       107.34        23.44 
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-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z 
       45.11        35.01         6.35        12.20        29.82         8.65 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N 
      151.27        78.87        80.61        39.62         2.60        18.61 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       56.42        14.47        67.43       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M8 
       54.74        75.48        14.30        55.59        44.88        19.76 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       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 
      144.76       203.05       167.90        47.54        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 
      136.47       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        33.40       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-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        7.00       216.92       228.59        20.91        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZY 
       27.72        53.52        40.27        23.93        74.73        27.09 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC 
       77.82        50.14        66.67       174.84        12.43        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16         2.40         9.90 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D 
       14.04       120.46        84.72        10.13        39.58 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             3.25              0.16 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           357.37            268.93 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            47.54             48.72 
[1] "3.2 - 357.4 (47.5)" "0.2 - 268.9 (48.7)"
[1] "hr=" "1.1"
D51V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q LOSS MUTATED                   20             3
  6Q LOSS WILD-TYPE                 17             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  6Q LOSS MUTATED                                          33
  6Q LOSS WILD-TYPE                                        27
                   vv
clus                REGIONAL LYMPH NODE
  6Q LOSS MUTATED                    80
  6Q LOSS WILD-TYPE                  99
D51V4, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     20                17
  PRIMARY TUMOR                                           3                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              33                27
  REGIONAL LYMPH NODE                                    80                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
  6Q LOSS MUTATED             6       4      10        6       13        8
  6Q LOSS WILD-TYPE           4       2      13        4       12        9
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  6Q LOSS MUTATED           4         5         3        14          8
  6Q LOSS WILD-TYPE         6         9         7        18          6
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           12         25        5
  6Q LOSS WILD-TYPE         11         23        7
D51V5, multiclass
             clus
vv            6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  I OR II NOS               6                 4
  STAGE 0                   4                 2
  STAGE I                  10                13
  STAGE IA                  6                 4
  STAGE IB                 13                12
  STAGE II                  8                 9
  STAGE IIA                 4                 6
  STAGE IIB                 5                 9
  STAGE IIC                 3                 7
  STAGE III                14                18
  STAGE IIIA                8                 6
  STAGE IIIB               12                11
  STAGE IIIC               25                23
  STAGE IV                  5                 7
[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      26 33 27 21
  6Q LOSS WILD-TYPE    27 27 28 36
D51V6, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1              26                27
  T2                 33                27
  T3                 27                28
  T4                 21                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                N0 N1 N2 N3
  6Q LOSS MUTATED   65 28 17 18
  6Q LOSS WILD-TYPE 76 23 15 19
D51V7, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              65                76
  N1              28                23
  N2              17                15
  N3              18                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
  6Q LOSS MUTATED   125   1   1   1   3
  6Q LOSS WILD-TYPE 127   3   1   1   2
D51V8, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              125               127
  M1                1                 3
  M1A               1                 1
  M1B               1                 1
  M1C               3                 2
[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
  6Q LOSS MUTATED   47 37
  6Q LOSS WILD-TYPE 57 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     47   37
  6Q LOSS WILD-TYPE   57   35
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               47                57
  YES              37                35
[1] 2 2
[1] FALSE
D51V10, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    18 118
  6Q LOSS WILD-TYPE  16 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     18  118
  6Q LOSS WILD-TYPE   16  129
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               18                16
  YES             118               129
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   53 83
  6Q LOSS WILD-TYPE 55 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     53   83
  6Q LOSS WILD-TYPE   55   90
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              53                55
  MALE                83                90
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       1                         1   134
  6Q LOSS WILD-TYPE     4                         0   141
D51V13, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                 134               141
[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
  6Q LOSS MUTATED     1 133
  6Q LOSS WILD-TYPE   2 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1  133
  6Q LOSS WILD-TYPE    2  141
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO             133               141
[1] 2 2
[1] FALSE

Clustering(52) Variable = 7P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     8   7
  7P LOSS WILD-TYPE 129 126
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               15               255 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                7               126 
$`7P LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A20C 
       45.83        13.32         5.39        14.83         0.20         4.34 
TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A198 TCGA-FR-A7U8 
       27.12         9.67        22.22        33.60        38.40         3.58 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
       49.15        40.64         8.68 

$`7P 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-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-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       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-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 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       20.48        13.94        95.38        52.01        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        6.97        23.11         4.01         2.89         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-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-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       13.15         0.13         0.00         0.00        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        36.07         5.13         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        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55         4.41         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         6.48         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        49.22        23.90         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        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        30.84         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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       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        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       16.14        27.35         0.46        13.94        31.40        18.61 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       12.95         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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        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-A729 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
       85.74         4.90         6.71         5.36        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-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
        8.81        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         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       10.65        11.05         5.79 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              0.2               0.0 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            49.15            124.31 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            14.83             13.94 
[1] "0.2 - 49.1 (14.8)"  "0.0 - 124.3 (13.9)"
[1] "hr=" "1"  
D52V2, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     8   7
  7P LOSS WILD-TYPE 134 127
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               15               261 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                7               127 
$`7P LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A20C 
       90.90        60.23        21.47        15.68        10.16       151.27 
TCGA-EE-A29M TCGA-EE-A2A5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A198 TCGA-FR-A7U8 
       44.35        39.29        53.19       148.08        50.76        15.16 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU 
      148.80        53.16        26.56 

$`7P 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-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-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       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-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 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       51.68        15.06       110.93       135.75       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
        7.43       125.19       151.53        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       11.34         3.25         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 
       45.11        35.01         3.55        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       109.64        78.87       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        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         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       345.96        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       46.82       102.90        24.43        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       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       101.95        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       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       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        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-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 
       34.32        27.35        33.40       101.79        31.40        35.44 
TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       13.94         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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       61.05        44.05       162.08        50.89        37.25       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-A729 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
      174.21         4.90       210.08         7.00       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-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
       11.41        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         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            10.16              0.16 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           151.27            357.37 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            50.76             47.54 
[1] "10.2 - 151.3 (50.8)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1.1"
D52V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P LOSS MUTATED                    4             0
  7P LOSS WILD-TYPE                 33             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7P LOSS MUTATED                                           3
  7P LOSS WILD-TYPE                                        57
                   vv
clus                REGIONAL LYMPH NODE
  7P LOSS MUTATED                     8
  7P LOSS WILD-TYPE                 171
D52V4, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  DISTANT METASTASIS                                      4                33
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               3                57
  REGIONAL LYMPH NODE                                     8               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
  7P LOSS MUTATED             0       1       1        0        4        1
  7P LOSS WILD-TYPE          10       5      22       10       21       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7P LOSS MUTATED           0         0         1         2          0
  7P LOSS WILD-TYPE        10        14         9        30         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED            3          1        0
  7P LOSS WILD-TYPE         20         47       12
D52V5, multiclass
             clus
vv            7P LOSS MUTATED 7P LOSS WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   1                 5
  STAGE I                   1                22
  STAGE IA                  0                10
  STAGE IB                  4                21
  STAGE II                  1                16
  STAGE IIA                 0                10
  STAGE IIB                 0                14
  STAGE IIC                 1                 9
  STAGE III                 2                30
  STAGE IIIA                0                14
  STAGE IIIB                3                20
  STAGE IIIC                1                47
  STAGE IV                  0                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
  7P LOSS MUTATED       1  9  0  1
  7P LOSS WILD-TYPE    52 51 55 56
D52V6, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               1                52
  T2                  9                51
  T3                  0                55
  T4                  1                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
  7P LOSS MUTATED     8   2   3   1
  7P LOSS WILD-TYPE 133  49  29  36
D52V7, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               8               133
  N1               2                49
  N2               3                29
  N3               1                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
  7P LOSS MUTATED    15   0   0   0   0
  7P LOSS WILD-TYPE 237   4   2   2   5
D52V8, multiclass
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               15               237
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 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
  7P LOSS MUTATED    6  3
  7P LOSS WILD-TYPE 98 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      6    3
  7P LOSS WILD-TYPE   98   69
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                6                98
  YES               3                69
[1] 2 2
[1] FALSE
D52V10, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2  13
  7P LOSS WILD-TYPE  32 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   13
  7P LOSS WILD-TYPE   32  234
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                2                32
  YES              13               234
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     4  11
  7P LOSS WILD-TYPE 104 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4   11
  7P LOSS WILD-TYPE  104  162
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               4               104
  MALE                11               162
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         0    14
  7P LOSS WILD-TYPE     4                         1   261
D52V13, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  14               261
[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
  7P LOSS MUTATED     0  15
  7P LOSS WILD-TYPE   3 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   15
  7P LOSS WILD-TYPE    3  259
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              15               259
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     7   7
  7Q LOSS WILD-TYPE 130 126
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               256 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7               126 
$`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        27.12         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 
        8.68        53.85 

$`7Q 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-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-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       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-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 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
        8.84        20.48        13.94        95.38        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         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         0.00         0.00 
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-A184 TCGA-EE-A185 TCGA-EE-A20B 
        1.12         1.35        12.20         5.13         4.31        36.07 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
        4.34         5.13         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-A29N 
       37.97        38.63         8.55         4.41         1.08         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         6.48         2.43 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        8.68         8.09        11.31        49.22        23.90         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
       19.43        16.01        35.54        28.31        30.84         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-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       111.78       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        29.65        27.16        23.05 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
        5.56       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       21.60        16.14        27.35         0.46        13.94        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-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       36.07        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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       18.41        85.74         4.90         6.71         3.58         5.36 
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-A1ZF 
        7.33         7.30         3.39        20.38         8.22        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-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.65         8.81        49.15        27.39         0.82         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-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        11.05         5.79 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              0.2               0.0 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            53.85            124.31 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           20.875            13.875 
[1] "0.2 - 53.9 (20.9)"  "0.0 - 124.3 (13.9)"
[1] "hr=" "1.1"
D53V2, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     7   7
  7Q LOSS WILD-TYPE 135 127
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               262 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7               127 
$`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        44.35        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 
       26.56        77.82 

$`7Q 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-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-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       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-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 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       10.03        51.68        15.06       110.93       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       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         3.25         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-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        45.11        35.01         3.55        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       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       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-A29N 
       47.84        39.62        72.07        32.19         2.60        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        37.35        14.47        55.92       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
      171.55        17.92        46.82       102.90        24.43        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GP 
       89.33        54.74        79.66        75.48       101.95        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-A2MG 
       28.83        19.76        61.51        47.28       103.27       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       144.76       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       103.56       136.47        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       64.08        34.32        27.35        33.40       101.79        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-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-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25        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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21         4.90       210.08        15.16         7.00 
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-A1ZF 
        7.79        27.72        48.85       357.37        53.52        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-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
      133.55        11.41       148.80        49.48        27.09        27.02 
TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       50.14        66.67        28.73       174.84        12.43        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
       49.45        77.88         0.20        22.92        47.54         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            10.16              0.16 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           148.18            357.37 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           53.175            47.540 
[1] "10.2 - 148.2 (53.2)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1.1"
D53V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q LOSS MUTATED                    3             0
  7Q LOSS WILD-TYPE                 34             4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  7Q LOSS MUTATED                                           4
  7Q LOSS WILD-TYPE                                        56
                   vv
clus                REGIONAL LYMPH NODE
  7Q LOSS MUTATED                     7
  7Q LOSS WILD-TYPE                 172
D53V4, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      3                34
  PRIMARY TUMOR                                           0                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               4                56
  REGIONAL LYMPH NODE                                     7               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
  7Q LOSS MUTATED             0       0       1        0        4        0
  7Q LOSS WILD-TYPE          10       6      22       10       21       17
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  7Q LOSS MUTATED           1         1         2         2          0
  7Q LOSS WILD-TYPE         9        13         8        30         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED            1          1        0
  7Q LOSS WILD-TYPE         22         47       12
D53V5, multiclass
             clus
vv            7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  I OR II NOS               0                10
  STAGE 0                   0                 6
  STAGE I                   1                22
  STAGE IA                  0                10
  STAGE IB                  4                21
  STAGE II                  0                17
  STAGE IIA                 1                 9
  STAGE IIB                 1                13
  STAGE IIC                 2                 8
  STAGE III                 2                30
  STAGE IIIA                0                14
  STAGE IIIB                1                22
  STAGE IIIC                1                47
  STAGE IV                  0                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
  7Q LOSS MUTATED       1  7  1  3
  7Q LOSS WILD-TYPE    52 53 54 54
D53V6, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               1                52
  T2                  7                53
  T3                  1                54
  T4                  3                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
  7Q LOSS MUTATED     9   3   1   0
  7Q LOSS WILD-TYPE 132  48  31  37
D53V7, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               9               132
  N1               3                48
  N2               1                31
  N3               0                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
  7Q LOSS MUTATED    13   0   0   0   0
  7Q LOSS WILD-TYPE 239   4   2   2   5
D53V8, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               13               239
  M1                0                 4
  M1A               0                 2
  M1B               0                 2
  M1C               0                 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"
D53V9, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    7  4
  7Q LOSS WILD-TYPE 97 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      7    4
  7Q LOSS WILD-TYPE   97   68
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                7                97
  YES               4                68
[1] 2 2
[1] FALSE
D53V10, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  13
  7Q LOSS WILD-TYPE  33 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   13
  7Q LOSS WILD-TYPE   33  234
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                33
  YES              13               234
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     5   9
  7Q LOSS WILD-TYPE 103 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      5    9
  7Q LOSS WILD-TYPE  103  164
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               5               103
  MALE                 9               164
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       1                         0    13
  7Q LOSS WILD-TYPE     4                         1   262
D53V13, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  13               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"
D53V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  14
  7Q LOSS WILD-TYPE   3 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   14
  7Q LOSS WILD-TYPE    3  260
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              14               260
[1] 2 2
[1] FALSE

Clustering(54) Variable = 8P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    24  25
  8P LOSS WILD-TYPE 113 108
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               49               221 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               25               108 
$`8P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 
       16.47        88.50        11.41         7.50        92.42        15.25 
TCGA-D3-A3MO TCGA-D3-A51N TCGA-D3-A5GN TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EB-A6L9 
        9.34         8.84        52.01        11.31         4.93         0.20 
TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
        8.12        12.20         4.34        37.97         4.41        27.12 
TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MG TCGA-EE-A2MI 
        2.43         9.67        30.08        13.02        44.25        14.56 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
       56.02        25.08        26.99        27.16         5.56       124.31 
TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19S 
       25.84         3.22        33.60        12.95         5.72        36.07 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZA 
        1.87         1.51         1.71        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 
        5.79 

$`8P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       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-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       21.14        68.22        69.90        30.87        36.16         6.31 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        64.44        45.11       114.67        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR 
       82.29        61.38        13.32        24.00         6.31       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       26.37         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
       17.72        20.48        13.94        95.38        47.87         1.55 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC 
        6.97        23.11         4.01         2.89         9.90        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-A1IB 
       13.68         9.99        44.52        36.69        25.15        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-A5UN TCGA-EE-A17X 
        0.20         0.13         0.00         0.00        13.22        11.57 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 
       10.55         6.31         1.12         1.35         5.13         4.31 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       36.07         5.13         9.21         1.18         7.99         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         8.55         1.08         9.50        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
        8.09         8.84         9.99         6.48         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       11.31        49.22        23.90         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       17.98        34.92        47.21        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT 
       28.31        33.83        30.84         5.42         1.15        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-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
        9.53        29.46         7.96        63.42       111.78       111.91 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       21.60        29.65        23.05       122.73         3.68        30.15 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       13.81        15.95        12.72        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         0.46        13.94        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       18.61        38.40        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-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       28.60        42.84        34.68         9.57        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
       11.80        13.08        12.62        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       22.49        18.41        85.74         4.90         6.71         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 
        5.36        64.47         3.45        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-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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        6.41         2.27         0.20         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 
        9.90         7.23        12.85        24.85        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       15.42        12.16        14.70        11.84        10.65 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              0.2               0.0 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           124.31            122.73 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            12.95             14.24 
[1] "0.2 - 124.3 (12.9)" "0.0 - 122.7 (14.2)"
[1] "hr=" "1.1"
D54V2, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    26  25
  8P LOSS WILD-TYPE 116 109
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               51               225 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               25               109 
$`8P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL TCGA-D3-A3C6 
       16.57       115.53        11.87       113.52       171.58        58.06 
TCGA-D3-A3MO TCGA-D3-A51N TCGA-D3-A5GN TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6EA 
        9.34        10.03       135.75       151.53         3.65        25.18 
TCGA-DA-A1IA TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29C 
       65.92        12.20        94.98        26.89       151.27        47.84 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GS 
       32.19        44.35        25.87        39.29        48.72        55.59 
TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS 
      103.20       204.66       167.90        47.54       248.65       136.47 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J3 TCGA-EE-A3JI TCGA-ER-A197 
       53.26       124.31        25.84       172.18       148.08        13.94 
TCGA-ER-A199 TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FS-A1YY 
        9.17        37.25        23.34        20.15        33.21       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 
       84.72       294.77         6.67 

$`8P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       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-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       23.77       168.00        69.90        48.76        42.08        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 
       56.19        66.08        45.11       130.72        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR 
      166.52        86.93        60.23        24.53        13.87       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
       39.75        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
       18.38        51.68        15.06       110.93       137.92       166.19 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
        7.43       125.19        54.67         6.41        11.34         3.25 
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-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-DA-A3F3 TCGA-DA-A3F5 
       53.92        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        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        3.55        52.01         6.35        29.82        27.22         8.65 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
       33.73        14.70        68.15         4.96       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
      168.26        13.55        63.35        80.61        13.97        39.62 
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-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       55.92       345.96       171.55        17.92        46.82       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        58.75        47.54        67.43       314.56       135.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      208.04        89.33        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      101.95        13.91        14.30        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-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ TCGA-EE-A2MR 
       16.96        96.23       144.76       203.05        43.23       103.56 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       41.59       122.73         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       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-A198 
       27.35        33.40       101.79        31.40        35.44        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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF 
      162.08        50.89       148.18        79.99        43.82        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-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
      174.21         4.90       210.08        15.16         7.00       216.92 
TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD 
       48.59        20.91        28.08         7.79        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-A1ZU 
      101.26        74.73       133.55        11.41       148.80        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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20        47.54         0.16         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       14.04       120.46        10.13        64.44        62.79        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 
       39.58        46.36        12.62 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             3.65              0.16 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           357.37            345.96 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            53.16             47.38 
[1] "3.6 - 357.4 (53.2)" "0.2 - 346.0 (47.4)"
[1] "hr=" "1.3"
D54V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P LOSS MUTATED                   12             1
  8P LOSS WILD-TYPE                 25             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8P LOSS MUTATED                                           6
  8P LOSS WILD-TYPE                                        54
                   vv
clus                REGIONAL LYMPH NODE
  8P LOSS MUTATED                    31
  8P LOSS WILD-TYPE                 148
D54V4, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  DISTANT METASTASIS                                     12                25
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               6                54
  REGIONAL LYMPH NODE                                    31               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
  8P LOSS MUTATED             2       3       6        4        6        1
  8P LOSS WILD-TYPE           8       3      17        6       19       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8P LOSS MUTATED           1         1         0         6          2
  8P LOSS WILD-TYPE         9        13        10        26         12
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED            3          8        2
  8P LOSS WILD-TYPE         20         40       10
D54V5, multiclass
             clus
vv            8P LOSS MUTATED 8P LOSS WILD-TYPE
  I OR II NOS               2                 8
  STAGE 0                   3                 3
  STAGE I                   6                17
  STAGE IA                  4                 6
  STAGE IB                  6                19
  STAGE II                  1                16
  STAGE IIA                 1                 9
  STAGE IIB                 1                13
  STAGE IIC                 0                10
  STAGE III                 6                26
  STAGE IIIA                2                12
  STAGE IIIB                3                20
  STAGE IIIC                8                40
  STAGE IV                  2                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
  8P LOSS MUTATED      12 14  5  7
  8P LOSS WILD-TYPE    41 46 50 50
D54V6, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              12                41
  T2                 14                46
  T3                  5                50
  T4                  7                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
  8P LOSS MUTATED    26   8   5   8
  8P LOSS WILD-TYPE 115  43  27  29
D54V7, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              26               115
  N1               8                43
  N2               5                27
  N3               8                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
  8P LOSS MUTATED    45   0   1   1   1
  8P LOSS WILD-TYPE 207   4   1   1   4
D54V8, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               45               207
  M1                0                 4
  M1A               1                 1
  M1B               1                 1
  M1C               1                 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"
D54V9, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   23  7
  8P LOSS WILD-TYPE 81 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     23    7
  8P LOSS WILD-TYPE   81   65
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               23                81
  YES               7                65
[1] 2 2
[1] FALSE
D54V10, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     6  45
  8P LOSS WILD-TYPE  28 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      6   45
  8P LOSS WILD-TYPE   28  202
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                6                28
  YES              45               202
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    19  32
  8P LOSS WILD-TYPE  89 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     19   32
  8P LOSS WILD-TYPE   89  141
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              19                89
  MALE                32               141
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       1                         0    50
  8P LOSS WILD-TYPE     4                         1   225
D54V13, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  50               225
[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
  8P LOSS MUTATED     0  51
  8P LOSS WILD-TYPE   3 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   51
  8P LOSS WILD-TYPE    3  223
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              51               223
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     9  11
  8Q LOSS WILD-TYPE 128 122
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               250 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               122 
$`8Q LOSS MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EE-A180 TCGA-EE-A20C 
       11.41        92.42        11.31         4.93         8.12         4.34 
TCGA-EE-A29M TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
       27.12        14.56        56.02        26.99        27.16         5.56 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FS-A1ZA 
       33.60         5.72        11.90         1.51         1.71         7.30 
TCGA-FS-A1ZC TCGA-FW-A3R5 
       20.38         0.99 

$`8Q 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-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-A2JF 
        8.38        21.14        88.50        68.22        69.90        30.87 
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        45.11 
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 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
        8.84        20.48        13.94        95.38        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         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-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         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.20        11.57        10.55         6.31         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        36.07         5.13         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        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        8.55         4.41         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         6.48         2.43         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       11.31        49.22        23.90         9.67         8.94        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        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        30.84         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-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ 
        7.96        63.42       111.78       111.91        25.08        21.60 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       29.65        23.05       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       13.94        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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       36.07        17.72        78.44        11.80         1.87        13.08 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
       12.62        11.74         9.04         6.58        22.49        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       85.74         4.90         6.71         3.58         5.36        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-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       11.84        10.65        11.05         5.79 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.99              0.00 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            92.42            124.31 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            11.36             14.42 
[1] "1.0 - 92.4 (11.4)"  "0.0 - 124.3 (14.4)"
[1] "hr=" "1.5"
D55V2, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     9  11
  8Q LOSS WILD-TYPE 133 123
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               256 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               123 
$`8Q LOSS MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D9-A6EA TCGA-DA-A1IA TCGA-EE-A180 TCGA-EE-A20C 
       11.87       171.58        25.18        65.92        94.98       151.27 
TCGA-EE-A29M TCGA-EE-A2MI TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
       44.35       204.66       167.90       248.65       136.47        53.26 
TCGA-EE-A3JI TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A2NE TCGA-ER-A3PL TCGA-FS-A1ZA 
      148.08         9.17        13.02        20.15        33.21        27.72 
TCGA-FS-A1ZC TCGA-FW-A3R5 
      357.37        22.92 

$`8Q 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-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-A2JF 
       65.49        23.77       115.53       168.00        69.90        48.76 
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        45.11 
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 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       10.03        51.68        15.06       110.93       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       151.53        54.67         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        6.41        11.34         3.25         9.90        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-A1IB TCGA-DA-A1IC 
       35.93       107.34        61.18        53.92        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        45.11        35.01         3.55        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       12.20        29.82        27.22         8.65        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       109.64        78.87       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        39.62 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       72.07        32.19         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       345.96        25.87       171.55        17.92 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       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       101.95        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-A2MG 
       28.83        19.76        61.51        47.28       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ 
       16.96        96.23       144.76       203.05        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
      103.56        41.59       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
      101.79        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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NF 
       37.25       148.18        79.99        43.82        23.34        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-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
      174.21         4.90       210.08        15.16         7.00       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-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
       46.36        12.62       294.77         6.67 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             9.17              0.16 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           357.37            345.96 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            59.59             47.54 
[1] "9.2 - 357.4 (59.6)" "0.2 - 346.0 (47.5)"
[1] "hr=" "1.4"
D55V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q LOSS MUTATED                    6             1
  8Q LOSS WILD-TYPE                 31             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  8Q LOSS MUTATED                                           2
  8Q LOSS WILD-TYPE                                        58
                   vv
clus                REGIONAL LYMPH NODE
  8Q LOSS MUTATED                    11
  8Q LOSS WILD-TYPE                 168
D55V4, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      6                31
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               2                58
  REGIONAL LYMPH NODE                                    11               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
  8Q LOSS MUTATED             2       2       3        1        2        1
  8Q LOSS WILD-TYPE           8       4      20        9       23       16
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  8Q LOSS MUTATED           0         1         0         2          0
  8Q LOSS WILD-TYPE        10        13        10        30         14
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED            2          3        1
  8Q LOSS WILD-TYPE         21         45       11
D55V5, multiclass
             clus
vv            8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  I OR II NOS               2                 8
  STAGE 0                   2                 4
  STAGE I                   3                20
  STAGE IA                  1                 9
  STAGE IB                  2                23
  STAGE II                  1                16
  STAGE IIA                 0                10
  STAGE IIB                 1                13
  STAGE IIC                 0                10
  STAGE III                 2                30
  STAGE IIIA                0                14
  STAGE IIIB                2                21
  STAGE IIIC                3                45
  STAGE IV                  1                11
[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  6  2  6
  8Q LOSS WILD-TYPE    52 54 53 51
D55V6, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               1                52
  T2                  6                54
  T3                  2                53
  T4                  6                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
  8Q LOSS MUTATED    14   2   2   2
  8Q LOSS WILD-TYPE 127  49  30  35
D55V7, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              14               127
  N1               2                49
  N2               2                30
  N3               2                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
  8Q LOSS MUTATED    19   0   1   0   0
  8Q LOSS WILD-TYPE 233   4   1   2   5
D55V8, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               19               233
  M1                0                 4
  M1A               1                 1
  M1B               0                 2
  M1C               0                 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"
D55V9, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    8  4
  8Q LOSS WILD-TYPE 96 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      8    4
  8Q LOSS WILD-TYPE   96   68
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                8                96
  YES               4                68
[1] 2 2
[1] FALSE
D55V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  20
  8Q LOSS WILD-TYPE  34 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   20
  8Q LOSS WILD-TYPE   34  227
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                34
  YES              20               227
[1] 2 2
[1] FALSE
D55V11, continuous
D55V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     8  12
  8Q LOSS WILD-TYPE 100 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      8   12
  8Q LOSS WILD-TYPE  100  161
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               8               100
  MALE                12               161
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         0    20
  8Q LOSS WILD-TYPE     5                         1   255
D55V13, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  20               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"
D55V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  20
  8Q LOSS WILD-TYPE   3 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   20
  8Q LOSS WILD-TYPE    3  254
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              20               254
[1] 2 2
[1] FALSE

Clustering(56) Variable = 9P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   84 92
  9P LOSS WILD-TYPE 53 41
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              176                94 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               92                41 
$`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        69.90        30.87         6.31        92.42 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF 
       56.19        45.11        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         5.39        80.22 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
       41.10         8.84        13.94        95.38        47.87         1.55 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV 
       23.11         4.01         2.89         9.90        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-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R 
       25.15         4.93         6.64        17.56        13.15         0.20 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
        0.00        13.22        11.57        10.55         8.12         1.12 
TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
        1.35         4.31        36.07         4.34         5.13         9.21 
TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
        1.18        37.97        11.15        38.63         8.55         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
        9.50        12.03         8.09         9.99         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
        8.09        11.31         9.67        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
       34.92        47.21        30.08        35.54        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       30.84         5.42         1.15        13.02        36.33        98.27 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
        6.18         9.53         7.96       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB 
       25.08        26.99        29.65        27.16       124.31       122.73 
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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       21.60        16.14        22.22        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       18.61        12.95         5.72        25.18         3.78         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19P 
       11.90        11.11        34.88        13.45        28.60        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A2NH 
        9.57        36.07        17.72         1.87        12.62        11.74 
TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        9.04        22.49         1.71        18.41        85.74         4.90 
TCGA-FR-A729 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 
        6.71        64.47         3.45        11.01        14.24         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.30         3.39        20.38         8.22        11.08        30.87 
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-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-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 
        6.41         0.20         0.99         0.13         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 
       24.85        84.72        15.42        12.16        14.70        10.65 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

$`9P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
        8.52       110.79        22.55        45.83        81.24         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO 
       21.14        88.50        11.41         7.50        36.16        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51F TCGA-D3-A51H 
      114.67        46.32        82.29        13.32        42.71        15.09 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D9-A6EA TCGA-D9-A6EC 
       17.72        20.48        52.01         6.97        11.31        13.22 
TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       10.03        36.69        22.36        19.36         7.00        14.83 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 
        0.13         0.00         0.20         6.31        12.20         5.13 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T 
        7.99         9.90         4.41        27.12         8.84         6.48 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT 
       49.22        23.90         8.94        19.43        16.01        34.98 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
        8.84         2.70        47.51        29.46        44.25        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 
       63.42        21.60        23.05         5.56        25.84        22.92 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19G 
       21.60        27.35         0.46        38.40        76.41       114.15 
TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
        4.21        42.84        78.44        11.80         1.51        13.08 
TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE 
        6.58         3.58         5.36        23.80        15.52        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU 
        7.17        12.92        12.89        52.08        40.64         8.68 
TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        5.23        14.20         2.27         0.16         0.43         9.90 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 
       31.33        10.13        16.24        11.84 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                0                 0 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           124.31            114.67 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           13.745            14.960 
[1] "0.0 - 124.3 (13.7)" "0.0 - 114.7 (15.0)"
[1] "hr=" "1.2"
D56V2, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   87 92
  9P LOSS WILD-TYPE 55 42
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              179                97 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               92                42 
$`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        69.90        48.76        12.10       171.58 
TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3CF 
       56.19        45.11        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        21.47       161.85 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D3-A5GR 
      131.90        10.03        15.06       110.93       137.92       166.19 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      125.19       151.53        54.67        11.34         3.25         9.90 
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-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
       35.93       107.34        53.92        65.92        68.09       215.44 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X 
       13.87        10.16        45.11         3.55        52.01        29.82 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B 
       27.22        94.98        33.73        14.70         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
      151.27        78.87       168.26        13.55        47.84        13.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       39.62        72.07         2.60        18.61        56.42        37.35 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 
       55.92        25.87       171.55        17.92        46.82        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       208.04        48.72 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       79.66        75.48        90.97       101.95        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MH 
       55.59        94.82       129.27        19.76        47.28        16.96 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR 
      144.76       203.05       167.90        47.54       248.65       103.56 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      136.47       124.31       122.73         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
       23.47       138.81       172.18        64.08        34.32        53.19 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 
      101.79       148.08        31.40        35.44        13.94         9.17 
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-A19L TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
      131.51        61.05       162.08        50.89        37.25       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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YW TCGA-FS-A1YX 
       92.98       174.21         4.90       210.08       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC 
      228.59        20.91         7.79        27.72        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52        15.45        32.75       101.26       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
      148.80        49.48        27.09        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-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 
       47.54         7.23        14.04       120.46        84.72        62.79 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        39.58        12.62       294.77         6.67 

$`9P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J8 
       16.67       133.25        31.59        90.90        95.74        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JO 
       23.77       115.53        11.87       113.52        42.08        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A51F TCGA-D3-A51H 
      130.72        46.32       166.52        60.23        43.69        40.14 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D9-A1JW TCGA-D9-A1JX 
       18.38        51.68       135.75         7.43         3.65         6.41 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 
       25.18        66.25        20.38        61.18        23.44        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 
       10.49        15.68        17.85        35.01         6.35        12.20 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H 
        8.65        26.89        68.15        63.35        80.61        32.19 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       44.35        14.47       345.96       102.90        24.43        58.75 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2MC 
       89.33        54.74        44.88        21.67        28.83        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MQ TCGA-EE-A2MT 
      103.27       103.20       204.66        96.23        43.23        41.59 
TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE 
       53.26        25.84       127.20        36.95        27.35        33.40 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 
       50.76        77.75       268.93         6.44        44.05        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ET TCGA-FR-A7U8 TCGA-FR-A7U9 
       43.82        20.15        16.37        80.32        15.16         7.00 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      202.65        28.08        40.27         9.70        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F8 TCGA-FS-A4FD 
       74.73        53.16        26.56        27.02       174.84        77.88 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        0.16         2.40         9.90       117.93        10.13        64.44 
TCGA-GN-A4U8 
       46.36 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.20              0.16 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           357.37            345.96 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            49.45             43.69 
[1] "0.2 - 357.4 (49.5)" "0.2 - 346.0 (43.7)"
[1] "hr=" "1.1"
D56V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P LOSS MUTATED                   25             1
  9P LOSS WILD-TYPE                 12             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9P LOSS MUTATED                                          44
  9P LOSS WILD-TYPE                                        16
                   vv
clus                REGIONAL LYMPH NODE
  9P LOSS MUTATED                   112
  9P LOSS WILD-TYPE                  67
D56V4, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  DISTANT METASTASIS                                     25                12
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              44                16
  REGIONAL LYMPH NODE                                   112                67
[1] 4 2
[1] 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             9       3      14        5       16       13
  9P LOSS WILD-TYPE           1       3       9        5        9        4
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9P LOSS MUTATED           8         9         7        21          7
  9P LOSS WILD-TYPE         2         5         3        11          7
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           15         30        8
  9P LOSS WILD-TYPE          8         18        4
D56V5, multiclass
             clus
vv            9P LOSS MUTATED 9P LOSS WILD-TYPE
  I OR II NOS               9                 1
  STAGE 0                   3                 3
  STAGE I                  14                 9
  STAGE IA                  5                 5
  STAGE IB                 16                 9
  STAGE II                 13                 4
  STAGE IIA                 8                 2
  STAGE IIB                 9                 5
  STAGE IIC                 7                 3
  STAGE III                21                11
  STAGE IIIA                7                 7
  STAGE IIIB               15                 8
  STAGE IIIC               30                18
  STAGE IV                  8                 4
[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      32 42 37 36
  9P LOSS WILD-TYPE    21 18 18 21
D56V6, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              32                21
  T2                 42                18
  T3                 37                18
  T4                 36                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
  9P LOSS MUTATED   96 33 18 23
  9P LOSS WILD-TYPE 45 18 14 14
D56V7, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              96                45
  N1              33                18
  N2              18                14
  N3              23                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  9P LOSS MUTATED   163   2   1   2   4
  9P LOSS WILD-TYPE  89   2   1   0   1
D56V8, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              163                89
  M1                2                 2
  M1A               1                 1
  M1B               2                 0
  M1C               4                 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"
D56V9, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   65 49
  9P LOSS WILD-TYPE 39 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     65   49
  9P LOSS WILD-TYPE   39   23
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               65                39
  YES              49                23
[1] 2 2
[1] FALSE
D56V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    22 161
  9P LOSS WILD-TYPE  12  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     22  161
  9P LOSS WILD-TYPE   12   86
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               22                12
  YES             161                86
[1] 2 2
[1] FALSE
D56V11, continuous
D56V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    79 104
  9P LOSS WILD-TYPE  29  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     79  104
  9P LOSS WILD-TYPE   29   69
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              79                29
  MALE               104                69
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       3                         1   179
  9P LOSS WILD-TYPE     2                         0    96
D56V13, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                 179                96
[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
  9P LOSS MUTATED     0 180
  9P LOSS WILD-TYPE   3  94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0  180
  9P LOSS WILD-TYPE    3   94
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO             180                94
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   68 70
  9Q LOSS WILD-TYPE 69 63
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              138               132 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               70                63 
$`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-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MR 
       92.42        45.11        15.25        46.98        61.38       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       26.37         5.39        41.10         8.84        13.94        95.38 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
       47.87        23.11         9.90        48.79        35.80        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
       13.68         9.99        44.52        25.15         4.93         6.64 
TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A180 
       17.56         0.20         0.00        13.22        10.55         8.12 
TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        1.12        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       11.15         8.55         1.08         9.50        12.03         8.09 
TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB 
        9.99         8.68         8.09        11.31        23.90        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       34.29        17.98        34.92        47.21        30.08        19.43 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M6 
       35.54        28.31        33.83         5.42        13.02        98.27 
TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP 
        6.18         7.96       111.78       111.91        56.02        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       21.60        29.65        27.16       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3J8 TCGA-EE-A3JA 
       30.15        13.81        15.95        21.60        16.14        22.22 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        33.60        31.40        18.61        12.95 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H 
        5.72        25.18         3.78         3.52        11.11        34.88 
TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A2NH TCGA-ER-A3EV 
       28.60        34.68         9.57        17.72        11.74        22.49 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        1.71         4.90         6.71        64.47        11.01        14.24 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.30         3.39        20.38         8.22        11.08        30.87 
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-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FC 
        5.23        53.85         3.22        28.73         5.98         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.20         0.99         0.16         7.23        12.85        24.85 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-OD-A75X 
       84.72        15.42        12.16        14.70        10.65        11.05 

$`9Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
        8.52       111.09       110.79        22.55        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        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       30.87         7.50        36.16         6.31        56.19        64.44 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
      114.67        46.32        82.29        13.32        24.00         6.31 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
        9.34        80.22        42.71        15.09        17.72        20.48 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EA 
       52.01         1.55         6.97         4.01         2.89        11.31 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB 
       13.22        14.60        51.12        10.03        36.69        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH 
       19.36         7.00        14.83        13.15         0.13         0.00 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        0.20        11.57         6.31         1.35        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
        4.31         7.99         9.90        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A5 
       27.12         8.84         6.48         2.43        49.22         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU 
        8.94        16.01        30.84         1.15        34.98        36.33 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
        8.84         2.70        47.51         9.53        29.46        44.25 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MN TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC 
       14.56        63.42        25.08        23.05         5.56        25.84 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A198 
       12.72         3.22        22.92        21.60        27.35        38.40 
TCGA-ER-A19A TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
       76.41        11.90       114.15         4.21        13.45        42.84 
TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       36.07        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 
       12.62         9.04         6.58        18.41        85.74         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE 
        5.36         3.45        23.80        15.52         7.33        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU 
        7.17        12.92        12.89        52.08        40.64         8.68 
TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY 
        7.36        14.20        10.78         2.27         0.13         0.43 
TCGA-GF-A3OT TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 TCGA-QB-A6FS 
        9.90        31.33        10.13        16.24        11.84         5.79 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                0                 0 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           124.31            114.67 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           15.335            13.185 
[1] "0.0 - 124.3 (15.3)" "0.0 - 114.7 (13.2)"
[1] "hr=" "1"  
D57V2, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   70 70
  9Q LOSS WILD-TYPE 72 64
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              140               136 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               70                64 
$`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-A2JL TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CC TCGA-D3-A3MR 
      171.58        45.11        58.06        46.98        86.93       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL 
       39.75        21.47       131.90        10.03        15.06       110.93 
TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A6E9 TCGA-DA-A1HV 
      137.92       125.19       151.53        54.67         9.90        48.89 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       36.03       194.83       176.55        35.93       107.34        53.92 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5UN 
       65.92        68.09       215.44        10.16        45.11        52.01 
TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F 
       27.22        94.98        33.73       109.64       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N 
      168.26        13.55        13.97        72.07         2.60        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 
       56.42        37.35        55.92       171.55        17.92        46.82 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       24.43        47.54        67.43       314.56       135.95       208.04 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       48.72        89.33        79.66        75.48        90.97        13.91 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2ML 
       55.59       129.27        19.76        16.96       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA 
      167.90       248.65        43.23       103.56       136.47       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J5 
      122.73         3.68        54.51        13.81        23.47        36.95 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       34.32        53.19        33.40       101.79       148.08        31.40 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       35.44        13.94         9.17        98.40        48.89        12.59 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       26.37       152.35        61.05       162.08        50.89       148.18 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A729 TCGA-FS-A1YW 
       32.05        46.98        33.21         4.90       210.08       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD 
      228.59        20.91        27.72        48.85       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       15.45        32.75       101.26       133.55        11.41       148.80 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F5 
       49.48        27.09        27.02        77.82        50.14        28.73 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A4EO 
       26.73        49.45         0.20        22.92         0.16         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       14.04       120.46        84.72        62.79        32.48        39.58 
TCGA-GN-A4U9 TCGA-OD-A75X 
       12.62       294.77 

$`9Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.67       112.04       133.25        31.59        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        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO 
       48.76       113.52        42.08        12.10        56.19        66.08 
TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML 
      130.72        46.32       166.52        60.23        24.53        13.87 
TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R 
        9.34       161.85        43.69        40.14        18.38        51.68 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      135.75       166.19         7.43         3.65         6.41        11.34 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 
        3.25        25.18        66.25        22.95       117.21        20.38 
TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
       61.18        23.44        28.60        10.49        15.68        13.87 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       17.85        35.01         3.55         6.35        12.20        29.82 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A29A 
        8.65        14.70        26.89        68.15         4.96        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R 
       80.61        47.84        39.62        32.19        44.35        14.47 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GK 
      345.96        25.87       102.90        39.29        58.75        54.74 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 
      101.95        14.30        44.88        94.82        21.67        28.83 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51        47.28       103.27       103.20       204.66        96.23 
TCGA-EE-A2MN TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AC TCGA-EE-A3AH TCGA-EE-A3J3 
       47.54        41.59        53.26        25.84       138.81       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19E 
      127.20        64.08        27.35        50.76        77.75        13.02 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19S TCGA-ER-A1A1 
      268.93         6.44       131.51        44.05        37.25        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        31.27       247.04 
TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YX 
       80.32        92.98       174.21        15.16         7.00        48.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ 
      202.65        28.08         7.79        40.27         9.70        47.38 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A4F4 TCGA-FS-A4F8 
       23.93        74.73        53.16        26.56        66.67       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A264 
       12.43        77.88        47.54         2.40         9.90       117.93 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 TCGA-QB-A6FS 
       10.13        64.44        46.36         6.67 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.16              2.40 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           357.37            345.96 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           52.600            43.935 
[1] "0.2 - 357.4 (52.6)" "2.4 - 346.0 (43.9)"
[1] "hr=" "1.2"
D57V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q LOSS MUTATED                   20             1
  9Q LOSS WILD-TYPE                 17             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  9Q LOSS MUTATED                                          36
  9Q LOSS WILD-TYPE                                        24
                   vv
clus                REGIONAL LYMPH NODE
  9Q LOSS MUTATED                    84
  9Q LOSS WILD-TYPE                  95
D57V4, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  DISTANT METASTASIS                                     20                17
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              36                24
  REGIONAL LYMPH NODE                                    84                95
[1] 4 2
[1] 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             7       2      11        3       12        8
  9Q LOSS WILD-TYPE           3       4      12        7       13        9
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  9Q LOSS MUTATED           7         9         7        18          6
  9Q LOSS WILD-TYPE         3         5         3        14          8
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           13         17        8
  9Q LOSS WILD-TYPE         10         31        4
D57V5, multiclass
             clus
vv            9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  I OR II NOS               7                 3
  STAGE 0                   2                 4
  STAGE I                  11                12
  STAGE IA                  3                 7
  STAGE IB                 12                13
  STAGE II                  8                 9
  STAGE IIA                 7                 3
  STAGE IIB                 9                 5
  STAGE IIC                 7                 3
  STAGE III                18                14
  STAGE IIIA                6                 8
  STAGE IIIB               13                10
  STAGE IIIC               17                31
  STAGE IV                  8                 4
[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      26 30 29 30
  9Q LOSS WILD-TYPE    27 30 26 27
D57V6, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              26                27
  T2                 30                30
  T3                 29                26
  T4                 30                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                N0 N1 N2 N3
  9Q LOSS MUTATED   78 25 16 14
  9Q LOSS WILD-TYPE 63 26 16 23
D57V7, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              78                63
  N1              25                26
  N2              16                16
  N3              14                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
  9Q LOSS MUTATED   126   2   1   2   4
  9Q LOSS WILD-TYPE 126   2   1   0   1
D57V8, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              126               126
  M1                2                 2
  M1A               1                 1
  M1B               2                 0
  M1C               4                 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
  9Q LOSS MUTATED   53 36
  9Q LOSS WILD-TYPE 51 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     53   36
  9Q LOSS WILD-TYPE   51   36
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               53                51
  YES              36                36
[1] 2 2
[1] FALSE
D57V10, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    18 124
  9Q LOSS WILD-TYPE  16 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     18  124
  9Q LOSS WILD-TYPE   16  123
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               18                16
  YES             124               123
[1] 2 2
[1] FALSE
D57V11, continuous
D57V12, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   62 80
  9Q LOSS WILD-TYPE 46 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     62   80
  9Q LOSS WILD-TYPE   46   93
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              62                46
  MALE                80                93
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       2                         0   140
  9Q LOSS WILD-TYPE     3                         1   135
D57V13, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                 140               135
[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
  9Q LOSS MUTATED     1 140
  9Q LOSS WILD-TYPE   2 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1  140
  9Q LOSS WILD-TYPE    2  134
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO             140               134
[1] 2 2
[1] FALSE

Clustering(58) Variable = 10P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   75 76
  10P LOSS WILD-TYPE 62 57
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               151                119 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                76                 57 
$`10P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       22.55        88.50        69.90        11.41         7.50         6.31 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF 
       56.19        64.44        45.11        46.98        13.32        24.00 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
        9.34        26.37         5.39        42.71        41.10        17.72 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       13.94        52.01        47.87         1.55         6.97        23.11 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 
        2.89         9.90        11.31        14.60        35.80        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-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 
       17.56         0.20         0.00        13.22         6.31         8.12 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29G 
        1.12         4.31        36.07         9.21         1.18         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T 
        4.41         1.08        27.12        12.03         8.09         6.48 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC 
        8.68         8.09        23.90         9.67        39.39        34.29 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN 
       34.92        47.21        30.08        19.43        28.31        33.83 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
       30.84         5.42         1.15        13.02        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM 
        2.70         6.18        44.25         7.96       111.78        56.02 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD 
       26.99        27.16         5.56       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       30.15        12.72         3.22        22.92        21.60        21.60 
TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A199 
       16.14        22.22         0.46        13.94        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-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH 
       17.72        11.80         1.87         1.51        12.62        11.74 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
        6.71         3.58         3.45        23.80        14.24         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
        7.30        20.38         8.22        11.08         7.17        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW 
       12.92        47.38         8.65         8.81         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO 
        0.82         7.36        28.73         2.27         0.16         7.23 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 
       31.33        10.13        16.24        15.42        12.16        10.65 
TCGA-OD-A75X 
       11.05 

$`10P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
        8.52        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A3BZ 
       21.14        68.22        30.87        36.16        92.42       114.67 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MR 
       15.25        46.32        82.29        61.38         6.31       103.59 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D9-A3Z1 
       80.22        15.09         8.84        20.48        95.38         4.01 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC 
       13.22        48.79        51.12        10.03        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       19.36         7.00        14.83        13.15         0.13         0.00 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
        0.20        11.57        10.55         1.35        12.20         5.13 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        4.34         5.13         7.99         9.90        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 
       38.63         9.50         8.84         9.99         2.43        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT 
       49.22         8.94        17.98        16.01        35.54        34.98 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ 
        8.84        47.51         9.53        29.46        14.56        63.42 
TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC 
      111.91        25.08        21.60        29.65        23.05        25.84 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
       13.81        15.95        27.35        31.40        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G 
       38.40        76.41        25.18         3.78        11.11       114.15 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NF 
        4.21        28.60        42.84         9.57        78.44        13.08 
TCGA-ER-A3ES TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB 
        9.04         5.36        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         0.43         9.90        12.85 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       24.85        84.72        14.70        11.84         5.79 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                  0 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            124.31             114.67 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             13.68              14.70 
[1] "0.0 - 124.3 (13.7)" "0.0 - 114.7 (14.7)"
[1] "hr=" "1.2"
D58V2, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   77 76
  10P LOSS WILD-TYPE 65 58
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               153                123 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                76                 58 
$`10P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       31.59       115.53        69.90        11.87       113.52        12.10 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CE TCGA-D3-A3CF 
       56.19        66.08        45.11        46.98        60.23        24.53 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F TCGA-D3-A51J TCGA-D3-A51K 
        9.34        39.75        21.47        43.69       131.90        18.38 
TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       15.06       135.75       137.92       166.19         7.43       125.19 
TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HW 
       54.67         3.25         9.90        25.18        22.95        36.03 
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-A3F5 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       65.92       215.44        10.16        35.01         3.55        52.01 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H 
        8.65        94.98        33.73         4.96       109.64       168.26 
TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P 
       13.55        72.07        32.19         2.60        44.35        56.42 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
       37.35       345.96       171.55        17.92        24.43        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       47.54        67.43       135.95       208.04        48.72        89.33 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       75.48        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH 
       94.82       129.27        28.83        19.76       103.20        16.96 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA 
      144.76       167.90       248.65       136.47        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
      122.73         3.68        54.51       138.81       172.18       127.20 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JH 
       36.95        64.08        34.32        53.19        33.40       101.79 
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-A19W TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
      162.08        37.25       148.18        43.82        23.34        20.15 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       31.27        32.05        80.32        46.98        33.21        92.98 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 
      174.21         4.90       210.08        15.16        48.59       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-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        32.75        47.38       101.26       133.55        11.41 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD 
       26.56        49.48        27.09        66.67        28.73        77.88 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.16         7.23       117.93        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       32.48        12.62       294.77 

$`10P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       16.67        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A3BZ 
       23.77       168.00        48.76        42.08       171.58       130.72 
TCGA-D3-A3C6 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MR 
       58.06        46.32       166.52        86.93        13.87       103.59 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D9-A148 
      161.85        40.14        10.03        51.68       110.93       151.53 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HY 
        3.65         6.41        11.34        66.25        48.89       117.21 
TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       20.38        23.44        68.09        28.60        10.49        15.68 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.87        17.85        45.11         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20F 
       27.22        14.70        26.89        68.15       151.27        78.87 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N 
       63.35        80.61        47.84        13.97        39.62        18.61 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       14.47        55.92        25.87        46.82       102.90        58.75 
TCGA-EE-A2GD TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC 
      314.56        54.74        79.66        44.88        21.67        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
       47.28       103.27       204.66        96.23       203.05        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
       43.23       103.56        41.59        25.84        13.81        23.47 
TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A 
       27.35        31.40        35.44        13.94        50.76        77.75 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M 
       98.40        48.89        26.37       268.93         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FR-A7U9 
       44.05        50.89        79.99        16.37       247.04         7.00 
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-GN-A262 TCGA-GN-A265 
       47.54         2.40         9.90        14.04       120.46        84.72 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       39.58        46.36         6.67 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.16               0.20 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            357.37             314.56 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             49.48              47.28 
[1] "0.2 - 357.4 (49.5)" "0.2 - 314.6 (47.3)"
[1] "hr=" "1"  
D58V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10P LOSS MUTATED                   21             2
  10P LOSS WILD-TYPE                 16             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10P LOSS MUTATED                                          42
  10P LOSS WILD-TYPE                                        18
                    vv
clus                 REGIONAL LYMPH NODE
  10P LOSS MUTATED                    92
  10P LOSS WILD-TYPE                  87
D58V4, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  DISTANT METASTASIS                                      21                 16
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               42                 18
  REGIONAL LYMPH NODE                                     92                 87
[1] 4 2
[1] 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             6       3      13        7       14       11
  10P LOSS WILD-TYPE           4       3      10        3       11        6
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10P LOSS MUTATED           3         5         5        21         10
  10P LOSS WILD-TYPE         7         9         5        11          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           13         28        7
  10P LOSS WILD-TYPE         10         20        5
D58V5, multiclass
             clus
vv            10P LOSS MUTATED 10P LOSS WILD-TYPE
  I OR II NOS                6                  4
  STAGE 0                    3                  3
  STAGE I                   13                 10
  STAGE IA                   7                  3
  STAGE IB                  14                 11
  STAGE II                  11                  6
  STAGE IIA                  3                  7
  STAGE IIB                  5                  9
  STAGE IIC                  5                  5
  STAGE III                 21                 11
  STAGE IIIA                10                  4
  STAGE IIIB                13                 10
  STAGE IIIC                28                 20
  STAGE IV                   7                  5
[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      32 36 23 38
  10P LOSS WILD-TYPE    21 24 32 19
D58V6, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1               32                 21
  T2                  36                 24
  T3                  23                 32
  T4                  38                 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                 N0 N1 N2 N3
  10P LOSS MUTATED   77 34 18 19
  10P LOSS WILD-TYPE 64 17 14 18
D58V7, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               77                 64
  N1               34                 17
  N2               18                 14
  N3               19                 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
  10P LOSS MUTATED   143   1   1   1   4
  10P LOSS WILD-TYPE 109   3   1   1   1
D58V8, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               143                109
  M1                 1                  3
  M1A                1                  1
  M1B                1                  1
  M1C                4                  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"
D58V9, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   56 43
  10P LOSS WILD-TYPE 48 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     56   43
  10P LOSS WILD-TYPE   48   29
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                56                 48
  YES               43                 29
[1] 2 2
[1] FALSE
D58V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    18 139
  10P LOSS WILD-TYPE  16 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     18  139
  10P LOSS WILD-TYPE   16  108
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                18                 16
  YES              139                108
[1] 2 2
[1] FALSE
D58V11, continuous
D58V12, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   68 89
  10P LOSS WILD-TYPE 40 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     68   89
  10P LOSS WILD-TYPE   40   84
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               68                 40
  MALE                 89                 84
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       1                         0   156
  10P LOSS WILD-TYPE     4                         1   119
D58V13, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  156                119
[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
  10P LOSS MUTATED     1 155
  10P LOSS WILD-TYPE   2 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1  155
  10P LOSS WILD-TYPE    2  119
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO              155                119
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   84 82
  10Q LOSS WILD-TYPE 53 51
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               166                104 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                82                 51 
$`10Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       22.55        88.50        69.90        11.41         7.50         6.31 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
       92.42        56.19        64.44        45.11        15.25        46.98 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       13.32         9.34       103.59        26.37         5.39        42.71 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
       41.10        17.72         8.84        13.94        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA 
        1.55         6.97        23.11         2.89         9.90        11.31 
TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       13.22        14.60        35.80        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 TCGA-DA-A3F8 
       44.52        36.69        25.15         4.93        17.56        14.83 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        0.20         0.00        13.22         6.31         8.12         1.12 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D 
        4.31        36.07         5.13         9.21         1.18        11.15 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q 
        8.55         4.41         1.08        27.12        12.03         8.09 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        6.48         8.68         8.09        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        47.21        30.08 
TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
       19.43        28.31        33.83        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD 
       13.02        36.33        98.27         2.70         6.18         9.53 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP 
       44.25         7.96        14.56       111.78        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-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        22.22         0.46        13.94        33.60        31.40 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L 
        5.72         3.78         3.52        11.90        34.88        13.45 
TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG 
       34.68        36.07        17.72        11.80         1.51        12.62 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
       11.74        22.49         1.71        18.41        85.74         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        6.71         3.58         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.33         7.30        20.38         8.22        11.08        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW 
       12.92        47.38         8.65         8.81         8.68        27.39 
TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TV 
        0.82         7.36        28.73         5.98         2.27         0.16 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
        7.23        12.85        24.85        31.33        10.13        16.24 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X 
       12.16        11.84        10.65        11.05 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
        8.52        45.83        81.24        10.29        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3BZ TCGA-D3-A3C8 
       21.14        68.22        30.87        36.16       114.67        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H 
       82.29        61.38        24.00         6.31        80.22        15.09 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       20.48        95.38         4.01        48.79        51.12        10.03 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5KH 
       22.36         6.64        19.36         7.00        13.15         0.13 
TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 
        0.00         0.20        11.57        10.55         1.35        12.20 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E 
        5.13         4.34         7.99         9.90        37.97        38.63 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.50         8.84         9.99         2.43        11.31        49.22 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME 
       16.01        35.54        34.98         8.84        47.51        29.46 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       63.42       111.91        25.08        21.60        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3JD TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       23.05        25.84        27.35        18.61        12.95        38.40 
TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19M 
       76.41        25.18        11.11       114.15         4.21        28.60 
TCGA-ER-A19N TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES 
       42.84         9.57        78.44         1.87        13.08         9.04 
TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE 
        6.58         5.36        64.47        15.52         3.39        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ 
        7.17        12.89        52.08        49.15        40.64         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
       53.85         3.22        14.20        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A268 
        0.99         0.13         0.43         9.90        84.72        15.42 
TCGA-GN-A26D TCGA-QB-A6FS 
       14.70         5.79 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 0                  0 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            124.31             114.67 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            13.565             15.470 
[1] "0.0 - 124.3 (13.6)" "0.0 - 114.7 (15.5)"
[1] "hr=" "1.1"
D59V2, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   87 82
  10Q LOSS WILD-TYPE 55 52
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               169                107 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                82                 52 
$`10Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JK 
       31.59       115.53        69.90        11.87       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 
      171.58        56.19        66.08        45.11        58.06        46.98 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51F 
       60.23         9.34       103.59        39.75        21.47        43.69 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO 
      131.90        18.38        10.03        15.06       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 
      166.19         7.43       125.19       151.53        54.67         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I1 
        9.90        25.18        66.25        22.95        36.03       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-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
      215.44        15.68        10.16        35.01         3.55        52.01 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        8.65        94.98        33.73         4.96       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
      168.26        13.55        13.97        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A29X 
       44.35        56.42        37.35       345.96       171.55        17.92 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       24.43        39.29        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN 
      135.95       208.04        48.72        89.33        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M6 
      101.95        13.91        14.30        55.59        94.82       129.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       28.83        19.76        47.28       103.20        16.96       204.66 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      144.76       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-A3JE 
      127.20        36.95        64.08        34.32        53.19        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
      101.79       148.08        31.40         9.17        48.89        12.59 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W 
       13.02       152.35       131.51       162.08        37.25       148.18 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL 
       43.82        20.15        31.27        32.05        46.98        33.21 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YX 
       92.98       174.21         4.90       210.08        15.16        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
      228.59       202.65        20.91         7.79        27.72       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       53.52        15.45        32.75        47.38       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F4 TCGA-FS-A4F5 
       11.41        26.56        49.48        27.09        66.67        28.73 
TCGA-FS-A4FB TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       26.73        77.88         0.16         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
      117.93        10.13        64.44        32.48        46.36        12.62 
TCGA-OD-A75X 
      294.77 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 
       16.67        90.90        95.74        43.43       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A3BZ TCGA-D3-A3C8 
       23.77       168.00        48.76        42.08       130.72        46.32 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51H 
      166.52        86.93        24.53        13.87       161.85        40.14 
TCGA-D3-A51R TCGA-D3-A5GL TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-DA-A1HV 
       51.68       110.93         3.65         6.41        11.34        48.89 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
      117.21        20.38        23.44        68.09        28.60        10.49 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       13.87        17.85        45.11         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A29A 
       27.22        14.70        26.89        68.15       151.27        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       80.61        47.84        39.62        18.61        14.47        55.92 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT 
       25.87        46.82       102.90        54.74        79.66        44.88 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
       21.67        61.51       103.27        96.23       203.05        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3JD 
       43.23       103.56       136.47        41.59        25.84        27.35 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19F 
       35.44        13.94        50.76        77.75        98.40        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-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A7U9 TCGA-FS-A1YW 
       23.34        16.37       247.04        80.32         7.00       216.92 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP 
       28.08        48.85        40.27         9.70        23.93        74.73 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 
      148.80        53.16        27.02        77.82        50.14       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         2.40 
TCGA-GF-A3OT TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
        9.90        84.72        62.79        39.58         6.67 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.16               0.20 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            357.37             268.93 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             49.48              46.32 
[1] "0.2 - 357.4 (49.5)" "0.2 - 268.9 (46.3)"
[1] "hr=" "1.2"
D59V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10Q LOSS MUTATED                   21             3
  10Q LOSS WILD-TYPE                 16             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  10Q LOSS MUTATED                                          45
  10Q LOSS WILD-TYPE                                        15
                    vv
clus                 REGIONAL LYMPH NODE
  10Q LOSS MUTATED                   104
  10Q LOSS WILD-TYPE                  75
D59V4, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      21                 16
  PRIMARY TUMOR                                            3                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               45                 15
  REGIONAL LYMPH NODE                                    104                 75
[1] 4 2
[1] 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             7       3      15        8       15       11
  10Q LOSS WILD-TYPE           3       3       8        2       10        6
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  10Q LOSS MUTATED           4         8         5        24         10
  10Q LOSS WILD-TYPE         6         6         5         8          4
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           14         27        8
  10Q LOSS WILD-TYPE          9         21        4
D59V5, multiclass
             clus
vv            10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  I OR II NOS                7                  3
  STAGE 0                    3                  3
  STAGE I                   15                  8
  STAGE IA                   8                  2
  STAGE IB                  15                 10
  STAGE II                  11                  6
  STAGE IIA                  4                  6
  STAGE IIB                  8                  6
  STAGE IIC                  5                  5
  STAGE III                 24                  8
  STAGE IIIA                10                  4
  STAGE IIIB                14                  9
  STAGE IIIC                27                 21
  STAGE IV                   8                  4
[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      37 40 27 37
  10Q LOSS WILD-TYPE    16 20 28 20
D59V6, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1               37                 16
  T2                  40                 20
  T3                  27                 28
  T4                  37                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10Q LOSS MUTATED   84 37 19 20
  10Q LOSS WILD-TYPE 57 14 13 17
D59V7, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               84                 57
  N1               37                 14
  N2               19                 13
  N3               20                 17
[1] 4 2
[1] 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   155   1   1   2   5
  10Q LOSS WILD-TYPE  97   3   1   0   0
D59V8, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               155                 97
  M1                 1                  3
  M1A                1                  1
  M1B                2                  0
  M1C                5                  0
[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
  10Q LOSS MUTATED   61 45
  10Q LOSS WILD-TYPE 43 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     61   45
  10Q LOSS WILD-TYPE   43   27
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                61                 43
  YES               45                 27
[1] 2 2
[1] FALSE
D59V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    22 151
  10Q LOSS WILD-TYPE  12  96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     22  151
  10Q LOSS WILD-TYPE   12   96
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                22                 12
  YES              151                 96
[1] 2 2
[1] FALSE
D59V11, continuous
D59V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    73 100
  10Q LOSS WILD-TYPE  35  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     73  100
  10Q LOSS WILD-TYPE   35   73
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               73                 35
  MALE                100                 73
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       1                         0   172
  10Q LOSS WILD-TYPE     4                         1   103
D59V13, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                  172                103
[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
  10Q LOSS MUTATED     1 171
  10Q LOSS WILD-TYPE   2 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1  171
  10Q LOSS WILD-TYPE    2  103
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO              171                103
[1] 2 2
[1] FALSE

Clustering(60) Variable = 11P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   44 49
  11P LOSS WILD-TYPE 93 84
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                93                177 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                49                 84 
$`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         5.39        80.22        52.01         1.55         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
       23.11         2.89        11.31        14.60        48.79        35.80 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5SG 
       39.19        44.52        25.15        17.56         0.20         0.00 
TCGA-EB-A5SH TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29C 
        0.00         1.35        36.07         4.34         1.18        37.97 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       11.15         1.08        27.12         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
        8.84         2.43         8.09        23.90         9.67        34.29 
TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN 
       34.92        28.31        98.27        63.42        56.02        25.08 
TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE 
       26.99        27.16         5.56       122.73         3.68        30.15 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 
       21.60        21.60        16.14        22.22        13.94        12.95 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A2ND 
        5.72         3.78         3.52        13.45        36.07         1.87 
TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1Z3 
        1.51         6.58        22.49        18.41         4.90        14.24 
TCGA-FS-A1ZA TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F4 
        7.30        11.08        30.87        47.38        27.39         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 
       28.73        14.20        10.78         0.20        24.85        31.33 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U9 
       16.24        12.16        10.65 

$`11P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.52       111.09        70.16       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
       81.24         8.38        21.14        88.50        69.90        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
        7.50        36.16         6.31        64.44        45.11       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        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6E9 
       20.48        13.94        95.38        47.87         4.01         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-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
       13.15         0.13        13.22         0.20        11.57        10.55 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        6.31         8.12         1.12        12.20         5.13         4.31 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
        5.13         9.21         7.99         9.90        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
        4.41         9.99         6.48         8.68        11.31        49.22 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
        8.94        39.39        17.98        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        30.84         5.42         1.15 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98        36.33         8.84         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA 
      111.78       111.91        21.60        29.65        23.05       124.31 
TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       27.35         0.46        33.60        31.40        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-A19W 
        4.21        28.60        42.84        34.68         9.57        17.72 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       78.44        11.80        13.08        12.62        11.74         9.04 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
        1.71        85.74         6.71         3.58         5.36        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
        3.45        11.01        23.80        15.52         7.33         3.39 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       20.38         8.22        19.53         7.17        12.92        12.89 
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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FC 
        0.82         5.23        53.85         3.22         5.98         6.41 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
        2.27         0.99         0.13         0.16         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
        7.23        12.85        84.72        10.13        15.42        14.70 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        11.05         5.79 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.00               0.13 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            122.73             124.31 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             16.14              13.22 
[1] "0.0 - 122.7 (16.1)" "0.1 - 124.3 (13.2)"
[1] "hr=" "1.1"
D60V2, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   46 50
  11P LOSS WILD-TYPE 96 84
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                96                180 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                50                 84 
$`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        21.47       161.85       135.75       166.19         7.43 
TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JX TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG 
      125.19        54.67         6.41         3.25        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-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A182 TCGA-EE-A20B 
       10.16        45.11        35.01         3.55        14.70       109.64 
TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
      151.27        13.55        47.84        13.97         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X 
       18.61        56.42        37.35        14.47        25.87        17.92 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 
       24.43        39.29        67.43       135.95        75.48       129.27 
TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU 
       96.23       167.90        47.54       248.65       136.47        53.26 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
      122.73         3.68        54.51        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
       53.19       101.79        13.94         9.17        48.89        12.59 
TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ET TCGA-ER-A3EV 
      131.51        37.25        23.34        20.15        80.32        46.98 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZF TCGA-FS-A1ZH 
       92.98         4.90        20.91        27.72        15.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
      101.26        49.48        66.67        28.73       174.84        12.43 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A4U9 
        0.20       120.46       117.93        64.44        32.48        12.62 

$`11P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04        71.80       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF 
       95.74        65.49        23.77       115.53        69.90        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10        66.08        45.11       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        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A1JW 
       51.68        15.06       110.93       137.92       151.53         3.65 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       11.34         9.90        66.25       117.21        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93        61.18        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV 
       10.49        15.68        13.87        17.85        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-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       26.89        68.15         4.96        78.87       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29T 
       80.61        39.62        72.07        32.19        55.92       345.96 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
      171.55        46.82       102.90        58.75        47.54       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 
      101.95        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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ 
      103.20        16.96       204.66       144.76       203.05        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG 
      103.56        41.59       124.31        25.84        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI 
      138.81       172.18       127.20        27.35        33.40       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E 
       31.40        35.44        50.76        77.75        98.40        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93       152.35         6.44        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF 
      162.08        50.89       148.18        79.99        43.82        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A729 
       31.27        32.05       247.04        33.21       174.21       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
       15.16         7.00       216.92        48.59       228.59       202.65 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       28.08         7.79        48.85       357.37        53.52        40.27 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        9.70        47.38        23.93        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        53.16        26.56        27.09        27.02        77.82 
TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU 
       50.14        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-A265 
        0.16         2.40         9.90         7.23        14.04        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       10.13        62.79        39.58        46.36       294.77         6.67 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.20               0.16 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            248.65             357.37 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             46.98              48.74 
[1] "0.2 - 248.7 (47.0)" "0.2 - 357.4 (48.7)"
[1] "hr=" "1.3"
D60V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P LOSS MUTATED                   12             1
  11P LOSS WILD-TYPE                 25             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11P LOSS MUTATED                                          24
  11P LOSS WILD-TYPE                                        36
                    vv
clus                 REGIONAL LYMPH NODE
  11P LOSS MUTATED                    59
  11P LOSS WILD-TYPE                 120
D60V4, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  DISTANT METASTASIS                                      12                 25
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               24                 36
  REGIONAL LYMPH NODE                                     59                120
[1] 4 2
[1] 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             5       3       9        2       11        2
  11P LOSS WILD-TYPE           5       3      14        8       14       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11P LOSS MUTATED           1         3         4        12          5
  11P LOSS WILD-TYPE         9        11         6        20          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED            9         18        6
  11P LOSS WILD-TYPE         14         30        6
D60V5, multiclass
             clus
vv            11P LOSS MUTATED 11P LOSS WILD-TYPE
  I OR II NOS                5                  5
  STAGE 0                    3                  3
  STAGE I                    9                 14
  STAGE IA                   2                  8
  STAGE IB                  11                 14
  STAGE II                   2                 15
  STAGE IIA                  1                  9
  STAGE IIB                  3                 11
  STAGE IIC                  4                  6
  STAGE III                 12                 20
  STAGE IIIA                 5                  9
  STAGE IIIB                 9                 14
  STAGE IIIC                18                 30
  STAGE IV                   6                  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
  11P LOSS MUTATED      19 23 13 23
  11P LOSS WILD-TYPE    34 37 42 34
D60V6, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               19                 34
  T2                  23                 37
  T3                  13                 42
  T4                  23                 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
  11P LOSS MUTATED   46 24  9 11
  11P LOSS WILD-TYPE 95 27 23 26
D60V7, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               46                 95
  N1               24                 27
  N2                9                 23
  N3               11                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B M1C
  11P LOSS MUTATED    85   2   0   0   4
  11P LOSS WILD-TYPE 167   2   2   2   1
D60V8, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                85                167
  M1                 2                  2
  M1A                0                  2
  M1B                0                  2
  M1C                4                  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
  11P LOSS MUTATED   33 30
  11P LOSS WILD-TYPE 71 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     33   30
  11P LOSS WILD-TYPE   71   42
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                33                 71
  YES               30                 42
[1] 2 2
[1] FALSE
D60V10, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    10  87
  11P LOSS WILD-TYPE  24 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     10   87
  11P LOSS WILD-TYPE   24  160
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                10                 24
  YES               87                160
[1] 2 2
[1] FALSE
D60V11, continuous
D60V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    47  50
  11P LOSS WILD-TYPE  61 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     47   50
  11P LOSS WILD-TYPE   61  123
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               47                 61
  MALE                 50                123
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                         1    95
  11P LOSS WILD-TYPE     4                         0   180
D60V13, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   95                180
[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
  11P LOSS MUTATED     0  96
  11P LOSS WILD-TYPE   3 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   96
  11P LOSS WILD-TYPE    3  178
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               96                178
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   54 53
  11Q LOSS WILD-TYPE 83 80
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               107                163 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                53                 80 
$`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         5.39        80.22 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z3 TCGA-D9-A6EA 
       52.01         1.55         6.97        23.11         2.89        11.31 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 
       14.60        48.79        35.80        39.19        44.52        25.15 
TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A180 
       17.56        13.15         0.20         0.00         0.00         8.12 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
        1.35        36.07        37.97        11.15         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         6.48         2.43 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GM 
       23.90         9.67        39.39        34.29        34.92        28.31 
TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       98.27         9.53        63.42        56.02        25.08        26.99 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 
       23.05         5.56       122.73         3.68        30.15        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 
       21.60        16.14        22.22        13.94        31.40        12.95 
TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19W 
        5.72         3.78         3.52        13.45        36.07        17.72 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
        1.87         1.51        12.62         6.58        22.49         1.71 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZE 
       18.41         4.90        14.24         7.33         7.30        19.53 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       11.08        30.87        12.92        47.38        27.39         5.23 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A266 
        7.36        28.73         2.27         0.20        31.33        10.13 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U9 TCGA-QB-A6FS 
       16.24        12.16        14.70        10.65         5.79 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 
        8.52       111.09        70.16        28.08        45.83         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        88.50        69.90        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
        6.31        45.11       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        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       41.10        17.72         8.84        20.48        13.94        95.38 
TCGA-D3-A5GO TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HY TCGA-DA-A1I0 
       47.87         4.01         9.90        13.22        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       13.68         9.99        36.69         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 
       19.36         7.00        14.83         0.13        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       11.57        10.55         6.31         1.12        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
        4.31         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29W 
        9.90        38.63         8.55         4.41         9.99         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GH 
        8.09        11.31        49.22         8.94        17.98        47.21 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GO 
       30.08        19.43        16.01        35.54        33.83        30.84 
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-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18        47.51        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
       14.56       111.78       111.91        21.60        29.65        27.16 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 
      124.31        25.84        13.81        15.95        12.72         3.22 
TCGA-EE-A3J4 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 
       22.92        27.35         0.46        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-FR-A44A TCGA-FR-A729 
       11.80        13.08        11.74         9.04        85.74         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        3.58         5.36        64.47         3.45        11.01        23.80 
TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZK 
       15.52         3.39        20.38         8.22         7.17        12.89 
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-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
        0.82        53.85         3.22        14.20        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         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 
        7.23        12.85        24.85        84.72        15.42        11.84 
TCGA-OD-A75X 
       11.05 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.00               0.13 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            122.73             124.31 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             15.25              13.32 
[1] "0.0 - 122.7 (15.2)" "0.1 - 124.3 (13.3)"
[1] "hr=" "1"  
D61V2, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   56 54
  11Q LOSS WILD-TYPE 86 80
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               110                166 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                54                 80 
$`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        21.47       161.85 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JX 
      135.75       166.19         7.43       125.19        54.67         6.41 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
        3.25        25.18        22.95        48.89        36.03       194.83 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5SG 
      107.34        53.92       215.44        13.87        10.16        45.11 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29C 
       35.01         3.55        94.98        14.70       109.64        47.84 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       13.97         2.60        44.35        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
       14.47       345.96        25.87        24.43        39.29        47.54 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GM TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ 
       67.43       135.95        75.48       129.27        47.28        96.23 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      167.90        47.54       248.65        41.59        53.26       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
        3.68        54.51        36.95        64.08        34.32        53.19 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19C TCGA-ER-A19D 
      101.79        31.40        13.94         9.17        48.89        12.59 
TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NG 
      131.51        37.25       148.18        23.34        20.15        31.27 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1Z3 
       80.32        46.98        33.21        92.98         4.90        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        7.79        27.72        40.27        15.45        32.75        47.38 
TCGA-FS-A1ZM TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4FD 
      101.26        49.48        27.02        66.67        28.73        77.88 
TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.20       117.93        10.13        64.44        32.48        39.58 
TCGA-GN-A4U9 TCGA-QB-A6FS 
       12.62         6.67 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A2J8 
       16.67       112.04        71.80        28.08        90.90        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53        69.90        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE 
       12.10        45.11       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        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      131.90        18.38        10.03        51.68        15.06       110.93 
TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC 
      137.92       151.53         3.65        11.34         9.90        66.25 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
      117.21        20.38       176.55        35.93        61.18        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A5KH 
       23.44        68.09        28.60        10.49        15.68        17.85 
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-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       33.73        26.89        68.15         4.96       151.27        78.87 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
      168.26        13.55        63.35        80.61        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       32.19        55.92       171.55        17.92        46.82       102.90 
TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       58.75       314.56       208.04        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       101.95        13.91        14.30        55.59 
TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       44.88        94.82        21.67        28.83        19.76        61.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27       103.20        16.96       204.66       144.76       203.05 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
       43.23       103.56       136.47       124.31        25.84        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JD TCGA-EE-A3JE 
       23.47       138.81       172.18       127.20        27.35        33.40 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19E 
      148.08        35.44        50.76        77.75        98.40        13.02 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       26.37       268.93       152.35         6.44        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A2NH 
      162.08        50.89        79.99        43.82        16.37        32.05 
TCGA-ER-A3ES TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
      247.04       174.21       210.08        15.16         7.00       216.92 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZC 
       48.59       228.59       202.65        28.08        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
       53.52         9.70        23.93        74.73       133.55        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4F0 TCGA-FS-A4F2 
      148.80        53.16        26.56        27.09        77.82        50.14 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
      174.84        12.43        26.73        49.45        22.92        47.54 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-OD-A75X 
       84.72        62.79        46.36       294.77 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.20               0.16 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            345.96             357.37 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            46.045             50.450 
[1] "0.2 - 346.0 (46.0)" "0.2 - 357.4 (50.5)"
[1] "hr=" "1.2"
D61V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q LOSS MUTATED                   14             1
  11Q LOSS WILD-TYPE                 23             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  11Q LOSS MUTATED                                          26
  11Q LOSS WILD-TYPE                                        34
                    vv
clus                 REGIONAL LYMPH NODE
  11Q LOSS MUTATED                    69
  11Q LOSS WILD-TYPE                 110
D61V4, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      14                 23
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               26                 34
  REGIONAL LYMPH NODE                                     69                110
[1] 4 2
[1] 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             5       2       9        2       12        2
  11Q LOSS WILD-TYPE           5       4      14        8       13       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  11Q LOSS MUTATED           1         5         6        14          5
  11Q LOSS WILD-TYPE         9         9         4        18          9
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           10         23        6
  11Q LOSS WILD-TYPE         13         25        6
D61V5, multiclass
             clus
vv            11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  I OR II NOS                5                  5
  STAGE 0                    2                  4
  STAGE I                    9                 14
  STAGE IA                   2                  8
  STAGE IB                  12                 13
  STAGE II                   2                 15
  STAGE IIA                  1                  9
  STAGE IIB                  5                  9
  STAGE IIC                  6                  4
  STAGE III                 14                 18
  STAGE IIIA                 5                  9
  STAGE IIIB                10                 13
  STAGE IIIC                23                 25
  STAGE IV                   6                  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
  11Q LOSS MUTATED      21 26 17 26
  11Q LOSS WILD-TYPE    32 34 38 31
D61V6, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               21                 32
  T2                  26                 34
  T3                  17                 38
  T4                  26                 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                 N0 N1 N2 N3
  11Q LOSS MUTATED   51 26 10 15
  11Q LOSS WILD-TYPE 90 25 22 22
D61V7, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               51                 90
  N1               26                 25
  N2               10                 22
  N3               15                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B M1C
  11Q LOSS MUTATED    97   2   1   0   3
  11Q LOSS WILD-TYPE 155   2   1   2   2
D61V8, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                97                155
  M1                 2                  2
  M1A                1                  1
  M1B                0                  2
  M1C                3                  2
[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
  11Q LOSS MUTATED   37 38
  11Q LOSS WILD-TYPE 67 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     37   38
  11Q LOSS WILD-TYPE   67   34
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                37                 67
  YES               38                 34
[1] 2 2
[1] FALSE
D61V10, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    13  98
  11Q LOSS WILD-TYPE  21 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     13   98
  11Q LOSS WILD-TYPE   21  149
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                13                 21
  YES               98                149
[1] 2 2
[1] FALSE
D61V11, continuous
D61V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    55  56
  11Q LOSS WILD-TYPE  53 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     55   56
  11Q LOSS WILD-TYPE   53  117
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               55                 53
  MALE                 56                117
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                         1   108
  11Q LOSS WILD-TYPE     3                         0   167
D61V13, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                  108                167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1 109
  11Q LOSS WILD-TYPE   2 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1  109
  11Q LOSS WILD-TYPE    2  165
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO              109                165
[1] 2 2
[1] FALSE

Clustering(62) Variable = 12P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    22  17
  12P LOSS WILD-TYPE 115 116
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                39                231 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                17                116 
$`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         8.84        47.87         1.55 
TCGA-D3-A5GS TCGA-D9-A6EA TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C 
        6.97        11.31        39.19         0.00        36.07         4.34 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2MG 
        8.55         8.09         9.99        23.90         5.42        44.25 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J3 
      111.78        26.99        27.16         5.56        30.15         3.22 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19E TCGA-ER-A2NG TCGA-FS-A1YX 
       21.60        22.22        12.95        11.90        12.62         3.45 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F2 
       15.52         7.30        30.87         8.65        40.64         3.22 
TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-OD-A75X 
       28.73         0.99        11.05 

$`12P 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-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-A2JF 
       21.14        88.50        68.22        69.90        11.41        30.87 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
        7.50        36.16         6.31        56.19        45.11       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         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       80.22        42.71        15.09        41.10        17.72        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.94        95.38        52.01        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.90        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-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-A5UN 
       14.83        13.15         0.20         0.13         0.00        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-A20F TCGA-EE-A20H 
        1.35        12.20         5.13         4.31         5.13         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        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        4.41         1.08        27.12         9.50        12.03         8.84 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        6.48         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
        9.67         8.94        39.39        34.29        17.98        34.92 
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-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       33.83        30.84         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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       29.46         7.96        14.56        63.42       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
       25.08        21.60        29.65        23.05       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       25.84         3.68        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         0.46        13.94        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-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-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       85.74         4.90         6.71         3.58         5.36        64.47 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
       11.01        23.80        14.24         7.33         3.39        20.38 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        8.22        19.53        11.08         7.17        12.92        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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
        0.82         5.23        53.85         7.36        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-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        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-QB-A6FS 
       11.84        10.65         5.79 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                  0 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            111.78             124.31 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             11.90              14.56 
[1] "0.0 - 111.8 (11.9)" "0.0 - 124.3 (14.6)"
[1] "hr=" "1"  
D62V2, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    22  17
  12P LOSS WILD-TYPE 120 117
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                39                237 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                17                117 
$`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        10.03       137.92       166.19 
TCGA-D3-A5GS TCGA-D9-A6EA TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C 
        7.43        25.18       194.83        35.01       109.64       151.27 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GP TCGA-EE-A2MG 
       72.07        37.35        55.92        24.43        13.91       103.20 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AE TCGA-EE-A3J3 
      144.76       248.65       136.47        53.26        54.51       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19E TCGA-ER-A2NG TCGA-FS-A1YX 
       64.08        53.19        13.94        13.02        31.27        48.59 
TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A4F2 
       28.08        27.72        32.75       133.55        53.16        50.14 
TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-OD-A75X 
       28.73        22.92       294.77 

$`12P 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-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-A2JF 
       23.77       115.53       168.00        69.90        11.87        48.76 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10        56.19        45.11       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        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
      161.85        43.69        40.14       131.90        18.38        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 
       15.06       110.93       135.75       125.19       151.53        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC 
        3.65         6.41        11.34         3.25         9.90        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-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-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       10.16        17.85        45.11         3.55        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-A20F TCGA-EE-A20H 
       14.70        26.89        68.15         4.96        78.87       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        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       32.19         2.60        44.35        18.61        56.42        14.47 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
      345.96        25.87       171.55        17.92        46.82       102.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
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       101.95        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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
      103.27        16.96       204.66        96.23       203.05       167.90 
TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AB 
       47.54        43.23       103.56        41.59       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
       25.84         3.68        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        33.40       101.79       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-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-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
      148.18        79.99        43.82        23.34        20.15        16.37 
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-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
      174.21         4.90       210.08        15.16         7.00       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
      228.59       202.65        20.91         7.79        48.85       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       53.52        40.27        15.45         9.70        47.38        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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.09        27.02        77.82        66.67       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-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       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-QB-A6FS 
       46.36        12.62         6.67 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              7.43               0.16 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            294.77             357.37 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             53.19              47.38 
[1] "7.4 - 294.8 (53.2)" "0.2 - 357.4 (47.4)"
[1] "hr=" "1.3"
D62V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P LOSS MUTATED                    6             1
  12P LOSS WILD-TYPE                 31             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12P LOSS MUTATED                                          12
  12P LOSS WILD-TYPE                                        48
                    vv
clus                 REGIONAL LYMPH NODE
  12P LOSS MUTATED                    20
  12P LOSS WILD-TYPE                 159
D62V4, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  DISTANT METASTASIS                                       6                 31
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               12                 48
  REGIONAL LYMPH NODE                                     20                159
[1] 4 2
[1] 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             3       1       5        2        4        3
  12P LOSS WILD-TYPE           7       5      18        8       21       14
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12P LOSS MUTATED           1         2         1         5          1
  12P LOSS WILD-TYPE         9        12         9        27         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED            3          5        3
  12P LOSS WILD-TYPE         20         43        9
D62V5, multiclass
             clus
vv            12P LOSS MUTATED 12P LOSS WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    1                  5
  STAGE I                    5                 18
  STAGE IA                   2                  8
  STAGE IB                   4                 21
  STAGE II                   3                 14
  STAGE IIA                  1                  9
  STAGE IIB                  2                 12
  STAGE IIC                  1                  9
  STAGE III                  5                 27
  STAGE IIIA                 1                 13
  STAGE IIIB                 3                 20
  STAGE IIIC                 5                 43
  STAGE IV                   3                  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
  12P LOSS MUTATED       7  9  7 10
  12P LOSS WILD-TYPE    46 51 48 47
D62V6, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                7                 46
  T2                   9                 51
  T3                   7                 48
  T4                  10                 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                  N0  N1  N2  N3
  12P LOSS MUTATED    24   6   4   5
  12P LOSS WILD-TYPE 117  45  28  32
D62V7, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               24                117
  N1                6                 45
  N2                4                 28
  N3                5                 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
  12P LOSS MUTATED    37   0   0   0   3
  12P LOSS WILD-TYPE 215   4   2   2   2
D62V8, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                37                215
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                3                  2
[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
  12P LOSS MUTATED   13 12
  12P LOSS WILD-TYPE 91 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     13   12
  12P LOSS WILD-TYPE   91   60
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                13                 91
  YES               12                 60
[1] 2 2
[1] FALSE
D62V10, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2  38
  12P LOSS WILD-TYPE  32 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   38
  12P LOSS WILD-TYPE   32  209
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 2                 32
  YES               38                209
[1] 2 2
[1] FALSE
D62V11, continuous
D62V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    18  22
  12P LOSS WILD-TYPE  90 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     18   22
  12P LOSS WILD-TYPE   90  151
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               18                 90
  MALE                 22                151
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0    40
  12P LOSS WILD-TYPE     5                         1   235
D62V13, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   40                235
[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
  12P LOSS MUTATED     0  40
  12P LOSS WILD-TYPE   3 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   40
  12P LOSS WILD-TYPE    3  234
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               40                234
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    25  22
  12Q LOSS WILD-TYPE 112 111
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                47                223 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                22                111 
$`12Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR 
       16.47        10.29        92.42         8.84        47.87         1.55 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C 
       11.31        13.22        39.19         0.00        36.07         4.34 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.55         8.09         9.99         8.09        23.90         9.67 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MP 
        5.42         1.15        36.33        44.25       111.78        26.99 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
       27.16         5.56       124.31         3.68        30.15         3.22 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19S 
       21.60        22.22        12.95         5.72        11.90        36.07 
TCGA-ER-A3PL TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ 
        1.71         3.45        15.52         7.30        30.87         8.65 
TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-OD-A75X 
       40.64         3.22        28.73         0.99        11.05 

$`12Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        70.16       110.79        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        81.24        85.32         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
       88.50        68.22        69.90        11.41        30.87         7.50 
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        45.11       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         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
       80.22        42.71        15.09        41.10        17.72        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       13.94        95.38        52.01         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        2.89         9.90        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-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-A5UN 
       14.83        13.15         0.20         0.13         0.00        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-A20F TCGA-EE-A20H 
        1.35        12.20         5.13         4.31         5.13         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        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        4.41         1.08        27.12         9.50        12.03         8.84 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
        6.48         2.43         8.68        11.31        49.22         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        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        30.84 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       13.02        34.98         8.84        98.27         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51         9.53        29.46         7.96        14.56        63.42 
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        29.65        23.05 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
      122.73        25.84        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         0.46        13.94        33.60 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       31.40        18.61        38.40        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 
       28.60        42.84        34.68         9.57        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         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        6.71         3.58         5.36        64.47        11.01        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       14.24         7.33         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-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        8.81        49.15         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       53.85         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         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        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-QB-A6FS 
        5.79 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 0                  0 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            124.31             122.73 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             11.31              14.60 
[1] "0.0 - 124.3 (11.3)" "0.0 - 122.7 (14.6)"
[1] "hr=" "1.1"
D63V2, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    25  22
  12Q LOSS WILD-TYPE 117 112
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                47                229 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                22                112 
$`12Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JL TCGA-D3-A51N TCGA-D3-A5GO TCGA-D3-A5GR 
       16.57        43.43       171.58        10.03       137.92       166.19 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-EB-A5SH TCGA-EE-A20B TCGA-EE-A20C 
       25.18        66.25       194.83        35.01       109.64       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        24.43        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       144.76       248.65 
TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3J3 
      136.47        53.26       124.31         3.68        54.51       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E TCGA-ER-A19S 
       64.08        53.19        13.94         9.17        13.02        37.25 
TCGA-ER-A3PL TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZQ 
       33.21        48.59        28.08        27.72        32.75       133.55 
TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FW-A3R5 TCGA-OD-A75X 
       53.16        50.14        28.73        22.92       294.77 

$`12Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        71.80       133.25        28.08 
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        95.74       103.10        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG 
      115.53       168.00        69.90        11.87        48.76       113.52 
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        45.11       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        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R 
      161.85        43.69        40.14       131.90        18.38        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       15.06       110.93       135.75         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         9.90 
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-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-A5UL TCGA-EB-A5UN TCGA-EB-A5VV 
       10.16        17.85        45.11         3.55        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-A20F TCGA-EE-A20H 
       14.70        26.89        68.15         4.96        78.87       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        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       32.19         2.60        44.35        18.61        56.42        14.47 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
      345.96        25.87       171.55        46.82       102.90        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       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       101.95 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        21.67       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       61.51        47.28       103.27        16.96       204.66        96.23 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      203.05       167.90        47.54        43.23       103.56        41.59 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 
      122.73        25.84        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        33.40       101.79       148.08 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       31.40        35.44        50.76        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-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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
      247.04        80.32        46.98        92.98       174.21         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
      210.08        15.16         7.00       216.92       228.59       202.65 
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-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP 
       15.45         9.70        47.38        23.93       101.26        74.73 
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-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FS-A4FC 
       77.82        66.67       174.84        12.43        26.73        49.45 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT 
       77.88         0.20        47.54         0.16         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       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-QB-A6FS 
        6.67 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              3.68               0.16 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            294.77             357.37 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             50.14              47.54 
[1] "3.7 - 294.8 (50.1)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.1"
D63V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q LOSS MUTATED                    6             2
  12Q LOSS WILD-TYPE                 31             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  12Q LOSS MUTATED                                          14
  12Q LOSS WILD-TYPE                                        46
                    vv
clus                 REGIONAL LYMPH NODE
  12Q LOSS MUTATED                    25
  12Q LOSS WILD-TYPE                 154
D63V4, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       6                 31
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               14                 46
  REGIONAL LYMPH NODE                                     25                154
[1] 4 2
[1] 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             3       1       5        3        6        4
  12Q LOSS WILD-TYPE           7       5      18        7       19       13
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  12Q LOSS MUTATED           1         2         1         7          2
  12Q LOSS WILD-TYPE         9        12         9        25         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED            3          5        3
  12Q LOSS WILD-TYPE         20         43        9
D63V5, multiclass
             clus
vv            12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    1                  5
  STAGE I                    5                 18
  STAGE IA                   3                  7
  STAGE IB                   6                 19
  STAGE II                   4                 13
  STAGE IIA                  1                  9
  STAGE IIB                  2                 12
  STAGE IIC                  1                  9
  STAGE III                  7                 25
  STAGE IIIA                 2                 12
  STAGE IIIB                 3                 20
  STAGE IIIC                 5                 43
  STAGE IV                   3                  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
  12Q LOSS MUTATED      10 11  8 12
  12Q LOSS WILD-TYPE    43 49 47 45
D63V6, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               10                 43
  T2                  11                 49
  T3                   8                 47
  T4                  12                 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
  12Q LOSS MUTATED    29   8   4   5
  12Q LOSS WILD-TYPE 112  43  28  32
D63V7, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               29                112
  N1                8                 43
  N2                4                 28
  N3                5                 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
  12Q LOSS MUTATED    44   0   1   0   2
  12Q LOSS WILD-TYPE 208   4   1   2   3
D63V8, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                44                208
  M1                 0                  4
  M1A                1                  1
  M1B                0                  2
  M1C                2                  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"
D63V9, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   17 12
  12Q LOSS WILD-TYPE 87 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     17   12
  12Q LOSS WILD-TYPE   87   60
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                17                 87
  YES               12                 60
[1] 2 2
[1] FALSE
D63V10, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     5  43
  12Q LOSS WILD-TYPE  29 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      5   43
  12Q LOSS WILD-TYPE   29  204
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 5                 29
  YES               43                204
[1] 2 2
[1] FALSE
D63V11, continuous
D63V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    22  26
  12Q LOSS WILD-TYPE  86 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     22   26
  12Q LOSS WILD-TYPE   86  147
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               22                 86
  MALE                 26                147
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0    48
  12Q LOSS WILD-TYPE     5                         1   227
D63V13, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   48                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"
D63V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  48
  12Q LOSS WILD-TYPE   3 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   48
  12Q LOSS WILD-TYPE    3  226
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               48                226
[1] 2 2
[1] FALSE

Clustering(64) Variable = 13Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    31  27
  13Q LOSS WILD-TYPE 106 106
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                58                212 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                27                106 
$`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        69.90        92.42       103.59 
TCGA-D3-A3MU TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z3 TCGA-D9-A6EA 
       26.37        95.38        52.01         1.55         2.89        11.31 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       48.79        35.80        13.68         9.99        44.52        25.15 
TCGA-DA-A1IC TCGA-EB-A5UN TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A20I TCGA-EE-A29C 
        6.64        13.22         1.12         5.13         1.18        37.97 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W 
       11.15        27.12         9.50         8.09         6.48         8.68 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2M5 TCGA-EE-A2MG 
        8.94        34.92        30.08        19.43         8.84        44.25 
TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD 
        7.96        29.65        27.16         5.56       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19B 
       30.15        12.72        21.60        13.94        31.40        25.18 
TCGA-ER-A19H TCGA-ER-A2NG TCGA-FR-A3YN TCGA-FR-A7U9 TCGA-FS-A1ZA TCGA-FS-A1ZH 
       34.88        12.62        18.41         5.36         7.30        30.87 
TCGA-FS-A1ZJ TCGA-FS-A4F4 TCGA-GN-A266 TCGA-GN-A26D 
       12.92         7.36        10.13        14.70 

$`13Q 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-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       22.55        45.83        81.24        10.29         8.38        21.14 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        11.41        30.87         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        45.11       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-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS 
       17.72         8.84        20.48        13.94        47.87         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY 
       23.11         4.01         9.90        13.22        14.60        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 
       10.03        39.19        36.69         4.93        22.36        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-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        0.00         0.00         0.20        11.57        10.55         6.31 
TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C 
        8.12         1.35        12.20         4.31        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
        5.13         9.21         7.99         9.90        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.41         1.08        12.03         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GB 
        8.09        11.31        49.22        23.90         9.67        39.39 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.29        17.98        47.21        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        30.84         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       36.33        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
       29.46        14.56        63.42       111.78       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
       25.08        26.99        21.60        23.05       124.31        25.84 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        15.95         3.22        22.92        21.60        16.14 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       22.22        27.35         0.46        33.60        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       38.40         5.72        76.41         3.78         3.52        11.90 
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-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-A2NH TCGA-ER-A3ES TCGA-ER-A3ET 
        1.87         1.51        13.08        11.74         9.04         6.58 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       22.49         1.71        85.74         4.90         6.71         3.58 
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-A1ZE TCGA-FS-A1ZF 
        7.33         3.39        20.38         8.22        19.53        11.08 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
        7.17        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-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FB 
       53.85         3.22        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-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       84.72        16.24        15.42        12.16        11.84        10.65 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.12               0.00 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            122.73             124.31 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            16.555             13.875 
[1] "1.1 - 122.7 (16.6)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1.2"
D64V2, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    34  27
  13Q LOSS WILD-TYPE 108 107
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                61                215 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                27                107 
$`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        69.90       171.58       103.59 
TCGA-D3-A3MU TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A148 TCGA-D9-A149 
       39.75       110.93       135.75       166.19       151.53        54.67 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
        3.25        25.18        48.89        36.03       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A181 
      107.34        53.92        68.09         3.55        52.01        33.73 
TCGA-EE-A184 TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N 
       68.15        13.55        47.84        13.97        44.35        18.61 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GI 
       37.35       345.96       171.55        58.75       135.95        48.72 
TCGA-EE-A2GJ TCGA-EE-A2M5 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MR TCGA-EE-A2MS 
       89.33        21.67       103.20        16.96       103.56       136.47 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3J5 
       53.26       122.73         3.68        54.51       138.81        36.95 
TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19B TCGA-ER-A19H TCGA-ER-A2NG TCGA-FR-A3YN 
      101.79        31.40        98.40       152.35        31.27        92.98 
TCGA-FR-A7U9 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A4F4 TCGA-GN-A266 
        7.00        27.72        32.75        47.38        66.67        10.13 
TCGA-GN-A26D 
       39.58 

$`13Q 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-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       31.59        90.90        95.74        43.43        65.49        23.77 
TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        11.87        48.76       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        45.11       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-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J 
        9.34        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GS 
       18.38        10.03        51.68        15.06       137.92         7.43 
TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC 
      125.19         3.65         6.41        11.34         9.90        66.25 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IA 
       22.95       117.21        20.38       194.83        61.18        65.92 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q 
       23.44        28.60        10.49       215.44        15.68        13.87 
TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 
       10.16        17.85        45.11        35.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 
       29.82        27.22         8.65        94.98        14.70        26.89 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
        4.96       109.64       151.27        78.87       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P 
       80.61        39.62        72.07        32.19         2.60        56.42 
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-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH 
       24.43        39.29        47.54        67.43       314.56       208.04 
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       101.95        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-A2MI TCGA-EE-A2MJ 
       19.76        61.51        47.28       103.27       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      144.76       203.05       167.90        47.54       248.65        43.23 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J3 
       41.59       124.31        25.84        13.81        23.47       172.18 
TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
      127.20        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A 
      148.08        35.44        13.94        50.76         9.17        77.75 
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-A19S 
      131.51        61.05        44.05       162.08        50.89        37.25 
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-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        33.21       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
        4.90       210.08        15.16       216.92        48.59       228.59 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
      202.65        20.91        28.08         7.79        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-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-A4F5 
       49.48        27.09        27.02        77.82        50.14        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         2.40         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       14.04       120.46       117.93        84.72        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       32.48        46.36        12.62       294.77         6.67 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              3.25               0.16 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            345.96             357.37 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             53.92              46.98 
[1] "3.2 - 346.0 (53.9)" "0.2 - 357.4 (47.0)"
[1] "hr=" "1.2"
D64V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q LOSS MUTATED                    4             1
  13Q LOSS WILD-TYPE                 33             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  13Q LOSS MUTATED                                          14
  13Q LOSS WILD-TYPE                                        46
                    vv
clus                 REGIONAL LYMPH NODE
  13Q LOSS MUTATED                    42
  13Q LOSS WILD-TYPE                 137
D64V4, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       4                 33
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               14                 46
  REGIONAL LYMPH NODE                                     42                137
[1] 4 2
[1] 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       1       6        5        6        3
  13Q LOSS WILD-TYPE           8       5      17        5       19       14
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  13Q LOSS MUTATED           1         2         2         8          2
  13Q LOSS WILD-TYPE         9        12         8        24         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED            5          8        4
  13Q LOSS WILD-TYPE         18         40        8
D64V5, multiclass
             clus
vv            13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  I OR II NOS                2                  8
  STAGE 0                    1                  5
  STAGE I                    6                 17
  STAGE IA                   5                  5
  STAGE IB                   6                 19
  STAGE II                   3                 14
  STAGE IIA                  1                  9
  STAGE IIB                  2                 12
  STAGE IIC                  2                  8
  STAGE III                  8                 24
  STAGE IIIA                 2                 12
  STAGE IIIB                 5                 18
  STAGE IIIC                 8                 40
  STAGE IV                   4                  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
  13Q LOSS MUTATED      15 13 14  8
  13Q LOSS WILD-TYPE    38 47 41 49
D64V6, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               15                 38
  T2                  13                 47
  T3                  14                 41
  T4                   8                 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
  13Q LOSS MUTATED    32  11   9   6
  13Q LOSS WILD-TYPE 109  40  23  31
D64V7, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               32                109
  N1               11                 40
  N2                9                 23
  N3                6                 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
  13Q LOSS MUTATED    54   0   0   2   3
  13Q LOSS WILD-TYPE 198   4   2   0   2
D64V8, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                54                198
  M1                 0                  4
  M1A                0                  2
  M1B                2                  0
  M1C                3                  2
[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
  13Q LOSS MUTATED   28 14
  13Q LOSS WILD-TYPE 76 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     28   14
  13Q LOSS WILD-TYPE   76   58
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                28                 76
  YES               14                 58
[1] 2 2
[1] FALSE
D64V10, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     7  54
  13Q LOSS WILD-TYPE  27 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      7   54
  13Q LOSS WILD-TYPE   27  193
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 7                 27
  YES               54                193
[1] 2 2
[1] FALSE
D64V11, continuous
D64V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    21  40
  13Q LOSS WILD-TYPE  87 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     21   40
  13Q LOSS WILD-TYPE   87  133
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               21                 87
  MALE                 40                133
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         0    61
  13Q LOSS WILD-TYPE     5                         1   214
D64V13, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   61                214
[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
  13Q LOSS MUTATED     0  60
  13Q LOSS WILD-TYPE   3 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0   60
  13Q LOSS WILD-TYPE    3  214
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               60                214
[1] 2 2
[1] FALSE

Clustering(65) Variable = 14Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   42 43
  14Q LOSS WILD-TYPE 95 90
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                85                185 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                43                 90 
$`14Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO 
       16.47       111.09        10.29        30.87        56.19        64.44 
TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51J 
       45.11        61.38        13.32       103.59         5.39        41.10 
TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A6EA TCGA-DA-A1HV 
        8.84        52.01        47.87         1.55        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-EE-A181 TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 
        1.12        37.97         8.55         2.43         8.09        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GP TCGA-EE-A2M6 TCGA-EE-A2M7 
        9.67         8.94        34.92         5.42        98.27         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MN 
        6.18         9.53        44.25         7.96       111.78        25.08 
TCGA-EE-A2MS TCGA-EE-A3AA TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J5 TCGA-EE-A3J7 
       27.16       124.31        12.72         3.22        21.60        21.60 
TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B 
       22.22         0.46        33.60        12.95         5.72        25.18 
TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3PL 
       11.90       114.15        34.88        36.07         1.87         1.71 
TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       85.74         3.45        15.52         7.33         7.30        20.38 
TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZT 
       19.53        30.87        47.38         8.65         8.81        40.64 
TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TU TCGA-GF-A4EO 
        3.22        28.73        14.20        10.78         0.13         7.23 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U9 
       12.85        31.33        16.24        15.42        12.16        10.65 
TCGA-OD-A75X 
       11.05 

$`14Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
        8.52        32.42        70.16       110.79        28.08        22.55 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       45.83        81.24        85.32         8.38        21.14        88.50 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
       68.22        69.90        11.41         7.50        36.16         6.31 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       92.42       114.67        15.25        46.98        46.32        82.29 
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        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS 
       15.09        17.72        20.48        13.94        95.38         6.97 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
       23.11         4.01         2.89         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         0.00         0.00        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        36.07         4.34         5.13         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        38.63         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         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 
        6.48         8.68        11.31        49.22        39.39        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        30.84         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ 
       36.33         8.84        47.51        29.46        14.56        63.42 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT 
      111.91        56.02        26.99        21.60        29.65        23.05 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
        5.56       122.73        25.84         3.68        30.15        13.81 
TCGA-EE-A3AG TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 
       15.95        22.92        16.14        27.35        13.94        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F 
       18.61        38.40        76.41         3.78         3.52        11.11 
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-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-FR-A3YN TCGA-FR-A69P 
       11.74         9.04         6.58        22.49        18.41         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 
        6.71         3.58         5.36        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         0.43         9.90        24.85 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       84.72        10.13        14.70        11.84         5.79 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.13               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            124.31             122.73 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             16.24              13.68 
[1] "0.1 - 124.3 (16.2)" "0.0 - 122.7 (13.7)"
[1] "hr=" "1"  
D65V2, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   44 43
  14Q LOSS WILD-TYPE 98 91
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                87                189 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                43                 91 
$`14Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JO 
       16.57       112.04        43.43        48.76        56.19        66.08 
TCGA-D3-A2JP TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51J 
       45.11        86.93        60.23       103.59        21.47       131.90 
TCGA-D3-A51N TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D9-A149 TCGA-D9-A6EA 
       10.03       135.75       137.92       166.19        54.67        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         3.55        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        24.43        39.29        58.75       135.95        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 
      144.76        47.54       136.47       124.31       138.81       172.18 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 
       36.95        64.08        53.19        33.40       148.08        13.94 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19S 
        9.17        98.40        13.02       268.93       152.35        37.25 
TCGA-ER-A2ND TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       23.34        33.21       174.21        48.59        28.08         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       27.72       357.37        40.27        32.75       101.26       133.55 
TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       11.41        53.16        50.14        28.73       174.84        12.43 
TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       47.54         7.23        14.04       117.93        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       32.48        12.62       294.77 

$`14Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.57        71.80       133.25        28.08        31.59 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA 
       90.90        95.74       103.10        65.49        23.77       115.53 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK 
      168.00        69.90        11.87       113.52        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
      171.58       130.72        58.06        46.98        46.32       166.52 
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       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GS 
       40.14        18.38        51.68        15.06       110.93         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      125.19       151.53         3.65         6.41        11.34         3.25 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 
        9.90        66.25        22.95        36.03        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93        61.18        65.92        23.44        68.09        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH 
       10.49        15.68        13.87        17.85        45.11        35.01 
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-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
       94.98        14.70        26.89        68.15         4.96       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        39.62        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W 
       56.42        37.35        14.47        55.92       345.96       171.55 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH 
       46.82       102.90        47.54        67.43       314.56       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-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
      101.95        14.30        55.59        44.88        94.82        21.67 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       61.51       103.27       204.66        96.23       203.05       167.90 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB 
      248.65        43.23       103.56        41.59        53.26       122.73 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J4 
       25.84         3.68        54.51        13.81        23.47       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       34.32        27.35       101.79        31.40        35.44        50.76 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       77.75        48.89        12.59        26.37         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-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       43.82        20.15        16.37        31.27        32.05       247.04 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       80.32        46.98        92.98         4.90       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZB 
        7.00       216.92       228.59       202.65        20.91        48.85 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       53.52        15.45         9.70        47.38        23.93        74.73 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
      148.80        26.56        49.48        27.09        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 
       66.67        26.73        49.45        77.88         0.20        22.92 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        0.16         2.40         9.90       120.46        84.72        10.13 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       39.58        46.36         6.67 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              3.55               0.16 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            357.37             345.96 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             48.89              46.98 
[1] "3.5 - 357.4 (48.9)" "0.2 - 346.0 (47.0)"
[1] "hr=" "1.1"
D65V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q LOSS MUTATED                   13             1
  14Q LOSS WILD-TYPE                 24             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  14Q LOSS MUTATED                                          24
  14Q LOSS WILD-TYPE                                        36
                    vv
clus                 REGIONAL LYMPH NODE
  14Q LOSS MUTATED                    49
  14Q LOSS WILD-TYPE                 130
D65V4, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      13                 24
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               24                 36
  REGIONAL LYMPH NODE                                     49                130
[1] 4 2
[1] 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             3       0      10        2        7        8
  14Q LOSS WILD-TYPE           7       6      13        8       18        9
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  14Q LOSS MUTATED           0         3         3        13          3
  14Q LOSS WILD-TYPE        10        11         7        19         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED            7         16        4
  14Q LOSS WILD-TYPE         16         32        8
D65V5, multiclass
             clus
vv            14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    0                  6
  STAGE I                   10                 13
  STAGE IA                   2                  8
  STAGE IB                   7                 18
  STAGE II                   8                  9
  STAGE IIA                  0                 10
  STAGE IIB                  3                 11
  STAGE IIC                  3                  7
  STAGE III                 13                 19
  STAGE IIIA                 3                 11
  STAGE IIIB                 7                 16
  STAGE IIIC                16                 32
  STAGE IV                   4                  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
  14Q LOSS MUTATED      20 21 14 19
  14Q LOSS WILD-TYPE    33 39 41 38
D65V6, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1               20                 33
  T2                  21                 39
  T3                  14                 41
  T4                  19                 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
  14Q LOSS MUTATED   42 20  7 13
  14Q LOSS WILD-TYPE 99 31 25 24
D65V7, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               42                 99
  N1               20                 31
  N2                7                 25
  N3               13                 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
  14Q LOSS MUTATED    80   0   1   0   3
  14Q LOSS WILD-TYPE 172   4   1   2   2
D65V8, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                80                172
  M1                 0                  4
  M1A                1                  1
  M1B                0                  2
  M1C                3                  2
[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
  14Q LOSS MUTATED   32 24
  14Q LOSS WILD-TYPE 72 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     32   24
  14Q LOSS WILD-TYPE   72   48
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                32                 72
  YES               24                 48
[1] 2 2
[1] FALSE
D65V10, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    11  77
  14Q LOSS WILD-TYPE  23 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11   77
  14Q LOSS WILD-TYPE   23  170
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                11                 23
  YES               77                170
[1] 2 2
[1] FALSE
D65V11, continuous
D65V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    36  52
  14Q LOSS WILD-TYPE  72 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     36   52
  14Q LOSS WILD-TYPE   72  121
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               36                 72
  MALE                 52                121
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       1                         0    87
  14Q LOSS WILD-TYPE     4                         1   188
D65V13, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   87                188
[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
  14Q LOSS MUTATED     0  88
  14Q LOSS WILD-TYPE   3 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   88
  14Q LOSS WILD-TYPE    3  186
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               88                186
[1] 2 2
[1] FALSE

Clustering(66) Variable = 15Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    17  22
  15Q LOSS WILD-TYPE 120 111
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                39                231 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                111 
$`15Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A6EC 
       15.25        61.38        26.37        52.01        47.87        13.22 
TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EE-A180 
       39.19        25.15         0.20         0.13         0.00         8.12 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH TCGA-EE-A2M5 
        1.08        12.03         8.09         9.67        47.21         8.84 
TCGA-EE-A2MC TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU TCGA-EE-A3AB 
       47.51         7.96       111.78        56.02         5.56       122.73 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19E 
       21.60        22.22         0.46        12.95         5.72        11.90 
TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZM TCGA-FS-A1ZT 
       22.49         3.45        23.80        15.52        47.38        40.64 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U9 
       10.13        16.24        10.65 

$`15Q 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-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        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         7.50        36.16         6.31        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       64.44        45.11       114.67        46.98        46.32        82.29 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
       13.32        24.00         6.31         9.34       103.59         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       20.48        13.94        95.38         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV 
        4.01         2.89         9.90        11.31        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-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-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 
       17.56        14.83        13.15         0.00        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-A20C TCGA-EE-A20F TCGA-EE-A20H 
        5.13         4.31        36.07         4.34         5.13         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        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
        8.55         4.41        27.12         9.50         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        6.48         2.43         8.68         8.09        11.31        49.22 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       23.90         8.94        39.39        34.29        17.98        34.92 
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 
       30.84         5.42         1.15        13.02        34.98        36.33 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
       98.27         2.70         6.18         9.53        29.46        44.25 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       14.56        63.42       111.91        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD 
       29.65        27.16        23.05       124.31        25.84         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-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       21.60        16.14        27.35        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D 
       18.61        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-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        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-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        9.04         6.58         1.71        18.41        85.74         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 
        6.71         3.58         5.36        64.47        11.01        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-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-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
        8.65         8.81        49.15         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-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.13         0.16         0.43         9.90         7.23        12.85 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       24.85        31.33        84.72        15.42        12.16        14.70 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       11.84        11.05         5.79 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                  0 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            122.73             124.31 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             15.25              13.94 
[1] "0.0 - 122.7 (15.2)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1.2"
D66V2, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    18  22
  15Q LOSS WILD-TYPE 124 112
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                40                236 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                112 
$`15Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D9-A148 
       58.06        86.93        39.75       135.75       137.92       151.53 
TCGA-D9-A6EC TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
       66.25       194.83        53.92        10.16        17.85        35.01 
TCGA-EE-A180 TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A2A5 TCGA-EE-A2GH 
       94.98         2.60        56.42        37.35        39.29       208.04 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MU 
       21.67        61.51        16.96       144.76       167.90        53.26 
TCGA-EE-A3AB TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A197 TCGA-ER-A199 
      122.73        64.08        53.19        33.40        13.94         9.17 
TCGA-ER-A19E TCGA-ER-A3EV TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZM 
       13.02        46.98        48.59       202.65        28.08       101.26 
TCGA-FS-A1ZT TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U9 
       53.16        10.13        64.44        12.62 

$`15Q 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-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        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       113.52        42.08        12.10       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       66.08        45.11       130.72        46.98        46.32       166.52 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MV 
       60.23        24.53        13.87         9.34       103.59        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       51.68        15.06       110.93       166.19         7.43       125.19 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         9.90 
TCGA-D9-A6EA TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       25.18        22.95        48.89        36.03       117.21        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
      176.55        35.93       107.34        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-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
       45.11         3.55        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       109.64       151.27        78.87       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        39.62        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       32.19        44.35        18.61        14.47        55.92       345.96 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.87       171.55        17.92        46.82       102.90        24.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       58.75        47.54        67.43       314.56       135.95        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       101.95 
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-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI 
       28.83        19.76        47.28       103.27       103.20       204.66 
TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR 
       96.23       203.05        47.54       248.65        43.23       103.56 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
      136.47        41.59       124.31        25.84         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-A3J8 TCGA-EE-A3JD TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       34.32        27.35       101.79       148.08        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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
      162.08        50.89        37.25       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-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       80.32        33.21        92.98       174.21         4.90       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       15.16         7.00       216.92       228.59        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-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
        9.70        32.75        47.38        23.93        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-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-GN-A262 
        0.16         2.40         9.90         7.23        14.04       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
      117.93        84.72        62.79        32.48        39.58        46.36 
TCGA-OD-A75X TCGA-QB-A6FS 
      294.77         6.67 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              2.60               0.16 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            208.04             357.37 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            53.225             47.460 
[1] "2.6 - 208.0 (53.2)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.2"
D66V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q LOSS MUTATED                    5             1
  15Q LOSS WILD-TYPE                 32             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  15Q LOSS MUTATED                                          12
  15Q LOSS WILD-TYPE                                        48
                    vv
clus                 REGIONAL LYMPH NODE
  15Q LOSS MUTATED                    22
  15Q LOSS WILD-TYPE                 157
D66V4, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       5                 32
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               12                 48
  REGIONAL LYMPH NODE                                     22                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
  15Q LOSS MUTATED             0       1       8        2        4        1
  15Q LOSS WILD-TYPE          10       5      15        8       21       16
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  15Q LOSS MUTATED           0         1         2         9          3
  15Q LOSS WILD-TYPE        10        13         8        23         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED            3          5        0
  15Q LOSS WILD-TYPE         20         43       12
D66V5, multiclass
             clus
vv            15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    1                  5
  STAGE I                    8                 15
  STAGE IA                   2                  8
  STAGE IB                   4                 21
  STAGE II                   1                 16
  STAGE IIA                  0                 10
  STAGE IIB                  1                 13
  STAGE IIC                  2                  8
  STAGE III                  9                 23
  STAGE IIIA                 3                 11
  STAGE IIIB                 3                 20
  STAGE IIIC                 5                 43
  STAGE IV                   0                 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
  15Q LOSS MUTATED       7 13  4 13
  15Q LOSS WILD-TYPE    46 47 51 44
D66V6, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1                7                 46
  T2                  13                 47
  T3                   4                 51
  T4                  13                 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                  N0  N1  N2  N3
  15Q LOSS MUTATED    24   6   4   6
  15Q LOSS WILD-TYPE 117  45  28  31
D66V7, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               24                117
  N1                6                 45
  N2                4                 28
  N3                6                 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
  15Q LOSS MUTATED    39   0   0   1   0
  15Q LOSS WILD-TYPE 213   4   2   1   5
D66V8, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                39                213
  M1                 0                  4
  M1A                0                  2
  M1B                1                  1
  M1C                0                  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"
D66V9, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   17 11
  15Q LOSS WILD-TYPE 87 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     17   11
  15Q LOSS WILD-TYPE   87   61
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                17                 87
  YES               11                 61
[1] 2 2
[1] FALSE
D66V10, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3  38
  15Q LOSS WILD-TYPE  31 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3   38
  15Q LOSS WILD-TYPE   31  209
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 3                 31
  YES               38                209
[1] 2 2
[1] FALSE
D66V11, continuous
D66V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    15  26
  15Q LOSS WILD-TYPE  93 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     15   26
  15Q LOSS WILD-TYPE   93  147
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               15                 93
  MALE                 26                147
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       2                         0    39
  15Q LOSS WILD-TYPE     3                         1   236
D66V13, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   39                236
[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
  15Q LOSS MUTATED     0  41
  15Q LOSS WILD-TYPE   3 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   41
  15Q LOSS WILD-TYPE    3  233
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               41                233
[1] 2 2
[1] FALSE

Clustering(67) Variable = 16P LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    25  28
  16P LOSS WILD-TYPE 112 105
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                53                217 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                28                105 
$`16P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
      111.09        32.42        22.55        45.83        68.22        69.90 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A51N 
       92.42        56.19        64.44       114.67        61.38         8.84 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EB-A44R TCGA-EE-A180 
       11.31        13.22        35.80        13.68         0.20         8.12 
TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29W 
        1.12         1.18        11.15         1.08        27.12         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2MK 
        8.09        11.31        34.29        30.84         8.84       111.78 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J5 TCGA-EE-A3JA 
       56.02        21.60         5.56       122.73        21.60        22.22 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19E TCGA-ER-A2ND TCGA-FS-A1Z0 
       33.60        31.40        12.95        11.90         1.87        23.80 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 
       40.64         8.68        27.39         0.99         0.13        24.85 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-OD-A75X 
       31.33        16.24        15.42        14.70        11.05 

$`16P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       16.47         8.52        70.16       110.79        28.08        81.24 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD 
       10.29        85.32         8.38        21.14        88.50        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 
       30.87         7.50        36.16         6.31        45.11        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         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       15.09        41.10        17.72        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        2.89         9.90        14.60        48.79        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19         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-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       13.15         0.13         0.00         0.00        13.22         0.20 
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-A29A 
        4.31        36.07         4.34         5.13         9.21         7.99 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
        9.90        37.97        38.63         8.55         4.41         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         6.48         2.43 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       49.22        23.90         9.67         8.94        39.39        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
       28.31        33.83         5.42         1.15        13.02        34.98 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       36.33        98.27         2.70         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML 
       29.46        44.25         7.96        14.56        63.42       111.91 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       25.08        26.99        29.65        27.16        23.05       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       25.84         3.68        30.15        13.81        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE 
        3.22        22.92        21.60        16.14        27.35         0.46 
TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
       13.94        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-FR-A3YN 
       11.74         9.04         6.58        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       85.74         4.90         6.71         3.58         5.36        64.47 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
        3.45        11.01        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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
        8.81        49.15         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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        2.27         0.20         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       12.85        84.72        10.13        12.16        11.84        10.65 
TCGA-QB-A6FS 
        5.79 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.13               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            122.73             124.31 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             21.60              13.32 
[1] "0.1 - 122.7 (21.6)" "0.0 - 124.3 (13.3)"
[1] "hr=" "1.1"
D67V2, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    26  28
  16P LOSS WILD-TYPE 116 106
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                54                222 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                28                106 
$`16P LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB TCGA-D3-A2JC 
      112.04       112.57        31.59        90.90       168.00        69.90 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A51N 
      171.58        56.19        66.08       130.72        86.93        10.03 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EB-A44R TCGA-EB-A5UL 
       25.18        66.25        36.03       176.55        10.16         3.55 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M 
       94.98        33.73        13.55        13.97         2.60        44.35 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2M5 
      171.55        17.92        46.82        67.43       101.95        21.67 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3J5 
      144.76       167.90        43.23        53.26       122.73        36.95 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19E TCGA-ER-A2ND 
       53.19       148.08        31.40        13.94        13.02        23.34 
TCGA-FS-A1Z0 TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FW-A3R5 TCGA-FW-A3TU 
      202.65        53.16        26.56        49.48        22.92        47.54 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-OD-A75X 
      120.46       117.93        64.44        62.79        39.58       294.77 

$`16P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       16.57        16.67        71.80       133.25        28.08        95.74 
TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD 
       43.43       103.10        65.49        23.77       115.53        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 
       48.76       113.52        42.08        12.10        45.11        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        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       40.14       131.90        18.38        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         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 
       45.11        35.01        52.01         6.35        12.20        29.82 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
       27.22         8.65        14.70        26.89        68.15         4.96 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
      109.64       151.27        78.87       168.26        63.35        80.61 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       47.84        39.62        72.07        32.19        18.61        56.42 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 
       37.35        14.47        55.92       345.96        25.87       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
       24.43        39.29        58.75        47.54       314.56       135.95 
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-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-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC 
      248.65       103.56       136.47        41.59       124.31        25.84 
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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
      127.20        64.08        34.32        27.35        33.40       101.79 
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-A19W 
       61.05        44.05       162.08        50.89        37.25       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH 
       79.99        43.82        20.15        16.37        31.27        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
        4.90       210.08        15.16         7.00       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-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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
      148.80        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
        0.20         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       84.72        10.13        32.48        46.36        12.62         6.67 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              2.60               0.16 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            294.77             357.37 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            53.225             47.330 
[1] "2.6 - 294.8 (53.2)" "0.2 - 357.4 (47.3)"
[1] "hr=" "1"  
D67V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P LOSS MUTATED                    8             2
  16P LOSS WILD-TYPE                 29             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16P LOSS MUTATED                                           7
  16P LOSS WILD-TYPE                                        53
                    vv
clus                 REGIONAL LYMPH NODE
  16P LOSS MUTATED                    37
  16P LOSS WILD-TYPE                 142
D67V4, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  DISTANT METASTASIS                                       8                 29
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                7                 53
  REGIONAL LYMPH NODE                                     37                142
[1] 4 2
[1] 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        2        5        2
  16P LOSS WILD-TYPE           7       4      20        8       20       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16P LOSS MUTATED           1         4         3         9          3
  16P LOSS WILD-TYPE         9        10         7        23         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED            5          7        2
  16P LOSS WILD-TYPE         18         41       10
D67V5, multiclass
             clus
vv            16P LOSS MUTATED 16P LOSS WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    2                  4
  STAGE I                    3                 20
  STAGE IA                   2                  8
  STAGE IB                   5                 20
  STAGE II                   2                 15
  STAGE IIA                  1                  9
  STAGE IIB                  4                 10
  STAGE IIC                  3                  7
  STAGE III                  9                 23
  STAGE IIIA                 3                 11
  STAGE IIIB                 5                 18
  STAGE IIIC                 7                 41
  STAGE IV                   2                 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
  16P LOSS MUTATED       8 12  8 14
  16P LOSS WILD-TYPE    45 48 47 43
D67V6, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1                8                 45
  T2                  12                 48
  T3                   8                 47
  T4                  14                 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                  N0  N1  N2  N3
  16P LOSS MUTATED    28  11   7   5
  16P LOSS WILD-TYPE 113  40  25  32
D67V7, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               28                113
  N1               11                 40
  N2                7                 25
  N3                5                 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
  16P LOSS MUTATED    49   0   0   0   2
  16P LOSS WILD-TYPE 203   4   2   2   3
D67V8, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                49                203
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                2                  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"
D67V9, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   24 13
  16P LOSS WILD-TYPE 80 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     24   13
  16P LOSS WILD-TYPE   80   59
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                24                 80
  YES               13                 59
[1] 2 2
[1] FALSE
D67V10, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     4  51
  16P LOSS WILD-TYPE  30 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4   51
  16P LOSS WILD-TYPE   30  196
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 4                 30
  YES               51                196
[1] 2 2
[1] FALSE
D67V11, continuous
D67V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    28  27
  16P LOSS WILD-TYPE  80 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     28   27
  16P LOSS WILD-TYPE   80  146
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               28                 80
  MALE                 27                146
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         1    53
  16P LOSS WILD-TYPE     4                         0   222
D67V13, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   53                222
[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
  16P LOSS MUTATED     1  54
  16P LOSS WILD-TYPE   2 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   54
  16P LOSS WILD-TYPE    2  220
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               54                220
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    37  43
  16Q LOSS WILD-TYPE 100  90
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                80                190 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                43                 90 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB 
      111.09        32.42       110.79        22.55        45.83        68.22 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       69.90        30.87        92.42        56.19        64.44       114.67 
TCGA-D3-A3CC TCGA-D3-A51N TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW 
       61.38         8.84         2.89        11.31        13.22        35.80 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EB-A5SG TCGA-EE-A17Z 
       13.68         9.99        14.83         0.20         0.00         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29B 
        8.12         1.12         4.31         4.34         1.18         9.90 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A29X 
       11.15         1.08        27.12        12.03         8.68         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GO TCGA-EE-A2GP 
       11.31         9.67        34.29        47.21        30.84         5.42 
TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ 
        8.84         9.53        63.42       111.78        56.02        21.60 
TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 
        5.56       122.73        30.15        13.81        22.92        21.60 
TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 TCGA-ER-A19B TCGA-ER-A19N 
       22.22        33.60        31.40        12.95        25.18        42.84 
TCGA-ER-A19W TCGA-ER-A2ND TCGA-FS-A1Z0 TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZP 
       17.72         1.87        23.80         3.39        11.08        52.08 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-FW-A3R5 
       40.64         8.68        27.39         3.22         0.20         0.99 
TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        0.13        24.85        31.33        16.24        15.42        14.70 
TCGA-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.47         8.52        70.16        28.08        81.24        10.29 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG 
       85.32         8.38        21.14        88.50        11.41         7.50 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       36.16         6.31        45.11        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         5.39        80.22        42.71        15.09        41.10 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       17.72        20.48        13.94        95.38        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EG 
        1.55         6.97        23.11         4.01         9.90        14.60 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       48.79        51.12        10.03        39.19        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-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 
       17.56        13.15         0.13         0.00        13.22         0.20 
TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B 
       11.57        10.55         1.35        12.20         5.13        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        5.13         9.21         7.99        37.97        38.63         8.55 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        4.41         9.50         8.09         8.84         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
        2.43        49.22        23.90         8.94        39.39        17.98 
TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        30.08        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       33.83         1.15        13.02        34.98        36.33        98.27 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
        2.70         6.18        47.51        29.46        44.25         7.96 
TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS 
       14.56       111.91        25.08        26.99        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH 
       23.05       124.31        25.84         3.68        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
        3.22        21.60        16.14        27.35         0.46        13.94 
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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       22.49         1.71        18.41        85.74         4.90         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z3 
        3.58         5.36        64.47         3.45        11.01        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         7.30        20.38         8.22        19.53 
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-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.81        49.15         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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 
        0.16         0.43         9.90         7.23        12.85        84.72 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U8 TCGA-GN-A4U9 
       10.13        12.16        11.84        10.65 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                  0 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            122.73             124.31 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            15.125             13.695 
[1] "0.0 - 122.7 (15.1)" "0.0 - 124.3 (13.7)"
[1] "hr=" "1.1"
D68V2, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    39  43
  16Q LOSS WILD-TYPE 103  91
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                82                194 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                43                 91 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JB 
      112.04       112.57       133.25        31.59        90.90       168.00 
TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3BZ 
       69.90        48.76       171.58        56.19        66.08       130.72 
TCGA-D3-A3CC TCGA-D3-A51N TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EA 
       86.93        10.03       151.53        54.67         3.25        25.18 
TCGA-D9-A6EC TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EB-A44R 
       66.25        36.03       176.55        35.93        15.68        10.16 
TCGA-EB-A5SG TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20C 
       45.11         8.65        94.98        33.73         4.96       151.27 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P 
       13.55        80.61        13.97         2.60        44.35        56.42 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GH 
      171.55        17.92        46.82        39.29        67.43       208.04 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2M5 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK 
      101.95        13.91        21.67        47.28        96.23       144.76 
TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AE TCGA-EE-A3AF 
      167.90        43.23        53.26       122.73        54.51        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A197 
      127.20        36.95        53.19       148.08        31.40        13.94 
TCGA-ER-A19B TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2ND TCGA-FS-A1Z0 TCGA-FS-A1ZB 
       98.40        44.05       148.18        23.34       202.65        48.85 
TCGA-FS-A1ZF TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F2 
       15.45        74.73        53.16        26.56        49.48        50.14 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
        0.20        22.92        47.54       120.46       117.93        64.44 
TCGA-GN-A268 TCGA-GN-A26D TCGA-OD-A75X TCGA-QB-A6FS 
       62.79        39.58       294.77         6.67 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J6 
       16.57        16.67        71.80        28.08        95.74        43.43 
TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JG 
      103.10        65.49        23.77       115.53        11.87       113.52 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 
       42.08        12.10        45.11        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        21.47       161.85        43.69        40.14       131.90 
TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       18.38        51.68        15.06       110.93       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
      166.19         7.43       125.19         3.65         6.41        11.34 
TCGA-D9-A6E9 TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        9.90        22.95        48.89       117.21        20.38       194.83 
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-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SH 
       28.60        10.49       215.44        13.87        17.85        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.55        52.01         6.35        12.20        29.82        27.22 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       14.70        26.89        68.15       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
       63.35        47.84        39.62        72.07        32.19        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 
       37.35        14.47        55.92       345.96        25.87       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI 
       24.43        58.75        47.54       314.56       135.95        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR 
       89.33        54.74        79.66        75.48        90.97        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        44.88        94.82       129.27        28.83        19.76 
TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2ML 
       61.51       103.27       103.20        16.96       204.66       203.05 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA 
       47.54       248.65       103.56       136.47        41.59       124.31 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J7 
       25.84         3.68        23.47       138.81       172.18        64.08 
TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 
       34.32        27.35        33.40       101.79        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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       92.98       174.21         4.90       210.08        15.16         7.00 
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-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH 
       27.72       357.37        53.52        40.27         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS 
       47.38        23.93       101.26       133.55        11.41       148.80 
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-A3TV TCGA-FW-A5DY 
       12.43        26.73        49.45        77.88         0.16         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A 
        9.90         7.23        14.04        84.72        10.13        32.48 
TCGA-GN-A4U8 TCGA-GN-A4U9 
       46.36        12.62 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.20               0.16 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            294.77             357.37 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            53.175             46.670 
[1] "0.2 - 294.8 (53.2)" "0.2 - 357.4 (46.7)"
[1] "hr=" "1.1"
D68V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q LOSS MUTATED                   14             2
  16Q LOSS WILD-TYPE                 23             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  16Q LOSS MUTATED                                          15
  16Q LOSS WILD-TYPE                                        45
                    vv
clus                 REGIONAL LYMPH NODE
  16Q LOSS MUTATED                    51
  16Q LOSS WILD-TYPE                 128
D68V4, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      14                 23
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               15                 45
  REGIONAL LYMPH NODE                                     51                128
[1] 4 2
[1] 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       4        4        6        6
  16Q LOSS WILD-TYPE           7       3      19        6       19       11
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  16Q LOSS MUTATED           1         6         6         9          3
  16Q LOSS WILD-TYPE         9         8         4        23         11
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED            8         11        3
  16Q LOSS WILD-TYPE         15         37        9
D68V5, multiclass
             clus
vv            16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    3                  3
  STAGE I                    4                 19
  STAGE IA                   4                  6
  STAGE IB                   6                 19
  STAGE II                   6                 11
  STAGE IIA                  1                  9
  STAGE IIB                  6                  8
  STAGE IIC                  6                  4
  STAGE III                  9                 23
  STAGE IIIA                 3                 11
  STAGE IIIB                 8                 15
  STAGE IIIC                11                 37
  STAGE IV                   3                  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
  16Q LOSS MUTATED      13 14 15 22
  16Q LOSS WILD-TYPE    40 46 40 35
D68V6, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               13                 40
  T2                  14                 46
  T3                  15                 40
  T4                  22                 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
  16Q LOSS MUTATED   45 13  9  9
  16Q LOSS WILD-TYPE 96 38 23 28
D68V7, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               45                 96
  N1               13                 38
  N2                9                 23
  N3                9                 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
  16Q LOSS MUTATED    72   1   0   1   2
  16Q LOSS WILD-TYPE 180   3   2   1   3
D68V8, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                72                180
  M1                 1                  3
  M1A                0                  2
  M1B                1                  1
  M1C                2                  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"
D68V9, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   36 22
  16Q LOSS WILD-TYPE 68 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     36   22
  16Q LOSS WILD-TYPE   68   50
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                36                 68
  YES               22                 50
[1] 2 2
[1] FALSE
D68V10, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     8  75
  16Q LOSS WILD-TYPE  26 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8   75
  16Q LOSS WILD-TYPE   26  172
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 8                 26
  YES               75                172
[1] 2 2
[1] FALSE
D68V11, continuous
D68V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    39  44
  16Q LOSS WILD-TYPE  69 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     39   44
  16Q LOSS WILD-TYPE   69  129
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               39                 69
  MALE                 44                129
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         1    81
  16Q LOSS WILD-TYPE     4                         0   194
D68V13, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   81                194
[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
  16Q LOSS MUTATED     1  82
  16Q LOSS WILD-TYPE   2 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   82
  16Q LOSS WILD-TYPE    2  192
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO               82                192
[1] 2 2
[1] FALSE

Clustering(69) Variable = 17P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   46 46
  17P LOSS WILD-TYPE 91 87
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                92                178 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                46                 87 
$`17P LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
       45.83        10.29        68.22        11.41         7.50        92.42 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51N TCGA-D3-A51T 
       56.19        64.44         6.31         9.34         8.84        13.94 
TCGA-D3-A5GO TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I5 
       47.87        11.31        48.79        35.80        51.12        44.52 
TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R TCGA-EB-A5UN TCGA-EE-A17X 
       25.15         7.00        17.56         0.20        13.22        11.57 
TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29E 
        8.12         5.13         4.31         4.34        37.97        38.63 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29T 
        8.55         4.41         1.08        27.12         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC 
        2.43         8.09        49.22        23.90         9.67        34.29 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       30.08        19.43         5.42        34.98         8.84        98.27 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
       47.51         9.53        44.25        25.08        26.99        21.60 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J5 
       29.65        27.16         5.56       124.31        25.84        21.60 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 
       21.60        16.14        13.94        31.40        18.61         5.72 
TCGA-ER-A19C TCGA-ER-A19S TCGA-ER-A2NG TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
        3.78        36.07        12.62        22.49        18.41        85.74 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        6.71         5.36         3.45        15.52        30.87        12.92 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 
        8.65        40.64         8.68        27.39         0.82         3.22 
TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       10.78         0.20         0.99        84.72        10.13        16.24 
TCGA-GN-A268 TCGA-GN-A4U9 
       15.42        10.65 

$`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        69.90        30.87        36.16         6.31        45.11 
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         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
       42.71        15.09        41.10        17.72        20.48        95.38 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       52.01         1.55         6.97        23.11         4.01         2.89 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.90        13.22        14.60        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69         4.93        22.36         6.64        19.36 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A6L9 
       14.83        13.15         0.13         0.00         0.00         0.20 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B 
       10.55         6.31         1.12         1.35        12.20        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D 
        5.13         9.21         1.18         7.99         9.90        11.15 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A0 
        9.50        12.03         8.09         8.84         8.68        11.31 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK 
        8.94        39.39        17.98        34.92        47.21        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        30.84         1.15        13.02 
TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI 
       36.33         2.70         6.18        29.46         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A3AB 
       63.42       111.78       111.91        56.02        23.05       122.73 
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-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 
       22.92        22.22        27.35         0.46        33.60        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       38.40        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-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       34.68         9.57        17.72        78.44        11.80         1.87 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
        1.51        13.08        11.74         9.04         6.58         1.71 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90         3.58        64.47        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-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
       11.08         7.17        12.89        47.38        52.08         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       49.15         5.23        53.85         7.36        28.73        14.20 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
        5.98         6.41         2.27         0.13         0.16         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A26A 
        9.90         7.23        12.85        24.85        31.33        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        11.05         5.79 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               0.2                0.0 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            124.31             122.73 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            15.470             13.745 
[1] "0.2 - 124.3 (15.5)" "0.0 - 122.7 (13.7)"
[1] "hr=" "1"  
D69V2, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   49 46
  17P LOSS WILD-TYPE 93 88
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                95                181 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                46                 88 
$`17P LOSS MUTATED`
TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JL 
       90.90        43.43       168.00        11.87       113.52       171.58 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A51N TCGA-D3-A51T 
       56.19        66.08        13.87         9.34        10.03        15.06 
TCGA-D3-A5GO TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
      137.92       151.53         3.65        25.18        48.89        36.03 
TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A44R 
      117.21       107.34        53.92        10.49       215.44        10.16 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A184 TCGA-EE-A185 
        3.55        52.01        29.82        94.98        68.15         4.96 
TCGA-EE-A20C TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L 
      151.27        47.84        39.62        72.07        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
       44.35        55.92       345.96        25.87        17.92       102.90 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GP 
       24.43        39.29        67.43        48.72        89.33        13.91 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MG 
       44.88        21.67       129.27        61.51        47.28       103.20 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MU 
       47.54       248.65        43.23       103.56       136.47        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH 
      124.31        25.84        36.95        64.08        34.32       101.79 
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-FS-A1YX 
       46.98        92.98       174.21       210.08         7.00        48.59 
TCGA-FS-A1Z4 TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU 
       28.08        32.75        47.38       133.55        53.16        26.56 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-FW-A3R5 
       49.48        27.09        50.14        12.43         0.20        22.92 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A4U9 
       84.72        10.13        64.44        62.79        12.62 

$`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        69.90        48.76        42.08        12.10        45.11 
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        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GL 
       43.69        40.14       131.90        18.38        51.68       110.93 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JX 
      135.75       166.19         7.43       125.19        54.67         6.41 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1I0 
       11.34         3.25         9.90        66.25        22.95        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-A3F8 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5SG 
       68.09        28.60        15.68        13.87        17.85        45.11 
TCGA-EB-A5SH TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 
       35.01         6.35        12.20        27.22         8.65        33.73 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       14.70        26.89       109.64        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       63.35        80.61        13.97        18.61        56.42        37.35 
TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD 
       14.47       171.55        46.82        58.75        47.54       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      135.95       208.04        54.74        79.66        75.48        90.97 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
      101.95        14.30        55.59        94.82        28.83        19.76 
TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      167.90        41.59       122.73         3.68        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JD 
       23.47       138.81       172.18       127.20        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19B 
       33.40       148.08        13.94        50.76        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-A19P TCGA-ER-A19Q TCGA-ER-A19W 
      131.51        61.05        44.05       162.08        50.89       148.18 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NH 
       79.99        43.82        23.34        20.15        16.37        32.05 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YW 
      247.04        80.32        33.21         4.90        15.16       216.92 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      228.59       202.65        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-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-A1ZZ TCGA-FS-A4F0 
      101.26        74.73        11.41       148.80        27.02        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD 
       66.67        28.73       174.84        26.73        49.45        77.88 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       47.54         0.16         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X 
      120.46       117.93        32.48        39.58        46.36       294.77 
TCGA-QB-A6FS 
        6.67 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.20               0.16 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            345.96             357.37 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             47.54              48.76 
[1] "0.2 - 346.0 (47.5)" "0.2 - 357.4 (48.8)"
[1] "hr=" "1.1"
D69V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P LOSS MUTATED                   14             1
  17P LOSS WILD-TYPE                 23             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17P LOSS MUTATED                                          14
  17P LOSS WILD-TYPE                                        46
                    vv
clus                 REGIONAL LYMPH NODE
  17P LOSS MUTATED                    69
  17P LOSS WILD-TYPE                 110
D69V4, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  DISTANT METASTASIS                                      14                 23
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               14                 46
  REGIONAL LYMPH NODE                                     69                110
[1] 4 2
[1] 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             4       3      13        5        9        4
  17P LOSS WILD-TYPE           6       3      10        5       16       13
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17P LOSS MUTATED           2         5         3        10          6
  17P LOSS WILD-TYPE         8         9         7        22          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED            7         16        4
  17P LOSS WILD-TYPE         16         32        8
D69V5, multiclass
             clus
vv            17P LOSS MUTATED 17P LOSS WILD-TYPE
  I OR II NOS                4                  6
  STAGE 0                    3                  3
  STAGE I                   13                 10
  STAGE IA                   5                  5
  STAGE IB                   9                 16
  STAGE II                   4                 13
  STAGE IIA                  2                  8
  STAGE IIB                  5                  9
  STAGE IIC                  3                  7
  STAGE III                 10                 22
  STAGE IIIA                 6                  8
  STAGE IIIB                 7                 16
  STAGE IIIC                16                 32
  STAGE IV                   4                  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
  17P LOSS MUTATED      18 24 17 22
  17P LOSS WILD-TYPE    35 36 38 35
D69V6, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               18                 35
  T2                  24                 36
  T3                  17                 38
  T4                  22                 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
  17P LOSS MUTATED   51 16 11 14
  17P LOSS WILD-TYPE 90 35 21 23
D69V7, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               51                 90
  N1               16                 35
  N2               11                 21
  N3               14                 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
  17P LOSS MUTATED    90   1   0   1   3
  17P LOSS WILD-TYPE 162   3   2   1   2
D69V8, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                90                162
  M1                 1                  3
  M1A                0                  2
  M1B                1                  1
  M1C                3                  2
[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
  17P LOSS MUTATED   43 25
  17P LOSS WILD-TYPE 61 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     43   25
  17P LOSS WILD-TYPE   61   47
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                43                 61
  YES               25                 47
[1] 2 2
[1] FALSE
D69V10, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    10  88
  17P LOSS WILD-TYPE  24 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     10   88
  17P LOSS WILD-TYPE   24  159
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                10                 24
  YES               88                159
[1] 2 2
[1] FALSE
D69V11, continuous
D69V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    32  66
  17P LOSS WILD-TYPE  76 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     32   66
  17P LOSS WILD-TYPE   76  107
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               32                 76
  MALE                 66                107
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       1                         1    96
  17P LOSS WILD-TYPE     4                         0   179
D69V13, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   96                179
[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
  17P LOSS MUTATED     0  97
  17P LOSS WILD-TYPE   3 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0   97
  17P LOSS WILD-TYPE    3  177
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               97                177
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    21  24
  17Q LOSS WILD-TYPE 116 109
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                45                225 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                109 
$`17Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A51N 
       10.29        11.41         7.50        56.19        64.44         8.84 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A180 TCGA-EE-A29C 
       11.31        35.80        44.52        25.15         8.12        37.97 
TCGA-EE-A29E TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GT 
       38.63         8.09         9.67        30.08         5.42        34.98 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A2MQ 
        8.84        98.27        47.51        44.25        26.99        21.60 
TCGA-EE-A3AA TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19C 
      124.31        21.60        16.14        13.94        31.40         3.78 
TCGA-ER-A19L TCGA-ER-A19S TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1Z4 TCGA-FS-A1ZH 
       13.45        36.07         6.71         5.36        15.52        30.87 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F9 
        8.65        40.64        27.39         0.82         3.22        10.78 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A267 
        0.20         0.99        16.24 

$`17Q 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-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-A2JF TCGA-D3-A2JH 
       21.14        88.50        68.22        69.90        30.87        36.16 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
        6.31        92.42        45.11       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         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       15.09        41.10        17.72        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
        2.89         9.90        13.22        14.60        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
       10.03        39.19        13.68         9.99        36.69         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         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.20        11.57        10.55         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        36.07         4.34         5.13 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G 
        9.21         1.18         7.99         9.90        11.15         8.55 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         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         6.48         2.43         8.68        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        23.90         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       34.92        47.21        19.43        16.01        35.54        28.31 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       33.83        30.84         1.15        13.02        36.33         2.70 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
        6.18         9.53        29.46         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS 
      111.78       111.91        56.02        25.08        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       23.05         5.56       122.73        25.84         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-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       22.22        27.35         0.46        33.60        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-A19M TCGA-ER-A19N 
       11.11       114.15        34.88         4.21        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
       34.68         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-A44A TCGA-FR-A69P TCGA-FR-A7U8 
       22.49         1.71        18.41        85.74         4.90         3.58 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
       64.47         3.45        11.01        23.80        14.24         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-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-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       49.15         8.68         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-GN-A262 TCGA-GN-A264 
        0.43         9.90         7.23        12.85        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       84.72        10.13        15.42        12.16        14.70        11.84 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       10.65        11.05         5.79 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               0.2                0.0 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            124.31             122.73 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             16.14              13.81 
[1] "0.2 - 124.3 (16.1)" "0.0 - 122.7 (13.8)"
[1] "hr=" "1.1"
D70V2, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    21  24
  17Q LOSS WILD-TYPE 121 110
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                45                231 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                110 
$`17Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A51N 
       43.43        11.87       113.52        56.19        66.08        10.03 
TCGA-D9-A6EA TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A180 TCGA-EE-A29C 
       25.18        36.03       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 
       39.62        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-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A19C 
      124.31        64.08        34.32       101.79        31.40        48.89 
TCGA-ER-A19L TCGA-ER-A19S TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1Z4 TCGA-FS-A1ZH 
      131.51        37.25       210.08         7.00        28.08        32.75 
TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F9 
      133.55        53.16        49.48        27.09        50.14        12.43 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A267 
        0.20        22.92        64.44 

$`17Q 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-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-A2JF TCGA-D3-A2JH 
       23.77       115.53       168.00        69.90        48.76        42.08 
TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 
       12.10       171.58        45.11       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        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       40.14       131.90        18.38        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         9.90 
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-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-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        45.11        35.01         3.55        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       12.20        29.82        27.22         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       109.64       151.27        78.87 
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 
       32.19         2.60        44.35        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       345.96        25.87       171.55        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        24.43        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
      135.95       208.04        89.33        54.74        79.66        75.48 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2M7 
       90.97       101.95        14.30        55.59        94.82        28.83 
TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       19.76        47.28       103.27        16.96       204.66        96.23 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS 
      144.76       203.05       167.90        47.54       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       41.59        53.26       122.73        25.84         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-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A197 
       53.19        27.35        33.40       148.08        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-A19M TCGA-ER-A19N 
       26.37       268.93       152.35         6.44        61.05        44.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND 
      162.08        50.89       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-A7U8 
       46.98        33.21        92.98       174.21         4.90        15.16 
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-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       84.72        10.13        62.79        32.48        39.58        46.36 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.16 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            248.65             357.37 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             47.84              47.54 
[1] "0.2 - 248.7 (47.8)" "0.2 - 357.4 (47.5)"
[1] "hr=" "1.2"
D70V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q LOSS MUTATED                    7             1
  17Q LOSS WILD-TYPE                 30             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  17Q LOSS MUTATED                                           8
  17Q LOSS WILD-TYPE                                        52
                    vv
clus                 REGIONAL LYMPH NODE
  17Q LOSS MUTATED                    32
  17Q LOSS WILD-TYPE                 147
D70V4, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       7                 30
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                8                 52
  REGIONAL LYMPH NODE                                     32                147
[1] 4 2
[1] 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        1        4        0
  17Q LOSS WILD-TYPE           7       5      14        9       21       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  17Q LOSS MUTATED           1         3         1         5          4
  17Q LOSS WILD-TYPE         9        11         9        27         10
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED            4          6        4
  17Q LOSS WILD-TYPE         19         42        8
D70V5, multiclass
             clus
vv            17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    1                  5
  STAGE I                    9                 14
  STAGE IA                   1                  9
  STAGE IB                   4                 21
  STAGE II                   0                 17
  STAGE IIA                  1                  9
  STAGE IIB                  3                 11
  STAGE IIC                  1                  9
  STAGE III                  5                 27
  STAGE IIIA                 4                 10
  STAGE IIIB                 4                 19
  STAGE IIIC                 6                 42
  STAGE IV                   4                  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
  17Q LOSS MUTATED       9 13  9 10
  17Q LOSS WILD-TYPE    44 47 46 47
D70V6, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                9                 44
  T2                  13                 47
  T3                   9                 46
  T4                  10                 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                  N0  N1  N2  N3
  17Q LOSS MUTATED    25  11   3   6
  17Q LOSS WILD-TYPE 116  40  29  31
D70V7, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               25                116
  N1               11                 40
  N2                3                 29
  N3                6                 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
  17Q LOSS MUTATED    42   1   0   0   3
  17Q LOSS WILD-TYPE 210   3   2   2   2
D70V8, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                42                210
  M1                 1                  3
  M1A                0                  2
  M1B                0                  2
  M1C                3                  2
[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
  17Q LOSS MUTATED   21 12
  17Q LOSS WILD-TYPE 83 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21   12
  17Q LOSS WILD-TYPE   83   60
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                21                 83
  YES               12                 60
[1] 2 2
[1] FALSE
D70V10, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     5  43
  17Q LOSS WILD-TYPE  29 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5   43
  17Q LOSS WILD-TYPE   29  204
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 5                 29
  YES               43                204
[1] 2 2
[1] FALSE
D70V11, continuous
D70V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    17  31
  17Q LOSS WILD-TYPE  91 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     17   31
  17Q LOSS WILD-TYPE   91  142
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               17                 91
  MALE                 31                142
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0    48
  17Q LOSS WILD-TYPE     5                         1   227
D70V13, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   48                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"
D70V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  48
  17Q LOSS WILD-TYPE   3 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   48
  17Q LOSS WILD-TYPE    3  226
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               48                226
[1] 2 2
[1] FALSE

Clustering(71) Variable = 18P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   43 36
  18P LOSS WILD-TYPE 94 97
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                79                191 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                36                 97 
$`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        69.90        11.41        30.87 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MR 
       92.42        64.44        45.11        15.25        46.98       103.59 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A6EG 
       26.37        41.10        95.38         1.55        23.11        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         0.00 
TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G 
       13.22        36.07         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 
       27.12         6.48         2.43         8.68         8.09        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG 
       17.98        34.92        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 
      111.78        56.02        21.60        27.16         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        13.94        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-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1ZA TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       85.74         4.90         3.58         7.30        47.38         8.65 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU TCGA-GN-A268 
        8.81        49.15        27.39         0.82         0.13        15.42 
TCGA-GN-A4U9 
       10.65 

$`18P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
        8.52       111.09        32.42       110.79        28.08        22.55 
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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ 
       68.22         7.50        36.16         6.31        56.19       114.67 
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-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
        9.34         5.39        80.22        42.71        15.09        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
        8.84        20.48        13.94        52.01        47.87         6.97 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HW 
        4.01         2.89         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-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.13         0.00         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-A29B TCGA-EE-A29C 
        4.31         5.13         9.21         1.18         9.90        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       38.63         4.41         1.08         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.84         9.99        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
        8.94        39.39        47.21        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       28.31        33.83        30.84        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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN 
       29.46         7.96        14.56        63.42       111.91        25.08 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 
       26.99        29.65        23.05        25.84        13.81        22.92 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 
       21.60        21.60        27.35         0.46        18.61        12.95 
TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J 
       38.40        76.41         3.52        11.11       114.15         4.21 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 
       13.45        28.60        42.84        34.68        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-A3PL TCGA-FR-A3YN TCGA-FR-A729 
        9.04         6.58        22.49         1.71        18.41         6.71 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.36        64.47         3.45        11.01        23.80        14.24 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
       15.52         7.33         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-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
       40.64         8.68         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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        0.20         0.99         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       12.85        24.85        31.33        84.72        10.13        16.24 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       12.16        14.70        11.84        11.05         5.79 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 0                  0 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            124.31             114.67 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             17.98              13.02 
[1] "0.0 - 124.3 (18.0)" "0.0 - 114.7 (13.0)"
[1] "hr=" "1.3"
D71V2, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   43 37
  18P LOSS WILD-TYPE 99 97
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                80                196 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                37                 97 
$`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        69.90        11.87        48.76 
TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3MR 
      171.58        66.08        45.11        58.06        46.98       103.59 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GL TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A1JX 
       39.75       131.90       110.93       166.19       125.19         6.41 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       22.95        48.89       176.55        61.18        53.92       215.44 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29D 
       45.11        52.01       109.64       151.27        63.35        13.97 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       72.07        44.35       345.96        25.87       171.55        17.92 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GR 
       67.43       314.56       135.95        48.72        13.91        14.30 
TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MU 
      103.20       144.76       167.90        43.23       136.47        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH 
      124.31       122.73         3.68        54.51        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      172.18        34.32        53.19       101.79       148.08        31.40 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19Q 
        9.17        98.40        48.89        13.02       152.35        50.89 
TCGA-ER-A19S TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1ZA TCGA-FS-A1ZM 
       37.25       174.21         4.90        15.16        27.72       101.26 
TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FW-A3TU 
      133.55        11.41       148.80        49.48        27.09        47.54 
TCGA-GN-A268 TCGA-GN-A4U9 
       62.79        12.62 

$`18P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.67       112.04       112.57       133.25        28.08        31.59 
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-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A3BZ 
      168.00       113.52        42.08        12.10        56.19       130.72 
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-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
        9.34        21.47       161.85        43.69        40.14        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       10.03        51.68        15.06       135.75       137.92         7.43 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53        54.67         3.65        11.34         3.25         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        35.01 
TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        3.55         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 
       78.87       168.26        13.55        80.61        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       32.19         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        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.54       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       101.95        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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
       16.96       204.66        96.23       203.05        47.54       248.65 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 
      103.56        41.59        25.84        13.81       127.20        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       64.08        27.35        33.40        35.44        13.94        50.76 
TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L 
       77.75        12.59        26.37       268.93         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       61.05        44.05       162.08       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-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U9 
       80.32        46.98        33.21        92.98       210.08         7.00 
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         2.40         9.90         7.23        14.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
      120.46       117.93        84.72        10.13        64.44        32.48 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS 
       39.58        46.36       294.77         6.67 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              3.68               0.16 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            345.96             357.37 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            56.285             43.755 
[1] "3.7 - 346.0 (56.3)" "0.2 - 357.4 (43.8)"
[1] "hr=" "1.3"
D71V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P LOSS MUTATED                   11             0
  18P LOSS WILD-TYPE                 26             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18P LOSS MUTATED                                          20
  18P LOSS WILD-TYPE                                        40
                    vv
clus                 REGIONAL LYMPH NODE
  18P LOSS MUTATED                    50
  18P LOSS WILD-TYPE                 129
D71V4, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  DISTANT METASTASIS                                      11                 26
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               20                 40
  REGIONAL LYMPH NODE                                     50                129
[1] 4 2
[1] 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             3       2       5        4        9        7
  18P LOSS WILD-TYPE           7       4      18        6       16       10
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18P LOSS MUTATED           0         5         1        12          6
  18P LOSS WILD-TYPE        10         9         9        20          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED            5         14        0
  18P LOSS WILD-TYPE         18         34       12
D71V5, multiclass
             clus
vv            18P LOSS MUTATED 18P LOSS WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    2                  4
  STAGE I                    5                 18
  STAGE IA                   4                  6
  STAGE IB                   9                 16
  STAGE II                   7                 10
  STAGE IIA                  0                 10
  STAGE IIB                  5                  9
  STAGE IIC                  1                  9
  STAGE III                 12                 20
  STAGE IIIA                 6                  8
  STAGE IIIB                 5                 18
  STAGE IIIC                14                 34
  STAGE IV                   0                 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
  18P LOSS MUTATED      19 19 13 15
  18P LOSS WILD-TYPE    34 41 42 42
D71V6, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               19                 34
  T2                  19                 41
  T3                  13                 42
  T4                  15                 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
  18P LOSS MUTATED    38  16  11   9
  18P LOSS WILD-TYPE 103  35  21  28
D71V7, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               38                103
  N1               16                 35
  N2               11                 21
  N3                9                 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
  18P LOSS MUTATED    77   0   0   0   0
  18P LOSS WILD-TYPE 175   4   2   2   5
D71V8, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                77                175
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                0                  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"
D71V9, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   29 17
  18P LOSS WILD-TYPE 75 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     29   17
  18P LOSS WILD-TYPE   75   55
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                29                 75
  YES               17                 55
[1] 2 2
[1] FALSE
D71V10, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    14  67
  18P LOSS WILD-TYPE  20 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     14   67
  18P LOSS WILD-TYPE   20  180
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                14                 20
  YES               67                180
[1] 2 2
[1] FALSE
D71V11, continuous
D71V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    30  51
  18P LOSS WILD-TYPE  78 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     30   51
  18P LOSS WILD-TYPE   78  122
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               30                 78
  MALE                 51                122
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         0    81
  18P LOSS WILD-TYPE     5                         1   194
D71V13, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   81                194
[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
  18P LOSS MUTATED     0  80
  18P LOSS WILD-TYPE   3 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0   80
  18P LOSS WILD-TYPE    3  194
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               80                194
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   40 35
  18Q LOSS WILD-TYPE 97 98
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                75                195 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                35                 98 
$`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        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MR 
       30.87        92.42        64.44        15.25        13.32       103.59 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A6EC TCGA-DA-A1HV 
       26.37        41.10         1.55        23.11        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         0.00 
TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29G 
       13.22        36.07         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 
       27.12         6.48         2.43         8.68         8.09        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2MG 
       17.98        34.92        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 
      111.78        21.60         5.56       124.31       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J8 TCGA-EE-A3JA 
       30.15        15.95        12.72         3.22        16.14        22.22 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19C 
       13.94        33.60        31.40         5.72        25.18         3.78 
TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P 
       34.88        36.07        17.72        22.49        85.74         4.90 
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 
        0.13        15.42        10.65 

$`18Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
        8.52       111.09        32.42       110.79        28.08        45.83 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       81.24        10.29         8.38        21.14        88.50        68.22 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
        7.50        36.16         6.31        56.19        45.11       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-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
        9.34         5.39        80.22        42.71        15.09        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
        8.84        20.48        13.94        95.38        52.01        47.87 
TCGA-D3-A5GS TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EG 
        6.97         4.01         2.89         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-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.20         0.13         0.00         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-A29B TCGA-EE-A29C 
        4.31         5.13         9.21         1.18         9.90        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       38.63         4.41         1.08         9.50        12.03         8.09 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.84         9.99        11.31        49.22        23.90         9.67 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
        8.94        39.39        47.21        19.43        16.01        35.54 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
       28.31        33.83        30.84        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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM 
       29.46         7.96        14.56        63.42       111.91        56.02 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC 
       25.08        26.99        29.65        27.16        23.05        25.84 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JE 
       13.81        22.92        21.60        21.60        27.35         0.46 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E 
       18.61        12.95        38.40        76.41         3.52        11.90 
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-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       34.68         9.57        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-A3PL 
       13.08        12.62        11.74         9.04         6.58         1.71 
TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
       18.41         6.71         5.36        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-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU 
       12.92        12.89        52.08         8.81        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-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
        0.16         0.43         9.90         7.23        12.85        24.85 
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-OD-A75X TCGA-QB-A6FS 
       11.84        11.05         5.79 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 0                  0 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            124.31             114.67 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             17.72              12.95 
[1] "0.0 - 124.3 (17.7)" "0.0 - 114.7 (12.9)"
[1] "hr=" "1.2"
D72V2, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    41  35
  18Q LOSS WILD-TYPE 101  99
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                76                200 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                35                 99 
$`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        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MR 
       48.76       171.58        66.08        58.06        60.23       103.59 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GR TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A6EC 
       39.75       131.90       166.19       125.19       151.53        66.25 
TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F5 
       48.89       176.55        61.18        53.92        65.92       215.44 
TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A29A TCGA-EE-A29D 
       45.11        52.01       109.64       151.27        63.35        13.97 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X 
       72.07        44.35       345.96        25.87       171.55        17.92 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GI TCGA-EE-A2GP TCGA-EE-A2GR 
       67.43       314.56       135.95        48.72        13.91        14.30 
TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
      103.20       144.76        43.23        53.26       124.31       122.73 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J8 
        3.68        54.51        23.47       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       101.79       148.08        31.40         9.17        98.40 
TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A3EV TCGA-FR-A44A 
       48.89       152.35        37.25       148.18        46.98       174.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW 
        4.90        15.16       101.26       133.55       148.80        49.48 
TCGA-FS-A1ZY TCGA-FW-A3TU TCGA-GN-A268 TCGA-GN-A4U9 
       27.09        47.54        62.79        12.62 

$`18Q LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QA 
       16.67       112.04       112.57       133.25        28.08        90.90 
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB 
       95.74        43.43        65.49        23.77       115.53       168.00 
TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3BZ 
      113.52        42.08        12.10        56.19        45.11       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-A3MV TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K 
        9.34        21.47       161.85        43.69        40.14        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       10.03        51.68        15.06       110.93       135.75       137.92 
TCGA-D3-A5GS TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
        7.43        54.67         3.65         6.41        11.34         3.25 
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        35.01 
TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A17Z 
        3.55         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 
       78.87       168.26        13.55        80.61        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       32.19         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        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
       47.54       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       101.95        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-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-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AF 
      248.65       103.56       136.47        41.59        25.84        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-ER-A195 
      127.20        36.95        64.08        27.35        33.40        35.44 
TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F 
       13.94        50.76        77.75        12.59        13.02        26.37 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P 
      268.93         6.44       131.51        61.05        44.05       162.08 
TCGA-ER-A19Q TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       50.89        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       31.27        32.05       247.04        80.32        33.21        92.98 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
      210.08         7.00       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-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-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZZ 
       23.93        74.73        11.41        53.16        26.56        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-A3TV 
       26.73        49.45        77.88         0.20        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        2.40         9.90         7.23        14.04       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       84.72        10.13        64.44        32.48        39.58        46.36 
TCGA-OD-A75X TCGA-QB-A6FS 
      294.77         6.67 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              3.68               0.16 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            345.96             357.37 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            63.070             42.755 
[1] "3.7 - 346.0 (63.1)" "0.2 - 357.4 (42.8)"
[1] "hr=" "1.4"
D72V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q LOSS MUTATED                   12             1
  18Q LOSS WILD-TYPE                 25             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  18Q LOSS MUTATED                                          19
  18Q LOSS WILD-TYPE                                        41
                    vv
clus                 REGIONAL LYMPH NODE
  18Q LOSS MUTATED                    45
  18Q LOSS WILD-TYPE                 134
D72V4, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  DISTANT METASTASIS                                      12                 25
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               19                 41
  REGIONAL LYMPH NODE                                     45                134
[1] 4 2
[1] 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             3       2       4        4        7        5
  18Q LOSS WILD-TYPE           7       4      19        6       18       12
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  18Q LOSS MUTATED           0         5         1        13          6
  18Q LOSS WILD-TYPE        10         9         9        19          8
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED            6         13        0
  18Q LOSS WILD-TYPE         17         35       12
D72V5, multiclass
             clus
vv            18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    2                  4
  STAGE I                    4                 19
  STAGE IA                   4                  6
  STAGE IB                   7                 18
  STAGE II                   5                 12
  STAGE IIA                  0                 10
  STAGE IIB                  5                  9
  STAGE IIC                  1                  9
  STAGE III                 13                 19
  STAGE IIIA                 6                  8
  STAGE IIIB                 6                 17
  STAGE IIIC                13                 35
  STAGE IV                   0                 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
  18Q LOSS MUTATED      18 16 13 15
  18Q LOSS WILD-TYPE    35 44 42 42
D72V6, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               18                 35
  T2                  16                 44
  T3                  13                 42
  T4                  15                 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
  18Q LOSS MUTATED    33  17  11   9
  18Q LOSS WILD-TYPE 108  34  21  28
D72V7, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               33                108
  N1               17                 34
  N2               11                 21
  N3                9                 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
  18Q LOSS MUTATED    71   0   0   1   0
  18Q LOSS WILD-TYPE 181   4   2   1   5
D72V8, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                71                181
  M1                 0                  4
  M1A                0                  2
  M1B                1                  1
  M1C                0                  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"
D72V9, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   28 16
  18Q LOSS WILD-TYPE 76 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     28   16
  18Q LOSS WILD-TYPE   76   56
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                28                 76
  YES               16                 56
[1] 2 2
[1] FALSE
D72V10, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    13  64
  18Q LOSS WILD-TYPE  21 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     13   64
  18Q LOSS WILD-TYPE   21  183
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                13                 21
  YES               64                183
[1] 2 2
[1] FALSE
D72V11, continuous
D72V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    28  49
  18Q LOSS WILD-TYPE  80 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     28   49
  18Q LOSS WILD-TYPE   80  124
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               28                 80
  MALE                 49                124
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         0    77
  18Q LOSS WILD-TYPE     5                         1   198
D72V13, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   77                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"
D72V14, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     0  76
  18Q LOSS WILD-TYPE   3 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0   76
  18Q LOSS WILD-TYPE    3  198
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               76                198
[1] 2 2
[1] FALSE

Clustering(73) Variable = 19P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    25  30
  19P LOSS WILD-TYPE 112 103
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                55                215 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                30                103 
$`19P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A51T 
       16.47        22.55        11.41        92.42        13.32        13.94 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1HW 
       95.38        52.01         2.89        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-A5SH TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H 
        0.00        11.57         9.21         1.18        11.15         4.41 
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        27.16 
TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3JA 
       23.05       122.73         3.68        15.95        21.60        22.22 
TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19Q TCGA-ER-A2NH TCGA-ER-A3EV 
       27.35        25.18         3.78         9.57        11.74        22.49 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZT 
       85.74         4.90        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        24.85 
TCGA-GN-A268 
       15.42 

$`19P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
        8.52       111.09        32.42        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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
       88.50        68.22        69.90        30.87         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
        6.31        56.19        64.44        45.11       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         5.39        80.22        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO 
       15.09        41.10        17.72         8.84        20.48        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC 
        1.55         6.97        23.11         4.01         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-A5UN TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z 
        0.13         0.00        13.22         0.20        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-A29A TCGA-EE-A29B TCGA-EE-A29C 
       36.07         4.34         5.13         7.99         9.90        37.97 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         8.55         1.08        27.12         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         6.48         2.43         8.68 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        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        30.84         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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.51         9.53        29.46         7.96        14.56        63.42 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR 
      111.78       111.91        56.02        25.08        21.60        29.65 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
        5.56       124.31        25.84        30.15        13.81        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH 
        3.22        22.92        21.60        16.14         0.46        13.94 
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-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-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S 
        4.21        13.45        28.60        42.84        34.68        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-A2NG TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 
       12.62         9.04         6.58         1.71        18.41         6.71 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 
        3.58         5.36        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-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM 
        8.22        19.53        11.08         7.17        12.89        47.38 
TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       52.08         8.81        49.15         8.68         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-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT 
        6.41         0.20         0.99         0.13         0.43         9.90 
TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       12.85        31.33        84.72        10.13        16.24        12.16 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       14.70        11.84        10.65        11.05         5.79 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 0                  0 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            122.73             124.31 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             15.42              13.94 
[1] "0.0 - 122.7 (15.4)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1.2"
D73V2, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    27  30
  19P LOSS WILD-TYPE 115 104
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                57                219 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                30                104 
$`19P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A51T 
       16.57        31.59        11.87       171.58        60.23        15.06 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D9-A148 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV 
      110.93       135.75       151.53         3.25        25.18        48.89 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       36.03        20.38       107.34        61.18        53.92        65.92 
TCGA-EB-A44R TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A20H TCGA-EE-A20I 
       10.16        35.01         3.55        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        32.19        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-A3AG 
      248.65       136.47        41.59       122.73         3.68        23.47 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19Q 
       36.95        53.19        27.35        98.40        48.89        50.89 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       32.05        46.98       174.21         4.90        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 
        7.23       120.46        62.79 

$`19P LOSS WILD-TYPE`
TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.67       112.04       112.57        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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH 
      115.53       168.00        69.90        48.76       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       12.10        56.19        66.08        45.11       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        21.47       161.85        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GO 
       40.14       131.90        18.38        10.03        51.68       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX 
      166.19         7.43       125.19        54.67         3.65         6.41 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I1 
       11.34         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-A5UN 
      215.44        15.68        13.87        17.85        45.11        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 
        6.35        12.20        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       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       78.87        63.35        80.61        47.84        39.62        72.07 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        18.61        56.42        37.35        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A2 
       55.92       345.96        25.87       171.55       102.90        24.43 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
       39.29        58.75        47.54        67.43       314.56       135.95 
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 
      101.95        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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.27        16.96       204.66        96.23       144.76       203.05 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
      167.90        47.54        43.23       103.56        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       25.84        54.51        13.81       138.81       172.18       127.20 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       64.08        34.32        33.40       101.79       148.08        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-A19L 
       13.02        26.37       268.93       152.35         6.44       131.51 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       61.05        44.05       162.08        37.25       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       43.82        23.34        20.15        16.37        31.27       247.04 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
       80.32        33.21        92.98       210.08        15.16         7.00 
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-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR 
       15.45         9.70        23.93       101.26        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
      148.80        26.56        27.09        27.02        77.82        50.14 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
       66.67        28.73       174.84        12.43        49.45         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A264 
       22.92        47.54         2.40         9.90        14.04       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 
       84.72        10.13        64.44        32.48        39.58        46.36 
TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.16               0.20 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            248.65             357.37 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             46.98              48.59 
[1] "0.2 - 248.7 (47.0)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.3"
D73V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P LOSS MUTATED                    7             1
  19P LOSS WILD-TYPE                 30             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19P LOSS MUTATED                                           9
  19P LOSS WILD-TYPE                                        51
                    vv
clus                 REGIONAL LYMPH NODE
  19P LOSS MUTATED                    41
  19P LOSS WILD-TYPE                 138
D73V4, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  DISTANT METASTASIS                                       7                 30
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                9                 51
  REGIONAL LYMPH NODE                                     41                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
  19P LOSS MUTATED             3       0       6        2        4        2
  19P LOSS WILD-TYPE           7       6      17        8       21       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19P LOSS MUTATED           1         1         1        12          0
  19P LOSS WILD-TYPE         9        13         9        20         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED            8          9        4
  19P LOSS WILD-TYPE         15         39        8
D73V5, multiclass
             clus
vv            19P LOSS MUTATED 19P LOSS WILD-TYPE
  I OR II NOS                3                  7
  STAGE 0                    0                  6
  STAGE I                    6                 17
  STAGE IA                   2                  8
  STAGE IB                   4                 21
  STAGE II                   2                 15
  STAGE IIA                  1                  9
  STAGE IIB                  1                 13
  STAGE IIC                  1                  9
  STAGE III                 12                 20
  STAGE IIIA                 0                 14
  STAGE IIIB                 8                 15
  STAGE IIIC                 9                 39
  STAGE IV                   4                  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
  19P LOSS MUTATED      13 15  6 12
  19P LOSS WILD-TYPE    40 45 49 45
D73V6, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               13                 40
  T2                  15                 45
  T3                   6                 49
  T4                  12                 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
  19P LOSS MUTATED    25  13   9   8
  19P LOSS WILD-TYPE 116  38  23  29
D73V7, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               25                116
  N1               13                 38
  N2                9                 23
  N3                8                 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
  19P LOSS MUTATED    50   0   1   1   3
  19P LOSS WILD-TYPE 202   4   1   1   2
D73V8, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                50                202
  M1                 0                  4
  M1A                1                  1
  M1B                1                  1
  M1C                3                  2
[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
  19P LOSS MUTATED   22 11
  19P LOSS WILD-TYPE 82 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     22   11
  19P LOSS WILD-TYPE   82   61
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                22                 82
  YES               11                 61
[1] 2 2
[1] FALSE
D73V10, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     9  49
  19P LOSS WILD-TYPE  25 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9   49
  19P LOSS WILD-TYPE   25  198
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 9                 25
  YES               49                198
[1] 2 2
[1] FALSE
D73V11, continuous
D73V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    28  30
  19P LOSS WILD-TYPE  80 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     28   30
  19P LOSS WILD-TYPE   80  143
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               28                 80
  MALE                 30                143
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         0    57
  19P LOSS WILD-TYPE     4                         1   218
D73V13, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   57                218
[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
  19P LOSS MUTATED     0  57
  19P LOSS WILD-TYPE   3 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   57
  19P LOSS WILD-TYPE    3  217
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               57                217
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    27  27
  19Q LOSS WILD-TYPE 110 106
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                54                216 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                27                106 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       22.55        11.41        92.42        13.94        95.38        52.01 
TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
        2.89        11.31        48.79        10.03        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17X TCGA-EE-A20H 
       25.15         4.93         0.20         0.00        11.57         9.21 
TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29X 
        1.18        11.15         4.41        27.12         9.99         8.09 
TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB 
       44.25        56.02        26.99        27.16        23.05       122.73 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A19B 
        3.68        15.95        21.60        22.22        27.35        25.18 
TCGA-ER-A19C TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P TCGA-FS-A1ZH 
        3.78        11.74        22.49        85.74         4.90        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4FB TCGA-FS-A4FD 
       12.92        40.64        27.39         3.22         5.98         2.27 
TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
        0.16         7.23        24.85        15.42        12.16        14.70 

$`19Q 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-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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
       21.14        88.50        68.22        69.90        30.87         7.50 
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        45.11       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         5.39 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
       80.22        42.71        15.09        41.10        17.72         8.84 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       20.48        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        9.90        13.22        14.60        35.80        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       13.68         9.99        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-A5UN 
       17.56        14.83        13.15         0.13         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        0.20        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        36.07         4.34         5.13 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L 
        7.99         9.90        37.97        38.63         8.55         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
        9.50        12.03         8.09         8.84         6.48         2.43 
TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.68        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        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        30.84 
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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
        7.96        14.56        63.42       111.78       111.91        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
       21.60        29.65         5.56       124.31        25.84        30.15 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 
       13.81        12.72         3.22        22.92        21.60        16.14 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 
        0.46        13.94        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-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
        1.71        18.41         6.71         3.58         5.36        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-A1ZQ TCGA-FS-A1ZR 
        7.17        12.89        47.38        52.08         8.65         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
       49.15         8.68         0.82         5.23        53.85         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-GN-A264 TCGA-GN-A265 
        0.13         0.43         9.90        12.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       10.13        16.24        11.84        10.65        11.05         5.79 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                  0 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            122.73             124.31 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            15.060             13.875 
[1] "0.0 - 122.7 (15.1)" "0.0 - 124.3 (13.9)"
[1] "hr=" "1"  
D74V2, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    28  27
  19Q LOSS WILD-TYPE 114 107
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                55                221 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                27                107 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JL TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
       31.59        11.87       171.58        15.06       110.93       135.75 
TCGA-D9-A148 TCGA-D9-A3Z3 TCGA-D9-A6EA TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I5 
      151.53         3.25        25.18        48.89        20.38       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17X 
       61.18        53.92        65.92        10.16        35.01        29.82 
TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29S 
      168.26        13.55        13.97        32.19        44.35        55.92 
TCGA-EE-A29X TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
       17.92       103.20       167.90       248.65       136.47        41.59 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
      122.73         3.68        23.47        36.95        53.19        27.35 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A2NH TCGA-ER-A3EV TCGA-FR-A44A TCGA-FR-A69P 
       98.40        48.89        32.05        46.98       174.21         4.90 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F2 TCGA-FS-A4FB 
       32.75        47.38        53.16        49.48        50.14        26.73 
TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A 
       77.88         0.16         7.23       120.46        62.79        32.48 
TCGA-GN-A26D 
       39.58 

$`19Q 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-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-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JF TCGA-D3-A2JG 
       23.77       115.53       168.00        69.90        48.76       113.52 
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        45.11       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        21.47 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
      161.85        43.69        40.14       131.90        18.38        10.03 
TCGA-D3-A51R TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 
       51.68       137.92       166.19         7.43       125.19        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-D9-A6EG 
        3.65         6.41        11.34         9.90        66.25        22.95 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IB 
       36.03       117.21       194.83       176.55        35.93        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-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       17.85        45.11         3.55        52.01         6.35        12.20 
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-A29A 
       68.15         4.96       109.64       151.27        78.87        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29N 
       80.61        47.84        39.62        72.07         2.60        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
       56.42        37.35        14.47       345.96        25.87       171.55 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       46.82       102.90        24.43        39.29        58.75        47.54 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       67.43       314.56       135.95       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       101.95        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-A2MH 
       28.83        19.76        61.51        47.28       103.27        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MQ 
      204.66        96.23       144.76       203.05        47.54        43.23 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF 
      103.56        53.26       124.31        25.84        54.51        13.81 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JE 
      138.81       172.18       127.20        64.08        34.32        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       148.08        31.40        35.44        13.94        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G 
        9.17        77.75        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-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-A3ES TCGA-ER-A3ET TCGA-ER-A3PL 
       20.15        16.37        31.27       247.04        80.32        33.21 
TCGA-FR-A3YN TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
       92.98       210.08        15.16         7.00       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-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-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
       26.56        27.09        27.02        77.82        66.67        28.73 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
      174.84        12.43        49.45         0.20        22.92        47.54 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        2.40         9.90        14.04       117.93        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-OD-A75X TCGA-QB-A6FS 
       64.44        46.36        12.62       294.77         6.67 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.16               0.20 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            248.65             357.37 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             46.98              48.59 
[1] "0.2 - 248.7 (47.0)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1.1"
D74V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q LOSS MUTATED                    6             1
  19Q LOSS WILD-TYPE                 31             3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  19Q LOSS MUTATED                                          10
  19Q LOSS WILD-TYPE                                        50
                    vv
clus                 REGIONAL LYMPH NODE
  19Q LOSS MUTATED                    39
  19Q LOSS WILD-TYPE                 140
D74V4, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       6                 31
  PRIMARY TUMOR                                            1                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               10                 50
  REGIONAL LYMPH NODE                                     39                140
[1] 4 2
[1] 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       7        2        5        2
  19Q LOSS WILD-TYPE           8       6      16        8       20       15
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  19Q LOSS MUTATED           1         1         2        10          1
  19Q LOSS WILD-TYPE         9        13         8        22         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED            7          8        4
  19Q LOSS WILD-TYPE         16         40        8
D74V5, multiclass
             clus
vv            19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  I OR II NOS                2                  8
  STAGE 0                    0                  6
  STAGE I                    7                 16
  STAGE IA                   2                  8
  STAGE IB                   5                 20
  STAGE II                   2                 15
  STAGE IIA                  1                  9
  STAGE IIB                  1                 13
  STAGE IIC                  2                  8
  STAGE III                 10                 22
  STAGE IIIA                 1                 13
  STAGE IIIB                 7                 16
  STAGE IIIC                 8                 40
  STAGE IV                   4                  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
  19Q LOSS MUTATED      10 17  7 13
  19Q LOSS WILD-TYPE    43 43 48 44
D74V6, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1               10                 43
  T2                  17                 43
  T3                   7                 48
  T4                  13                 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                  N0  N1  N2  N3
  19Q LOSS MUTATED    26  11   9   7
  19Q LOSS WILD-TYPE 115  40  23  30
D74V7, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               26                115
  N1               11                 40
  N2                9                 23
  N3                7                 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
  19Q LOSS MUTATED    47   0   1   1   3
  19Q LOSS WILD-TYPE 205   4   1   1   2
D74V8, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                47                205
  M1                 0                  4
  M1A                1                  1
  M1B                1                  1
  M1C                3                  2
[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
  19Q LOSS MUTATED   21 12
  19Q LOSS WILD-TYPE 83 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     21   12
  19Q LOSS WILD-TYPE   83   60
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                21                 83
  YES               12                 60
[1] 2 2
[1] FALSE
D74V10, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     8  48
  19Q LOSS WILD-TYPE  26 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8   48
  19Q LOSS WILD-TYPE   26  199
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 8                 26
  YES               48                199
[1] 2 2
[1] FALSE
D74V11, continuous
D74V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    27  29
  19Q LOSS WILD-TYPE  81 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     27   29
  19Q LOSS WILD-TYPE   81  144
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               27                 81
  MALE                 29                144
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         0    55
  19Q LOSS WILD-TYPE     4                         1   220
D74V13, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   55                220
[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
  19Q LOSS MUTATED     0  55
  19Q LOSS WILD-TYPE   3 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   55
  19Q LOSS WILD-TYPE    3  219
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               55                219
[1] 2 2
[1] FALSE

Clustering(75) Variable = 20P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     7   8
  20P LOSS WILD-TYPE 130 125
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                255 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                125 
$`20P LOSS MUTATED`
TCGA-D3-A2JC TCGA-D3-A3CF TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29E TCGA-EE-A29G 
       69.90        24.00        48.79        39.19        38.63         8.55 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3PL 
        3.78        11.90        34.88        17.72        12.62         1.71 
TCGA-FS-A1ZE TCGA-FS-A1ZR TCGA-FS-A4F4 
       19.53         8.81         7.36 

$`20P 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-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-A2JD TCGA-D3-A2JF 
        8.38        21.14        88.50        68.22        11.41        30.87 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       114.67        15.25        46.98        46.32        82.29 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       61.38        13.32         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 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
        8.84        20.48        13.94        95.38        52.01        47.87 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
        1.55         6.97        23.11         4.01         2.89         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       11.31        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-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         0.00         0.00        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        36.07         4.34 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
        5.13         9.21         1.18         7.99         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       11.15         4.41         1.08        27.12         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         6.48         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        49.22        23.90         9.67         8.94 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       39.39        34.29        17.98        34.92        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        30.84 
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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       44.25         7.96        14.56        63.42       111.78       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        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE 
       21.60        21.60        16.14        22.22        27.35         0.46 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
       13.94        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-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       36.07        78.44        11.80         1.87         1.51        13.08 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       11.74         9.04         6.58        22.49        18.41        85.74 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
        4.90         6.71         3.58         5.36        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         0.43 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       10.65        11.05         5.79 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1.71               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             69.90             124.31 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             17.72              13.94 
[1] "1.7 - 69.9 (17.7)"  "0.0 - 124.3 (13.9)"
[1] "hr=" "1.1"
D75V2, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     7   8
  20P LOSS WILD-TYPE 135 126
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                261 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                126 
$`20P LOSS MUTATED`
TCGA-D3-A2JC TCGA-D3-A3CF TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29E TCGA-EE-A29G 
       69.90        24.53        48.89       194.83        39.62        72.07 
TCGA-ER-A19C TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3PL 
       48.89        13.02       152.35       148.18        31.27        33.21 
TCGA-FS-A1ZE TCGA-FS-A1ZR TCGA-FS-A4F4 
       40.27        11.41        66.67 

$`20P 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-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-A2JD TCGA-D3-A2JF 
       65.49        23.77       115.53       168.00        11.87        48.76 
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-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB 
       45.11       130.72        58.06        46.98        46.32       166.52 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU 
       86.93        60.23        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 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO 
       10.03        51.68        15.06       110.93       135.75       137.92 
TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
      166.19         7.43       125.19       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         3.25         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       22.95        36.03       117.21        20.38       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        45.11        35.01         3.55        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       109.64       151.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C 
       78.87       168.26        13.55        63.35        80.61        47.84 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       13.97        32.19         2.60        44.35        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       345.96        25.87       171.55 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
       17.92        46.82       102.90        24.43        39.29        58.75 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       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       101.95 
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-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
      103.20        16.96       204.66        96.23       144.76       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       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       41.59        53.26       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE 
       36.95        64.08        34.32        53.19        27.35        33.40 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
      101.79       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-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF 
       37.25        79.99        43.82        23.34        20.15        16.37 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A44A 
       32.05       247.04        80.32        46.98        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
        4.90       210.08        15.16         7.00       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         2.40 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        9.90         7.23        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
       12.62       294.77         6.67 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             11.41               0.16 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            194.83             357.37 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             48.89              47.54 
[1] "11.4 - 194.8 (48.9)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1.1"
D75V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P LOSS MUTATED                    1             0
  20P LOSS WILD-TYPE                 36             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20P LOSS MUTATED                                           7
  20P LOSS WILD-TYPE                                        53
                    vv
clus                 REGIONAL LYMPH NODE
  20P LOSS MUTATED                     7
  20P LOSS WILD-TYPE                 172
D75V4, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  DISTANT METASTASIS                                       1                 36
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                7                 53
  REGIONAL LYMPH NODE                                      7                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
  20P LOSS MUTATED             0       0       1        0        1        1
  20P LOSS WILD-TYPE          10       6      22       10       24       16
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20P LOSS MUTATED           1         0         1         1          1
  20P LOSS WILD-TYPE         9        14         9        31         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED            2          3        1
  20P LOSS WILD-TYPE         21         45       11
D75V5, multiclass
             clus
vv            20P LOSS MUTATED 20P LOSS WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    0                  6
  STAGE I                    1                 22
  STAGE IA                   0                 10
  STAGE IB                   1                 24
  STAGE II                   1                 16
  STAGE IIA                  1                  9
  STAGE IIB                  0                 14
  STAGE IIC                  1                  9
  STAGE III                  1                 31
  STAGE IIIA                 1                 13
  STAGE IIIB                 2                 21
  STAGE IIIC                 3                 45
  STAGE IV                   1                 11
[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       3  4  3  3
  20P LOSS WILD-TYPE    50 56 52 54
D75V6, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                3                 50
  T2                   4                 56
  T3                   3                 52
  T4                   3                 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
  20P LOSS MUTATED     6   1   3   3
  20P LOSS WILD-TYPE 135  50  29  34
D75V7, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                6                135
  N1                1                 50
  N2                3                 29
  N3                3                 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
  20P LOSS MUTATED    13   0   1   0   0
  20P LOSS WILD-TYPE 239   4   1   2   5
D75V8, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                13                239
  M1                 0                  4
  M1A                1                  1
  M1B                0                  2
  M1C                0                  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
  20P LOSS MUTATED    5  5
  20P LOSS WILD-TYPE 99 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5    5
  20P LOSS WILD-TYPE   99   67
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 5                 99
  YES                5                 67
[1] 2 2
[1] FALSE
D75V10, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3  12
  20P LOSS WILD-TYPE  31 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3   12
  20P LOSS WILD-TYPE   31  235
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 3                 31
  YES               12                235
[1] 2 2
[1] FALSE
D75V11, continuous
D75V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     6   9
  20P LOSS WILD-TYPE 102 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6    9
  20P LOSS WILD-TYPE  102  164
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                6                102
  MALE                  9                164
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         0    15
  20P LOSS WILD-TYPE     5                         1   260
D75V13, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   15                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"
D75V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  14
  20P LOSS WILD-TYPE   3 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   14
  20P LOSS WILD-TYPE    3  260
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               14                260
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     2   2
  20Q LOSS WILD-TYPE 135 131
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                266 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                131 
$`20Q LOSS MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29G TCGA-ER-A19C TCGA-FS-A1ZE 
       39.19         8.55         3.78        19.53 

$`20Q 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-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        69.90        11.41 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       30.87         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        45.11       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         5.39        80.22        42.71        15.09 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       41.10        17.72         8.84        20.48        13.94        95.38 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       52.01        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
        2.89         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-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.00         0.00        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-A20H TCGA-EE-A20I 
        4.31        36.07         4.34         5.13         9.21         1.18 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        7.99         9.90        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         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         6.48         2.43         8.68         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
       49.22        23.90         9.67         8.94        39.39        34.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
       17.98        34.92        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        30.84         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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       14.56        63.42       111.78       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        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       16.14        22.22        27.35         0.46        13.94        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-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-A2NC TCGA-ER-A2ND TCGA-ER-A2NE 
       36.07        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-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
        1.71        18.41        85.74         4.90         6.71         3.58 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        5.36        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-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-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-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         0.43         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        12.85        24.85        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-OD-A75X TCGA-QB-A6FS 
       11.05         5.79 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              3.78               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             39.19             124.31 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             14.04              14.07 
[1] "3.8 - 39.2 (14.0)"  "0.0 - 124.3 (14.1)"
[1] "hr=" "1.2"
D76V2, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     2   2
  20Q LOSS WILD-TYPE 140 132
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                272 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                132 
$`20Q LOSS MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29G TCGA-ER-A19C TCGA-FS-A1ZE 
      194.83        72.07        48.89        40.27 

$`20Q 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-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        69.90        11.87 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
       48.76       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        45.11       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        21.47       161.85        43.69        40.14 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
      131.90        18.38        10.03        51.68        15.06       110.93 
TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
      135.75       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         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-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-A5SH 
       15.68        13.87        10.16        17.85        45.11        35.01 
TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        3.55        52.01         6.35        12.20        29.82        27.22 
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-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
        4.96       109.64       151.27        78.87       168.26        13.55 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       63.35        80.61        47.84        13.97        39.62        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        2.60        44.35        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       345.96        25.87       171.55        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      102.90        24.43        39.29        58.75        47.54        67.43 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
      314.56       135.95       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       101.95        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       144.76       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       103.56       136.47        41.59        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         3.68        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-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       34.32        53.19        27.35        33.40       101.79       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-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-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-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 
       33.21        92.98       174.21         4.90       210.08        15.16 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        7.00       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-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         2.40         9.90 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        7.23        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
      294.77         6.67 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             40.27               0.16 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            194.83             357.37 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             60.48              47.54 
[1] "40.3 - 194.8 (60.5)" "0.2 - 357.4 (47.5)" 
[1] "hr=" "1.3"
D76V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20Q LOSS MUTATED                    1             0
  20Q LOSS WILD-TYPE                 36             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  20Q LOSS MUTATED                                           2
  20Q LOSS WILD-TYPE                                        58
                    vv
clus                 REGIONAL LYMPH NODE
  20Q LOSS MUTATED                     1
  20Q LOSS WILD-TYPE                 178
D76V4, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       1                 36
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                2                 58
  REGIONAL LYMPH NODE                                      1                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
  20Q LOSS MUTATED             0       0       1        0        0        0
  20Q LOSS WILD-TYPE          10       6      22       10       25       17
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  20Q LOSS MUTATED           0         0         1         0          1
  20Q LOSS WILD-TYPE        10        14         9        32         13
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED            0          1        0
  20Q LOSS WILD-TYPE         23         47       12
D76V5, multiclass
             clus
vv            20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  I OR II NOS                0                 10
  STAGE 0                    0                  6
  STAGE I                    1                 22
  STAGE IA                   0                 10
  STAGE IB                   0                 25
  STAGE II                   0                 17
  STAGE IIA                  0                 10
  STAGE IIB                  0                 14
  STAGE IIC                  1                  9
  STAGE III                  0                 32
  STAGE IIIA                 1                 13
  STAGE IIIB                 0                 23
  STAGE IIIC                 1                 47
  STAGE IV                   0                 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
  20Q LOSS MUTATED       1  1  0  2
  20Q LOSS WILD-TYPE    52 59 55 55
D76V6, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                1                 52
  T2                   1                 59
  T3                   0                 55
  T4                   2                 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
  20Q LOSS MUTATED     1   0   1   1
  20Q LOSS WILD-TYPE 140  51  31  36
D76V7, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                1                140
  N1                0                 51
  N2                1                 31
  N3                1                 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
  20Q LOSS MUTATED     4   0   0   0   0
  20Q LOSS WILD-TYPE 248   4   2   2   5
D76V8, multiclass
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                 4                248
  M1                 0                  4
  M1A                0                  2
  M1B                0                  2
  M1C                0                  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"
D76V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   1
  20Q LOSS WILD-TYPE 102  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    1
  20Q LOSS WILD-TYPE  102   71
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 2                102
  YES                1                 71
[1] 2 2
[1] FALSE
D76V10, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   3
  20Q LOSS WILD-TYPE  33 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    3
  20Q LOSS WILD-TYPE   33  244
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 1                 33
  YES                3                244
[1] 2 2
[1] FALSE
D76V11, continuous
D76V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   4
  20Q LOSS WILD-TYPE 108 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    4
  20Q LOSS WILD-TYPE  108  169
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                0                108
  MALE                  4                169
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     4
  20Q LOSS WILD-TYPE     5                         1   271
D76V13, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                271
[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
  20Q LOSS MUTATED     0   4
  20Q LOSS WILD-TYPE   3 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    4
  20Q LOSS WILD-TYPE    3  270
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                4                270
[1] 2 2
[1] FALSE

Clustering(77) Variable = 21Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    30  24
  21Q LOSS WILD-TYPE 107 109
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                54                216 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                24                109 
$`21Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
       32.42        68.22        69.90        36.16        92.42        56.19 
TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D3-A51T TCGA-D3-A5GS TCGA-D9-A6E9 TCGA-D9-A6EA 
       64.44        46.32        13.94         6.97         9.90        11.31 
TCGA-DA-A1I0 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A20B 
       10.03         0.20        10.55         8.12         1.12        36.07 
TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        1.18         8.55         4.41         6.48         2.43         8.68 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI 
        8.09        23.90         8.94        39.39        34.29        30.08 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2MN TCGA-EE-A2MS 
       30.84         8.84        98.27       111.78        25.08        27.16 
TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19E TCGA-FS-A1ZA 
       12.72        21.60        22.22        12.95        11.90         7.30 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       19.53         7.17        47.38        40.64         8.68        27.39 
TCGA-FW-A5DY TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U9 TCGA-OD-A75X 
        0.43        24.85        10.13        15.42        10.65        11.05 

$`21Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.47         8.52       111.09        70.16       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-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK 
       21.14        88.50        11.41        30.87         7.50         6.31 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       114.67        15.25        46.98        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 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        8.84        20.48        95.38        52.01        47.87         1.55 
TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV 
       23.11         4.01         2.89        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-A5KH TCGA-EB-A5SG 
        7.00        17.56        14.83        13.15         0.13         0.00 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
        0.00        13.22         0.20        11.57         6.31         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
       12.20         5.13         4.31         4.34         5.13         9.21 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        7.99         9.90        37.97        11.15        38.63         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.50        12.03         8.09         8.84         9.99 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       11.31        49.22         9.67        17.98        34.92        47.21 
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-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 
        1.15        13.02        34.98        36.33         2.70         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        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        29.65 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
       23.05         5.56       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        27.35         0.46        13.94        33.60        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C 
       18.61        38.40         5.72        76.41        25.18         3.78 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L 
        3.52        11.11       114.15        34.88         4.21        13.45 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
       28.60        42.84        34.68         9.57        36.07        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-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW 
       85.74         4.90         6.71         3.58         5.36        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-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ 
        3.39        20.38         8.22        11.08        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY 
       12.89        52.08         8.65         8.81        49.15         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-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 
        0.13         0.16         9.90         7.23        12.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       84.72        16.24        12.16        14.70        11.84         5.79 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               0.2                0.0 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            111.78             124.31 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            13.445             14.220 
[1] "0.2 - 111.8 (13.4)" "0.0 - 124.3 (14.2)"
[1] "hr=" "1.2"
D77V2, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    30  25
  21Q LOSS WILD-TYPE 112 109
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                55                221 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                25                109 
$`21Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN 
      112.57       168.00        69.90        42.08       171.58        56.19 
TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D3-A51T TCGA-D3-A5GS TCGA-D9-A1JX TCGA-D9-A6E9 
       66.08        46.32        15.06         7.43         6.41         9.90 
TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       25.18        20.38        10.16        27.22        94.98        33.73 
TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A29V 
      109.64        13.55        72.07        32.19       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
      171.55        17.92        24.43        58.75        47.54        67.43 
TCGA-EE-A2GI TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2MN 
       48.72       101.95        21.67       129.27       144.76        47.54 
TCGA-EE-A2MS TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-ER-A197 TCGA-ER-A19E 
      136.47       138.81        36.95        53.19        13.94        13.02 
TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU 
       27.72        40.27         9.70       101.26        53.16        26.56 
TCGA-FS-A1ZW TCGA-FW-A5DY TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A4U9 
       49.48         2.40       120.46        10.13        62.79        12.62 
TCGA-OD-A75X 
      294.77 

$`21Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 
       16.57        16.67       112.04        71.80       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-A2JD TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK 
       23.77       115.53        11.87        48.76       113.52        12.10 
TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CC 
       45.11       130.72        58.06        46.98       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 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       10.03        51.68       110.93       135.75       137.92       166.19 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 
      125.19       151.53        54.67         3.65        11.34         3.25 
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-A5KH TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        17.85        45.11        35.01         3.55        52.01 
TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
        6.35        12.20        29.82         8.65        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       68.15         4.96       151.27        78.87       168.26        63.35 
TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M 
       80.61        47.84        13.97        39.62         2.60        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 
       18.61        56.42        37.35        14.47        55.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GJ 
      102.90        39.29       314.56       135.95       208.04        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       54.74        79.66        75.48        90.97        13.91        14.30 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
       55.59        44.88        94.82        28.83        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
       47.28       103.27       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       103.56        41.59 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       148.08        31.40        35.44 
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-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-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-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-FR-A3YN TCGA-FR-A44A 
      247.04        80.32        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YX 
        4.90       210.08        15.16         7.00       216.92        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB 
      228.59       202.65        20.91        28.08         7.79        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      357.37        53.52        15.45        32.75        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       74.73       133.55        11.41       148.80        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-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A264 TCGA-GN-A265 
        0.16         9.90         7.23        14.04       117.93        84.72 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-QB-A6FS 
       64.44        32.48        39.58        46.36         6.67 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              2.40               0.16 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            345.96             357.37 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             47.54              48.59 
[1] "2.4 - 346.0 (47.5)" "0.2 - 357.4 (48.6)"
[1] "hr=" "1"  
D77V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q LOSS MUTATED                    7             2
  21Q LOSS WILD-TYPE                 30             2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  21Q LOSS MUTATED                                          14
  21Q LOSS WILD-TYPE                                        46
                    vv
clus                 REGIONAL LYMPH NODE
  21Q LOSS MUTATED                    32
  21Q LOSS WILD-TYPE                 147
D77V4, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       7                 30
  PRIMARY TUMOR                                            2                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE               14                 46
  REGIONAL LYMPH NODE                                     32                147
[1] 4 2
[1] 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             2       3       3        3        4        5
  21Q LOSS WILD-TYPE           8       3      20        7       21       12
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  21Q LOSS MUTATED           0         2         2         8          2
  21Q LOSS WILD-TYPE        10        12         8        24         12
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED            6          8        3
  21Q LOSS WILD-TYPE         17         40        9
D77V5, multiclass
             clus
vv            21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  I OR II NOS                2                  8
  STAGE 0                    3                  3
  STAGE I                    3                 20
  STAGE IA                   3                  7
  STAGE IB                   4                 21
  STAGE II                   5                 12
  STAGE IIA                  0                 10
  STAGE IIB                  2                 12
  STAGE IIC                  2                  8
  STAGE III                  8                 24
  STAGE IIIA                 2                 12
  STAGE IIIB                 6                 17
  STAGE IIIC                 8                 40
  STAGE IV                   3                  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
  21Q LOSS MUTATED       8 10 10 14
  21Q LOSS WILD-TYPE    45 50 45 43
D77V6, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1                8                 45
  T2                  10                 50
  T3                  10                 45
  T4                  14                 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                  N0  N1  N2  N3
  21Q LOSS MUTATED    27  13   6   5
  21Q LOSS WILD-TYPE 114  38  26  32
D77V7, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               27                114
  N1               13                 38
  N2                6                 26
  N3                5                 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
  21Q LOSS MUTATED    50   0   1   0   2
  21Q LOSS WILD-TYPE 202   4   1   2   3
D77V8, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                50                202
  M1                 0                  4
  M1A                1                  1
  M1B                0                  2
  M1C                2                  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"
D77V9, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   22 16
  21Q LOSS WILD-TYPE 82 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     22   16
  21Q LOSS WILD-TYPE   82   56
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                22                 82
  YES               16                 56
[1] 2 2
[1] FALSE
D77V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     3  53
  21Q LOSS WILD-TYPE  31 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3   53
  21Q LOSS WILD-TYPE   31  194
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 3                 31
  YES               53                194
[1] 2 2
[1] FALSE
D77V11, continuous
D77V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    24  32
  21Q LOSS WILD-TYPE  84 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     24   32
  21Q LOSS WILD-TYPE   84  141
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               24                 84
  MALE                 32                141
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       2                         1    53
  21Q LOSS WILD-TYPE     3                         0   222
D77V13, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   53                222
[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
  21Q LOSS MUTATED     0  55
  21Q LOSS WILD-TYPE   3 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0   55
  21Q LOSS WILD-TYPE    3  219
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               55                219
[1] 2 2
[1] FALSE

Clustering(78) Variable = 22Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED     9  18
  22Q LOSS WILD-TYPE 128 115
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                27                243 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                18                115 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A5GO TCGA-DA-A1I2 
       28.08        68.22        30.87        92.42        47.87        13.68 
TCGA-EB-A44R TCGA-EE-A184 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GP 
        0.20         5.13        37.97        38.63         8.94         5.42 
TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A3JA TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H 
       44.25        56.02        22.22         3.52        11.90        34.88 
TCGA-ER-A19P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZY TCGA-FS-A4F0 
       34.68        64.47         3.45        12.92         0.82        53.85 
TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A4U9 
        7.23        10.13        10.65 

$`22Q 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-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-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       21.14        88.50        69.90        11.41         7.50        36.16 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
        6.31        56.19        64.44        45.11       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         5.39        80.22 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       42.71        15.09        41.10        17.72         8.84        20.48 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       13.94        95.38        52.01         1.55         6.97        23.11 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
        4.01         2.89         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-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-A5KH 
       19.36         7.00        17.56        14.83        13.15         0.13 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Y 
        0.00         0.00        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-A185 
        6.31         8.12         1.12         1.35        12.20         4.31 
TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A 
       36.07         4.34         5.13         9.21         1.18         7.99 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        9.90        11.15         8.55         4.41         1.08        27.12 
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         6.48 
TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        2.43         8.68         8.09        11.31        49.22        23.90 
TCGA-EE-A2A5 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67        39.39        34.29        17.98        34.92        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-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
       30.84         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-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN 
        7.96        14.56        63.42       111.78       111.91        25.08 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
       26.99        21.60        29.65        27.16        23.05         5.56 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        25.84         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-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       16.14        27.35         0.46        13.94        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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P 
        6.58        22.49         1.71        18.41        85.74         4.90 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        6.71         3.58         5.36        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-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-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 
       27.39         5.23         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-A6C8 TCGA-GN-A262 
        0.13         0.16         0.43         9.90        12.85        24.85 
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-OD-A75X TCGA-QB-A6FS 
       11.84        11.05         5.79 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               0.2                0.0 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             92.42             124.31 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             22.22              13.94 
[1] "0.2 - 92.4 (22.2)"  "0.0 - 124.3 (13.9)"
[1] "hr=" "1.3"
D78V2, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    10  18
  22Q LOSS WILD-TYPE 132 116
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                28                248 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                18                116 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JB TCGA-D3-A2JF TCGA-D3-A2JL TCGA-D3-A5GO TCGA-D9-A149 
       28.08       168.00        48.76       171.58       137.92        54.67 
TCGA-DA-A1I2 TCGA-EB-A44R TCGA-EE-A184 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A6 
      176.55        10.16        68.15        47.84        39.62        58.75 
TCGA-EE-A2GP TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A3JA TCGA-ER-A19D TCGA-ER-A19E 
       13.91       103.20       167.90        53.19        12.59        13.02 
TCGA-ER-A19H TCGA-ER-A19P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1ZJ TCGA-FS-A1ZY 
      152.35       162.08       216.92        48.59        47.38        27.09 
TCGA-FS-A4F0 TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A4U9 
       77.82         7.23        10.13        12.62 

$`22Q 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-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-A2JC TCGA-D3-A2JD TCGA-D3-A2JG TCGA-D3-A2JH 
       23.77       115.53        69.90        11.87       113.52        42.08 
TCGA-D3-A2JK TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C6 
       12.10        56.19        66.08        45.11       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        21.47       161.85 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N TCGA-D3-A51R 
       43.69        40.14       131.90        18.38        10.03        51.68 
TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU 
       15.06       110.93       135.75       166.19         7.43       125.19 
TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
      151.53         3.65         6.41        11.34         3.25         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-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       194.83        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        45.11        35.01         3.55 
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       109.64 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
      151.27        78.87       168.26        13.55        63.35        80.61 
TCGA-EE-A29D TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       13.97        72.07        32.19         2.60        44.35        18.61 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       56.42        37.35        14.47        55.92       345.96        25.87 
TCGA-EE-A29W TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
      171.55        17.92        46.82       102.90        24.43        39.29 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       47.54        67.43       314.56       135.95       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       101.95 
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-A2MH 
       28.83        19.76        61.51        47.28       103.27        16.96 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
      204.66        96.23       144.76       203.05        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       103.56       136.47        41.59        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        25.84         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-A3J8 
      138.81       172.18       127.20        36.95        64.08        34.32 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 
       27.35        33.40       101.79       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-FR-A3YN TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 
       46.98        33.21        92.98       174.21         4.90       210.08 
TCGA-FR-A7U8 TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
       15.16         7.00       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-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-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
      133.55        11.41       148.80        53.16        26.56        49.48 
TCGA-FS-A1ZZ TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
       27.02        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-A6C8 TCGA-GN-A262 TCGA-GN-A264 
        0.16         2.40         9.90        14.04       120.46       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-OD-A75X TCGA-QB-A6FS 
      294.77         6.67 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              7.23               0.16 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            216.92             357.37 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            50.975             47.410 
[1] "7.2 - 216.9 (51.0)" "0.2 - 357.4 (47.4)"
[1] "hr=" "1.2"
D78V3, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q LOSS MUTATED                    4             0
  22Q LOSS WILD-TYPE                 33             4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  22Q LOSS MUTATED                                           7
  22Q LOSS WILD-TYPE                                        53
                    vv
clus                 REGIONAL LYMPH NODE
  22Q LOSS MUTATED                    17
  22Q LOSS WILD-TYPE                 162
D78V4, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  DISTANT METASTASIS                                       4                 33
  PRIMARY TUMOR                                            0                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE                7                 53
  REGIONAL LYMPH NODE                                     17                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
  22Q LOSS MUTATED             1       1       4        2        6        1
  22Q LOSS WILD-TYPE           9       5      19        8       19       16
                    vv
clus                 STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  22Q LOSS MUTATED           0         2         0         0          0
  22Q LOSS WILD-TYPE        10        12        10        32         14
                    vv
clus                 STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED            3          2        1
  22Q LOSS WILD-TYPE         20         46       11
D78V5, multiclass
             clus
vv            22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  I OR II NOS                1                  9
  STAGE 0                    1                  5
  STAGE I                    4                 19
  STAGE IA                   2                  8
  STAGE IB                   6                 19
  STAGE II                   1                 16
  STAGE IIA                  0                 10
  STAGE IIB                  2                 12
  STAGE IIC                  0                 10
  STAGE III                  0                 32
  STAGE IIIA                 0                 14
  STAGE IIIB                 3                 20
  STAGE IIIC                 2                 46
  STAGE IV                   1                 11
[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       4 10  2  4
  22Q LOSS WILD-TYPE    49 50 53 53
D78V6, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1                4                 49
  T2                  10                 50
  T3                   2                 53
  T4                   4                 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
  22Q LOSS MUTATED    19   3   2   2
  22Q LOSS WILD-TYPE 122  48  30  35
D78V7, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               19                122
  N1                3                 48
  N2                2                 30
  N3                2                 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
  22Q LOSS MUTATED    25   0   0   1   0
  22Q LOSS WILD-TYPE 227   4   2   1   5
D78V8, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                25                227
  M1                 0                  4
  M1A                0                  2
  M1B                1                  1
  M1C                0                  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"
D78V9, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   13  4
  22Q LOSS WILD-TYPE 91 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     13    4
  22Q LOSS WILD-TYPE   91   68
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                13                 91
  YES                4                 68
[1] 2 2
[1] FALSE
D78V10, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3  25
  22Q LOSS WILD-TYPE  31 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   25
  22Q LOSS WILD-TYPE   31  222
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 3                 31
  YES               25                222
[1] 2 2
[1] FALSE
D78V11, continuous
D78V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    11  17
  22Q LOSS WILD-TYPE  97 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     11   17
  22Q LOSS WILD-TYPE   97  156
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               11                 97
  MALE                 17                156
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         1    26
  22Q LOSS WILD-TYPE     4                         0   249
D78V13, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   26                249
[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
  22Q LOSS MUTATED     0  28
  22Q LOSS WILD-TYPE   3 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      0   28
  22Q LOSS WILD-TYPE    3  246
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               28                246
[1] 2 2
[1] FALSE

Clustering(79) Variable = XQ LOSS MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    31  36
  XQ LOSS WILD-TYPE 106  97
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               67               203 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               36                97 
$`XQ LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JL 
      111.09        32.42        28.08        10.29         7.50        92.42 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       15.25        46.98         8.84        13.94        95.38        47.87 
TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A17Y TCGA-EE-A185 
        2.89        35.80        44.52        25.15        10.55         4.31 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
        4.34         5.13         1.18        37.97        11.15         4.41 
TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR 
        8.09         2.43         8.09        23.90        34.29         1.15 
TCGA-EE-A2GS TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD TCGA-EE-A3AF 
       13.02       111.78        56.02        27.16         3.68        13.81 
TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-ER-A193 TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L 
       12.72        16.14        31.40        11.90       114.15        13.45 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-FR-A7U8 
        1.51        13.08        12.62        11.74         6.58         3.58 
TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH 
       64.47        11.01         7.30        20.38        11.08        30.87 
TCGA-FS-A1ZJ TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZZ TCGA-FS-A4F0 
       12.92         8.65         8.81        49.15         5.23        53.85 
TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FS-A4FB TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A262 
        7.36        10.78         5.98         0.13        12.85        24.85 
TCGA-OD-A75X 
       11.05 

$`XQ LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.47         8.52        70.16       110.79        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-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       69.90        11.41        30.87        36.16         6.31        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       64.44        45.11       114.67        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 
        5.39        80.22        42.71        15.09        41.10        17.72 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       20.48        52.01         1.55         6.97        23.11         4.01 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
        9.90        11.31        13.22        14.60        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IA 
       10.03        39.19        13.68         9.99        36.69         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         0.00         0.00        13.22 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
        0.20        11.57         6.31         8.12         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B 
       12.20         5.13        36.07         9.21         7.99         9.90 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         8.55         1.08        27.12         9.50        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.68        11.31        49.22 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
        9.67         8.94        39.39        17.98        34.92        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-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
       30.84         5.42        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-A2MG 
        2.70         6.18        47.51         9.53        29.46        44.25 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP 
        7.96        14.56        63.42       111.91        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
       21.60        29.65        23.05         5.56       124.31       122.73 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 
       25.84        30.15        15.95         3.22        22.92        21.60 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI 
       21.60        22.22        27.35         0.46        13.94        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-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
        3.78         3.52        11.11        34.88         4.21        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
       11.80         1.87         9.04        22.49         1.71        18.41 
TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z0 
       85.74         4.90         6.71         5.36         3.45        23.80 
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-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU 
        7.17        12.89        47.38        52.08        40.64         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FC 
       27.39         0.82         3.22        28.73        14.20         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         0.43         9.90 
TCGA-GF-A4EO TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        7.23        31.33        84.72        10.13        16.24        15.42 
TCGA-GN-A26A TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-QB-A6FS 
       12.16        14.70        11.84        10.65         5.79 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.13              0.00 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           114.15            124.31 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            12.72             15.42 
[1] "0.1 - 114.2 (12.7)" "0.0 - 124.3 (15.4)"
[1] "hr=" "1.2"
D79V2, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    32  36
  XQ LOSS WILD-TYPE 110  98
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               68               208 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               36                98 
$`XQ LOSS MUTATED`
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JL 
      112.04       112.57        28.08        43.43       113.52       171.58 
TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GO 
       58.06        46.98        10.03        15.06       110.93       137.92 
TCGA-D9-A148 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A17Y 
      151.53         3.25        36.03       107.34        53.92        27.22 
TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29D 
        4.96       151.27        78.87        13.55        47.84        13.97 
TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GC 
       32.19        37.35        25.87        17.92        24.43        67.43 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A3AD 
       14.30        55.59       144.76       167.90       136.47         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        14.04 
TCGA-GN-A262 TCGA-OD-A75X 
      120.46       294.77 

$`XQ LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA 
       16.57        16.67        71.80       133.25        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-A2JH TCGA-D3-A2JK TCGA-D3-A2JN 
       69.90        11.87        48.76        42.08        12.10        56.19 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC 
       66.08        45.11       130.72        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 
       21.47       161.85        43.69        40.14       131.90        18.38 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A149 
       51.68       135.75       166.19         7.43       125.19        54.67 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
        3.65         6.41        11.34         9.90        25.18        66.25 
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-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.93        61.18        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 
       45.11        35.01         3.55        52.01         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       29.82         8.65        94.98        33.73        14.70        26.89 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29E 
       68.15       109.64       168.26        63.35        80.61        39.62 
TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       72.07         2.60        44.35        18.61        56.42        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
       55.92       345.96       171.55        46.82       102.90        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       58.75        47.54       314.56       135.95       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       101.95 
TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
       13.91        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-A2MI TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
      204.66        96.23       203.05        47.54       248.65        43.23 
TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC 
      103.56        41.59        53.26       124.31       122.73        25.84 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
       54.51        23.47       172.18       127.20        36.95        64.08 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       53.19        27.35        33.40       101.79       148.08        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-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       12.59        26.37       152.35         6.44        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-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       23.34       247.04        46.98        33.21        92.98       174.21 
TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        4.90       210.08         7.00        48.59       202.65        20.91 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG 
       28.08         7.79        48.85        53.52        40.27         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW 
       23.93       101.26        74.73        53.16        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4FC TCGA-FS-A4FD 
       27.09        50.14        28.73       174.84        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         2.40         9.90         7.23 
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-QB-A6FS 
       39.58        46.36        12.62         6.67 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             3.25              0.16 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           357.37            345.96 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           45.205            48.805 
[1] "3.2 - 357.4 (45.2)" "0.2 - 346.0 (48.8)"
[1] "hr=" "1"  
D79V3, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ LOSS MUTATED                   14             1
  XQ LOSS WILD-TYPE                 23             3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE
  XQ LOSS MUTATED                                          11
  XQ LOSS WILD-TYPE                                        49
                   vv
clus                REGIONAL LYMPH NODE
  XQ LOSS MUTATED                    44
  XQ LOSS WILD-TYPE                 135
D79V4, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  DISTANT METASTASIS                                     14                23
  PRIMARY TUMOR                                           1                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE              11                49
  REGIONAL LYMPH NODE                                    44               135
[1] 4 2
[1] 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       2       3        1        7        6
  XQ LOSS WILD-TYPE           4       4      20        9       18       11
                   vv
clus                STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA
  XQ LOSS MUTATED           2         7         1         4          3
  XQ LOSS WILD-TYPE         8         7         9        28         11
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED            4         13        5
  XQ LOSS WILD-TYPE         19         35        7
D79V5, multiclass
             clus
vv            XQ LOSS MUTATED XQ LOSS WILD-TYPE
  I OR II NOS               6                 4
  STAGE 0                   2                 4
  STAGE I                   3                20
  STAGE IA                  1                 9
  STAGE IB                  7                18
  STAGE II                  6                11
  STAGE IIA                 2                 8
  STAGE IIB                 7                 7
  STAGE IIC                 1                 9
  STAGE III                 4                28
  STAGE IIIA                3                11
  STAGE IIIB                4                19
  STAGE IIIC               13                35
  STAGE IV                  5                 7
[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      10 13 17 14
  XQ LOSS WILD-TYPE    43 47 38 43
D79V6, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1              10                43
  T2                 13                47
  T3                 17                38
  T4                 14                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                 N0  N1  N2  N3
  XQ LOSS MUTATED    38  14   2  11
  XQ LOSS WILD-TYPE 103  37  30  26
D79V7, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              38               103
  N1              14                37
  N2               2                30
  N3              11                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B M1C
  XQ LOSS MUTATED    61   0   0   2   4
  XQ LOSS WILD-TYPE 191   4   2   0   1
D79V8, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               61               191
  M1                0                 4
  M1A               0                 2
  M1B               2                 0
  M1C               4                 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"
D79V9, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   23 21
  XQ LOSS WILD-TYPE 81 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     23   21
  XQ LOSS WILD-TYPE   81   51
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               23                81
  YES              21                51
[1] 2 2
[1] FALSE
D79V10, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     6  64
  XQ LOSS WILD-TYPE  28 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6   64
  XQ LOSS WILD-TYPE   28  183
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                6                28
  YES              64               183
[1] 2 2
[1] FALSE
D79V11, continuous
D79V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    35  35
  XQ LOSS WILD-TYPE  73 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     35   35
  XQ LOSS WILD-TYPE   73  138
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              35                73
  MALE                35               138
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         0    69
  XQ LOSS WILD-TYPE     4                         1   206
D79V13, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  69               206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1  67
  XQ LOSS WILD-TYPE   2 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   67
  XQ LOSS WILD-TYPE    2  207
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              67               207
[1] 2 2
[1] FALSE
