[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"        "-oTBLCA-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/11541262/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/11548710/transformed.cor.cli.txt"

nPatients in clinical file=281, in cluster file=408, common to both=278
[1]  80 278
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               56               222 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               56               222 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               82               196 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               82               196 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               66               212 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               66               212 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               29               249 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               29               249 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               88               190 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               88               190 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              115               163 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              115               163 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               28               250 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               28               250 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               261 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               261 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              102               176 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              102               176 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               34               244 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               34               244 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               41               237 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               41               237 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               23               255 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               23               255 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              112               166 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              112               166 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               98               180 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               98               180 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               55               223 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               55               223 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              129               149 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              129               149 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               46               232 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               46               232 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               36               242 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               36               242 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                76                202 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                76                202 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                25                253 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                25                253 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                25                253 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                25                253 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                37                241 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                37                241 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                77                201 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                77                201 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                58                220 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                58                220 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                65                213 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                65                213 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                44                234 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                44                234 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                22                256 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                22                256 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                49                229 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                49                229 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                54                224 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                54                224 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                39                239 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                39                239 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                92                186 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                92                186 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                78                200 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                78                200 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                40                238 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                40                238 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                52                226 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                52                226 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                88                190 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                88                190 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               132                146 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               132                146 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               154                124 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               154                124 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                77                201 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                77                201 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                36                242 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                36                242 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               29               249 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               29               249 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               19               259 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               19               259 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               258 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               258 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               30               248 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               30               248 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               61               217 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               61               217 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               36               242 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               36               242 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               15               263 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               15               263 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               91               187 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               91               187 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               89               189 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               89               189 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               42               236 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               42               236 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              105               173 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              105               173 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               65               213 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               65               213 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              101               177 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              101               177 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               10               268 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               10               268 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               15               263 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               15               263 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              125               153 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              125               153 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               256 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               256 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              116               162 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              116               162 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              110               168 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              110               168 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                49                229 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                49                229 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                87                191 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                87                191 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               113                165 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               113                165 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                81                197 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                81                197 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                33                245 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                33                245 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                34                244 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                34                244 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                52                226 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                52                226 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                77                201 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                77                201 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                93                185 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                93                185 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                68                210 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                68                210 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                63                215 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                63                215 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               117                161 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               117                161 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                26                252 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                26                252 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                211 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                211 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                96                182 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                96                182 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                68                210 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                68                210 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                40                238 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                40                238 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                21                257 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                21                257 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                269 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                269 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                44                234 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                44                234 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               106                172 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               106                172 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               54               224 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               54               224 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 278 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
         678           NA         2555         3148         2991          147 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
        1219           NA           NA           NA          377           NA 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
         363           NA           NA           NA           NA           NA 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
         522          170          111           NA          390           63 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
         469          873          304          864           NA           59 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
         700           14           13           21           NA           NA 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
          NA           NA            4            2            3            2 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CU-A0YN TCGA-CU-A0YO 
           3            3           NA           NA           NA           NA 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
         219          166          158          496           NA          284 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
          77           NA         2020          560          578          271 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
        3981         3420          491          536          475           55 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
         322           NA         3767         2656           67          121 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
         238           NA          319         1529          648          609 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
          NA          252           NA         4283         1460           NA 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
        1952         1264         2330         2049          477         1249 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
         933         1326           NA          796          750            3 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
          15           16           NA           18           17           20 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
          42           25          395          436           37           14 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
         392          477           NA          209           NA          378 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
         363          483         1397           NA          683          186 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
         390           NA          401           NA           NA           60 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
         699          454          455          454          110          369 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
         407         1130           NA          209           NA           NA 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
         208           NA          209         1511           81          147 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
          NA          194         1541          572          283          204 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
         125           63           81           67          122          330 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
         462          217          106          124           NA          197 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        1884          931          173           NA         1072          525 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
         214           NA           26         1602           NA          592 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
          88           68          481          137          484          428 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
         540           34           81          235           64           95 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
         638           67          224          195          231          344 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
          62          824          171           NA           NA          134 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QG TCGA-GV-A3QH 
         195          187          173          232           NA          237 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
         126          203          195          580          351           46 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
         205         1174           93           NA          250          266 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
         105          142           76          197          320           53 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
          55          130          194          193          105          359 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
         410          372          507          433           NA          114 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        1370           NA         2705         2964         1709           NA 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
          NA           NA           NA         2423           NA           NA 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
         640           NA          799           NA           68           NA 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
        2027           64           NA           NA           NA           NA 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
        2790           NA           NA           NA           NA           NA 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
          NA         2293           NA          315          147           NA 
TCGA-YF-AA3L TCGA-YF-AA3M 
         242          275 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=82,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=175,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=26,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "NUMBER.OF.LYMPH.NODES"       "RACE"                       
[11] "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 278 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=50, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1   1  80 136  39 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
      82      136       39 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   1  80 136  39 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
      82      136       39 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
166  28  55   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
166  28  55   7 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
166  28  55   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
166  28  55   7 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=60, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=19, binary=FALSE, numeric=TRUE
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    35  20
  1P GAIN WILD-TYPE 147  68
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               55               215 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20                68 
$`1P GAIN MUTATED`
TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CU-A0YN 
        5.06        17.16        12.82         8.98         1.94        12.92 
TCGA-CU-A5W6 TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM 
        1.84        10.59         7.79       123.85         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-E5-A4U1 TCGA-E7-A541 
        8.22        20.02        17.98        64.18        26.17         0.59 
TCGA-E7-A5KE TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SO 
        0.56         8.94         4.01        45.93        24.30         5.52 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A5C0 
       13.18        19.79         1.97        22.98         6.87         6.87 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A3IE 
        2.66         4.01        15.19         4.08         3.25        20.12 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GD-A3OS 
       19.46         2.89        15.81         4.50         1.12        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A6ZA 
        7.36         6.41         4.41         7.63         4.14        11.54 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A9T5 TCGA-XF-AAMT 
        6.35         3.45        13.48        88.93        66.64         2.96 
TCGA-YF-AA3M 
        9.04 

$`1P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB 
       14.89        14.96         5.06         8.35         8.25         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        3.65         4.67         2.07        15.42        28.70         9.99 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       28.41        23.01         0.46         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO 
        0.07         0.10         0.07         0.10         0.10         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
        7.20         5.46         5.19        16.31         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I6 
      112.44        16.14        17.62        15.62         1.81        87.32 
TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
        2.20        10.49        50.27        21.30         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       10.55       140.81        48.00        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       15.68        41.06        30.67        43.59        15.35        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         0.49         0.53         0.66         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.99        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM 
        6.87        12.43        11.93        15.88        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.82        46.78        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX 
       12.13        13.38        37.15        11.01         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        6.84        27.45        49.68         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.38        50.66        18.81         9.30         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A61P 
        2.07         2.20        10.85         7.13         3.48         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC 
        7.04         0.85        52.67         6.94         2.24        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        17.75         2.66         7.73         2.10         3.12 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        2.20         7.59        11.31         2.04        27.09         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH 
        4.73        10.65         6.41         6.15         5.69         7.79 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.67         6.41        19.07         1.51         6.74        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.50         6.48        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        6.38        11.80        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        3.75        45.04         6.58        97.45        56.19        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
        2.10        92.98        10.82        54.90         7.63        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        8.32         6.77        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.56              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           123.85            140.81 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             7.82             10.36 
[1] "0.6 - 123.8 (7.8)"  "0.1 - 140.8 (10.4)"
[1] "hr=" "1.3"
D1V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED          1       0       17        16       22
  1P GAIN WILD-TYPE        0       2       69        77       70
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               17                69
  STAGE III              16                77
  STAGE IV               22                70
[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"
                   vv
clus                T0+T1+T2  T3  T4
  1P GAIN MUTATED         17  27   8
  1P GAIN WILD-TYPE       65 109  31
D1V4, multiclass
          clus
vv         1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1+T2              17                65
  T3                    27               109
  T4                     8                31
[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"
                   vv
clus                 N0  N1  N2  N3
  1P GAIN MUTATED    29  10  10   3
  1P GAIN WILD-TYPE 137  18  45   4
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              29               137
  N1              10                18
  N2              10                45
  N3               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED    25   1  30
  1P GAIN WILD-TYPE 104   6 111
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              25               104
  M1               1                 6
  MX              30               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    13  43
  1P GAIN WILD-TYPE  64 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     13   43
  1P GAIN WILD-TYPE   64  158
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              13                64
  MALE                43               158
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       3                         3    46
  1P GAIN WILD-TYPE    28                        10   169
D1V11, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   3                28
  BLACK OR AFRICAN AMERICAN               3                10
  WHITE                                  46               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  53
  1P GAIN WILD-TYPE   4 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   53
  1P GAIN WILD-TYPE    4  205
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              53               205
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    52  29
  1Q GAIN WILD-TYPE 130  59
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               81               189 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               29                59 
$`1Q GAIN MUTATED`
TCGA-2F-A9KP TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LD 
       11.97         2.66         6.74         5.06        17.16         3.65 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A47V TCGA-CU-A0YN 
       28.70        28.41         8.98         1.94         0.10        12.92 
TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 
        5.46         1.84         2.53       112.44        10.59         7.79 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
        3.98         7.82         8.22        17.98        64.18        67.36 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A541 TCGA-E7-A5KF TCGA-FD-A3B5 
       26.17        24.66         0.10         0.59         0.66         8.94 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
        4.01        45.93        24.30        22.45         6.12         5.52 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BU 
       13.18        19.79         1.97        22.98         3.62         6.87 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE 
        6.87        49.68         2.66         4.01         3.48         3.25 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       19.46         2.89        15.81         4.50        17.75         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-AATO 
        7.73         2.10        20.98         7.36         6.41        10.65 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF 
        4.41         6.15         4.14        11.54        38.60         3.06 
TCGA-K4-A3WS TCGA-K4-A5RJ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        8.75         1.74         6.35         3.45        13.48        12.23 
TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-AAMT 
       88.93        15.35        17.88        11.90        66.64         2.96 
TCGA-XF-AAN0 TCGA-YC-A9TC TCGA-YF-AA3M 
       56.48         0.66         9.04 

$`1Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       22.29        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        7.33        12.39         6.58        11.93        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         8.25         5.59         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       15.42         9.99        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO 
        0.13         0.07         0.07         0.10         0.10         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        7.20         5.19        16.31         9.34         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00         8.91       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ 
       15.62         1.81       123.85        87.32         2.20        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
      140.81        48.00        41.56        76.60        15.68        41.06 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE 
       30.67        43.59        15.35         0.49         0.53         0.56 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        1.38         0.82        12.99        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       12.89        15.68         6.87        12.43        11.93        15.88 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y 
       12.82        46.78        14.93        14.96        14.93        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       13.38        37.15        11.01         5.36         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       27.45         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       18.81         9.30         6.71         4.11         2.07         2.20 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
       10.85        15.19         7.13         4.08         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC 
       20.12         0.85        52.67         6.94         2.24        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       14.07         2.66         3.12         2.20         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JZ 
        2.04        27.09         5.62         4.73         6.41         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        7.63         7.79         6.67         6.41        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        6.74         9.01         8.22         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A8JT 
        6.48        10.52         1.81         4.27         6.38        11.80 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       16.67        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX 
       97.45        56.19         1.87        64.80        79.66        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
        2.10        92.98        10.82        54.90         7.63        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        8.32         6.77        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YF-AA3L 
       10.36         4.83         7.96 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.10              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           112.44            140.81 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             7.79             10.52 
[1] "0.1 - 112.4 (7.8)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.4"
D2V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED          1       0       23        21       36
  1Q GAIN WILD-TYPE        0       2       63        72       56
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               23                63
  STAGE III              21                72
  STAGE IV               36                56
[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"
                   vv
clus                T0+T1+T2 T3 T4
  1Q GAIN MUTATED         24 38 14
  1Q GAIN WILD-TYPE       58 98 25
D2V4, multiclass
          clus
vv         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1+T2              24                58
  T3                    38                98
  T4                    14                25
[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"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED    41  11  22   3
  1Q GAIN WILD-TYPE 125  17  33   4
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              41               125
  N1              11                17
  N2              22                33
  N3               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED   34  5 43
  1Q GAIN WILD-TYPE 95  2 98
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              34                95
  M1               5                 2
  MX              43                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    19  63
  1Q GAIN WILD-TYPE  58 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     19   63
  1Q GAIN WILD-TYPE   58  138
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              19                58
  MALE                63               138
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       4                         4    67
  1Q GAIN WILD-TYPE    27                         9   148
D2V11, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   4                27
  BLACK OR AFRICAN AMERICAN               4                 9
  WHITE                                  67               148
[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"
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     1  75
  1Q GAIN WILD-TYPE   4 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   75
  1Q GAIN WILD-TYPE    4  183
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              75               183
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    47  18
  2P GAIN WILD-TYPE 135  70
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               65               205 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               18                70 
$`2P GAIN MUTATED`
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB 
       12.39        11.93        19.04         5.06         8.35         5.59 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
        3.65        12.82        28.70        28.41         8.98        23.01 
TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        0.43         0.10         7.20         2.53        66.41        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
      130.88       112.44        10.59         7.79        87.32         2.20 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
        7.82         8.22        48.00        17.98        64.18        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A541 TCGA-E7-A6ME TCGA-FD-A3NA 
       15.68        30.67        43.59         0.59        12.99        45.93 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A62O 
       46.78        19.79        14.93        14.93        27.45         4.83 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.11         2.07         2.66         2.20         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS 
        6.48         0.85        14.07         7.73         2.10        20.98 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
        7.63         7.79         6.67         6.74        38.60         8.75 
TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-XF-A8HD TCGA-XF-A8HG 
        4.67         1.81         4.27        88.93        15.35 

$`2P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20N 
       40.08         7.33         2.66         6.74         6.58        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16         4.67         2.07        15.42         9.99 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94         0.46         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.07         0.10        12.92         4.90         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       16.31         1.84         9.34         2.14        19.00         8.91 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL 
       16.14        17.62        15.62         1.81       123.85         3.98 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       10.49        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E5-A4TZ 
       10.55       140.81        41.56        76.60        41.06        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE 
       26.17        24.66         0.10         0.49         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.66         1.38         0.82        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       12.89        15.68         8.94         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        15.88        24.30        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X 
        5.52        13.18         1.97        22.98        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       12.13        13.38        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P 
        5.69         6.84         6.87        49.68         2.66         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TI 
        6.38        50.66        18.81         9.30         6.71         4.01 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.85        15.19         7.13         3.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        5.69        26.93        35.24        17.26         7.04        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       52.67         6.94        19.46         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ 
        4.50        15.91        17.75         1.12         2.66         3.12 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36         6.41         7.59        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
       27.09         5.62         4.73        10.65         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        6.15         5.69         4.14         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB 
        1.51         3.06         9.01         8.22         3.45         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        6.48        10.52         1.74         6.38         6.35         3.45 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       11.80        13.48        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
        3.75        45.04         6.58        97.45        56.19         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       17.88        64.80        79.66        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
        2.10        92.98        10.82        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
        2.96         8.32         6.77        56.48        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 
TCGA-YF-AA3M 
        9.04 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           130.88            140.81 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             8.98              9.30 
[1] "0.1 - 130.9 (9.0)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.4"
D3V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED          0       0       17        17       30
  2P GAIN WILD-TYPE        1       2       69        76       62
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               17                69
  STAGE III              17                76
  STAGE IV               30                62
[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"
                   vv
clus                T0+T1+T2  T3  T4
  2P GAIN MUTATED         17  33   9
  2P GAIN WILD-TYPE       65 103  30
D3V4, multiclass
          clus
vv         2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1+T2              17                65
  T3                    33               103
  T4                     9                30
[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"
                   vv
clus                 N0  N1  N2  N3
  2P GAIN MUTATED    28   9  21   2
  2P GAIN WILD-TYPE 138  19  34   5
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              28               138
  N1               9                19
  N2              21                34
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  2P GAIN MUTATED    32   3  30
  2P GAIN WILD-TYPE  97   4 111
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              32                97
  M1               3                 4
  MX              30               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    25  41
  2P GAIN WILD-TYPE  52 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     25   41
  2P GAIN WILD-TYPE   52  160
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              25                52
  MALE                41               160
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       6                         3    52
  2P GAIN WILD-TYPE    25                        10   163
D3V11, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   6                25
  BLACK OR AFRICAN AMERICAN               3                10
  WHITE                                  52               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  58
  2P GAIN WILD-TYPE   5 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   58
  2P GAIN WILD-TYPE    5  200
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              58               200
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    22   6
  2Q GAIN WILD-TYPE 160  82
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               28               242 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                82 
$`2Q GAIN MUTATED`
TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
       12.39        19.04         5.59        15.42        28.70        28.41 
TCGA-CU-A0YR TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IN 
        7.20        66.41       112.44        10.59         7.79         8.22 
TCGA-E5-A2PC TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A62O TCGA-FD-A6TG TCGA-FJ-A3ZF 
       43.59        45.93        46.78         4.83         2.66         4.08 
TCGA-G2-A3VY TCGA-GD-A3OS TCGA-GV-A3QF TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OF 
        0.85        20.98         7.63        19.07         6.74         3.06 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-XF-A8HD 
        8.75         4.67         1.81        88.93 

$`2Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25        17.16         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 
        4.67        12.82         2.07         9.99         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       23.01         0.46         0.43         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.10         0.07         0.10         0.10        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
        2.14        18.41        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       17.62        15.62         1.81       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        3.98         7.82        10.49        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67         8.28        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       30.67        15.35        26.17        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.53         0.59         0.56         0.66         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.99        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79         1.97        22.98        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        12.13        13.38        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         6.84        27.45         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.66         6.28         6.38        50.66        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        6.71         4.11         2.07         2.20         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       15.19         7.13         3.48         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       20.12        52.67         6.94        19.46         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B 
        2.66         7.73         2.10         3.12         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        6.41         7.59        11.31         2.04        27.09         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65         4.41         6.41         6.15         5.69 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.79         4.14         6.67         6.41        11.54         1.51 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         9.01         8.22         3.45         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
       10.52         1.74         4.27         6.38         6.35         3.45 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       11.80        13.48        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        3.75        45.04         6.58        97.45        56.19        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        92.98        10.82        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
       91.73         2.96         8.32         6.77        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.85              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           112.44            140.81 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             9.67              9.17 
[1] "0.8 - 112.4 (9.7)" "0.1 - 140.8 (9.2)"
[1] "hr=" "1.9"
D4V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED          0       0        9         9       11
  2Q GAIN WILD-TYPE        1       2       77        84       81
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                9                77
  STAGE III               9                84
  STAGE IV               11                81
[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"
                   vv
clus                T0+T1+T2  T3  T4
  2Q GAIN MUTATED          9  12   3
  2Q GAIN WILD-TYPE       73 124  36
D4V4, multiclass
          clus
vv         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1+T2               9                73
  T3                    12               124
  T4                     3                36
[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"
                   vv
clus                 N0  N1  N2  N3
  2Q GAIN MUTATED    15   4   6   1
  2Q GAIN WILD-TYPE 151  24  49   6
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              15               151
  N1               4                24
  N2               6                49
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  2Q GAIN MUTATED    11   1  16
  2Q GAIN WILD-TYPE 118   6 125
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              11               118
  M1               1                 6
  MX              16               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    10  19
  2Q GAIN WILD-TYPE  67 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     10   19
  2Q GAIN WILD-TYPE   67  182
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              10                67
  MALE                19               182
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       2                         1    23
  2Q GAIN WILD-TYPE    29                        12   192
D4V11, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   2                29
  BLACK OR AFRICAN AMERICAN               1                12
  WHITE                                  23               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  24
  2Q GAIN WILD-TYPE   5 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   24
  2Q GAIN WILD-TYPE    5  234
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              24               234
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    53  32
  3P GAIN WILD-TYPE 129  56
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               85               185 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               32                56 
$`3P GAIN MUTATED`
TCGA-2F-A9KO TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20W 
       22.29         7.33         2.66        12.39        19.04         8.35 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A0YR 
        3.65         4.67         2.07         0.46         4.90         7.20 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2HX 
       16.31         1.84         2.53         2.14       112.44         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 
       10.59        87.32         8.22        50.27        20.02        17.98 
TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 
       64.18        30.67        43.59        15.35        26.17         0.10 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A43U TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P 
        0.56        12.99        14.93         6.87         4.83         6.28 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE 
        4.11         2.07         2.66         2.20         4.01         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO 
        4.08         3.25         6.48        61.94        30.61        35.24 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GD-A3OP 
       17.26         0.85        19.46         2.24        15.81         2.10 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-AATO TCGA-GV-A3JV 
       20.98         7.36         6.41         2.04        10.65         4.41 
TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
        6.41         7.63         7.79         6.67        19.07        11.54 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        6.74        38.60         9.01         8.75         3.45         4.67 
TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HC TCGA-XF-A8HF 
        4.27        12.23        14.24         0.85         6.58        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-AAMF TCGA-XF-AAML 
       15.35         1.87        17.88        79.66        10.82         7.63 
TCGA-XF-AAMX 
        6.77 

$`3P GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        11.93        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
       17.16         5.59        12.82        15.42        28.70         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         8.98         1.94        23.01         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.13         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 
       12.92         5.46         5.19         9.34        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00         8.91       130.88        16.14        17.62        15.62 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ 
        7.79       123.85         2.20         3.98         7.82        10.49 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30         9.67         8.28        10.55       140.81        48.00 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E7-A3X6 
       41.56        76.60        67.36        15.68        41.06        24.66 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.49         0.53         0.59         0.66         1.38         0.82 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.33         1.22         0.46        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        6.87         4.01        12.43        11.93        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79         1.97        22.98        14.93        14.96 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        12.13        13.38        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         5.69         6.84        27.45        49.68         2.66 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TK 
        6.38        50.66        18.81         9.30         6.71        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
       15.19         7.13         5.69        26.93         7.04        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       52.67         6.94         2.89         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 
       17.75         1.12         2.66         7.73         3.12         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JX 
        7.59        11.31        27.09         5.62         4.73         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE 
        5.69         4.14         6.41         1.51         3.06         8.22 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        2.50         6.48        10.52         1.74         1.81         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 
        6.35         3.45        11.80        13.48        16.67         3.75 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX 
       45.04        88.93        97.45        64.80        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT 
       66.64         2.10        92.98        54.90        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        8.32        56.48        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       10.36         4.83         0.66         7.96         9.04 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           112.44            140.81 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             7.36             10.55 
[1] "0.1 - 112.4 (7.4)"  "0.1 - 140.8 (10.6)"
[1] "hr=" "1.5"
D5V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED          1       0       29        17       39
  3P GAIN WILD-TYPE        0       2       57        76       53
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               29                57
  STAGE III              17                76
  STAGE IV               39                53
[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"
                   vv
clus                T0+T1+T2  T3  T4
  3P GAIN MUTATED         27  35  16
  3P GAIN WILD-TYPE       55 101  23
D5V4, multiclass
          clus
vv         3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1+T2              27                55
  T3                    35               101
  T4                    16                23
[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"
                   vv
clus                 N0  N1  N2  N3
  3P GAIN MUTATED    41  10  28   2
  3P GAIN WILD-TYPE 125  18  27   5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              41               125
  N1              10                18
  N2              28                27
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  3P GAIN MUTATED   40  3 44
  3P GAIN WILD-TYPE 89  4 97
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              40                89
  M1               3                 4
  MX              44                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    21  67
  3P GAIN WILD-TYPE  56 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     21   67
  3P GAIN WILD-TYPE   56  134
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              21                56
  MALE                67               134
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       9                         2    71
  3P GAIN WILD-TYPE    22                        11   144
D5V11, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   9                22
  BLACK OR AFRICAN AMERICAN               2                11
  WHITE                                  71               144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  82
  3P GAIN WILD-TYPE   5 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   82
  3P GAIN WILD-TYPE    5  176
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              82               176
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    76  36
  3Q GAIN WILD-TYPE 106  52
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              112               158 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               36                52 
$`3Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX 
       22.29        40.08         7.33         2.66        12.39        11.93 
TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       19.04         5.06         8.35         8.25        17.16         3.65 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS 
        4.67         2.07        28.70         9.99         0.46         0.43 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
        4.90         7.20         5.46        16.31         1.84         2.53 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 
       66.41        18.41       130.88       112.44         1.81        10.59 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 
       87.32         2.20         8.22        50.27        20.02        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3Y1 
       64.18        15.68        30.67        43.59        15.35         0.10 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 
        0.49         0.59         0.56        12.99        12.89         6.87 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5C0 
       11.93        24.30        22.45        14.93        14.93         6.87 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
        4.83         6.28         9.30         4.11         2.07         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        2.20         4.01         3.48         4.08         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3I6 
       30.61        35.24        17.26         0.85        19.46         2.24 
TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OS 
       15.81        14.07        17.75         2.66         2.10        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
        7.36         6.41         2.04        10.65         4.41         6.41 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
        7.63         7.79         6.67        19.07        11.54         6.74 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6MB 
       38.60         9.01         8.75         3.45         4.67         4.27 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF 
       12.23        14.24         0.85        45.04         6.58        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SZ TCGA-XF-A9T5 
       15.35         1.87        17.88        79.66        28.24        66.64 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-YF-AA3M 
        7.63         2.96         6.77         9.04 

$`3Q GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A3JM 
       11.97        84.00       103.50        98.33         4.83         6.74 
TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.58        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F 
       14.89        14.96         5.59        12.82        15.42        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        8.98         1.94        23.01         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3QU 
        0.10         0.07         0.10         0.10        12.92         5.19 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
        9.34         2.14        19.00         8.91        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ 
       15.62         7.79       123.85         3.98         7.82        10.49 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30         9.67         8.28        10.55       140.81        48.00 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 
       41.56        76.60        67.36        41.06        26.17        24.66 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV 
        0.53         0.66         1.38         0.82        14.33         1.22 
TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
        0.46        15.68         8.94         4.01        12.43        15.88 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       45.93         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
       19.79         1.97        22.98        14.96         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       13.38        37.15        11.01         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA 
        6.84        27.45        49.68         2.66         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE 
       18.81         6.71        10.85        15.19         7.13         3.25 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
        5.69        26.93         7.04        20.12        52.67         6.94 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ 
        2.89         4.50        15.91         1.12         7.73         3.12 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        2.20         7.59        11.31        27.09         5.62         4.73 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OF 
        6.15         5.69         4.14         6.41         1.51         3.06 
TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        8.22         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
        6.38         6.35         3.45        11.80        13.48        16.67 
TCGA-S5-AA26 TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX 
        3.75        88.93        97.45        64.80        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        16.27         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 
       92.98        10.82        54.90        91.73         8.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L 
        0.66         7.96 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           130.88            140.81 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            8.550            10.425 
[1] "0.1 - 130.9 (8.6)"  "0.1 - 140.8 (10.4)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED          1       1       36        25       49
  3Q GAIN WILD-TYPE        0       1       50        68       43
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 1                 1
  STAGE II               36                50
  STAGE III              25                68
  STAGE IV               49                43
[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"
                   vv
clus                T0+T1+T2 T3 T4
  3Q GAIN MUTATED         36 50 18
  3Q GAIN WILD-TYPE       46 86 21
D6V4, multiclass
          clus
vv         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1+T2              36                46
  T3                    50                86
  T4                    18                21
[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"
                   vv
clus                 N0  N1  N2  N3
  3Q GAIN MUTATED    55  13  35   2
  3Q GAIN WILD-TYPE 111  15  20   5
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              55               111
  N1              13                15
  N2              35                20
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED   54  4 56
  3Q GAIN WILD-TYPE 75  3 85
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              54                75
  M1               4                 3
  MX              56                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    32  83
  3Q GAIN WILD-TYPE  45 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     32   83
  3Q GAIN WILD-TYPE   45  118
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              32                45
  MALE                83               118
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED      11                         5    91
  3Q GAIN WILD-TYPE    20                         8   124
D6V11, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                  11                20
  BLACK OR AFRICAN AMERICAN               5                 8
  WHITE                                  91               124
[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"
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     2 105
  3Q GAIN WILD-TYPE   3 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2  105
  3Q GAIN WILD-TYPE    3  153
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             105               153
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    21   6
  4P GAIN WILD-TYPE 161  82
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               27               243 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6                82 
$`4P GAIN MUTATED`
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A6 
        1.94        23.01         0.10         5.46         2.14        66.41 
TCGA-DK-A1AC TCGA-DK-A2I2 TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-E5-A4U1 
      130.88         7.79        48.00        64.18        67.36        26.17 
TCGA-E7-A541 TCGA-FD-A3NA TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TC TCGA-FD-A6TE 
        0.59        45.93         5.36        27.45         9.30         4.11 
TCGA-G2-A2EF TCGA-GD-A76B TCGA-GU-A42P TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A6FZ 
       61.94         7.36         6.41        11.54         9.01         1.81 
TCGA-MV-A51V TCGA-XF-A9T3 TCGA-YF-AA3L 
       13.48         2.24         7.96 

$`4P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR 
       15.42        28.70         9.99        28.41         8.98         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
        0.10        12.92         4.90         7.20         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        1.84         9.34         2.53        18.41        19.00         8.91 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       10.49        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
       10.55       140.81        17.98        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       41.06        30.67        43.59        15.35        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.49         0.53         0.56         0.66         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.99        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79         1.97        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93         3.62        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        6.87         5.69         6.84         6.87        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        4.83         6.28         6.38        50.66        18.81         6.71 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.07         2.66         2.20         4.01        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
        7.13         3.48         4.08         3.25         6.48        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        5.69        26.93        35.24        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
        0.85        52.67         6.94        19.46         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        2.66         7.73         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.59        11.31         2.04        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        7.79         4.14         6.67         6.41        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        6.74        38.60         3.06         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB 
        4.67         2.50         6.48        10.52         1.74         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38         6.35         3.45        11.80        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       14.24         0.85         3.75        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       97.45        56.19        15.35         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       79.66        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        91.73         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
        4.83         0.66         9.04 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.10              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           130.88            140.81 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             9.01              9.34 
[1] "0.1 - 130.9 (9.0)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.8"
D7V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED          1       0       12         8        7
  4P GAIN WILD-TYPE        0       2       74        85       85
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               12                74
  STAGE III               8                85
  STAGE IV                7                85
[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"
                   vv
clus                T0+T1+T2  T3  T4
  4P GAIN MUTATED         13  13   1
  4P GAIN WILD-TYPE       69 123  38
D7V4, multiclass
          clus
vv         4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1+T2              13                69
  T3                    13               123
  T4                     1                38
[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"
                   vv
clus                 N0  N1  N2  N3
  4P GAIN MUTATED    21   4   2   1
  4P GAIN WILD-TYPE 145  24  53   6
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              21               145
  N1               4                24
  N2               2                53
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  4P GAIN MUTATED    17   0  11
  4P GAIN WILD-TYPE 112   7 130
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0              17               112
  M1               0                 7
  MX              11               130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    11  17
  4P GAIN WILD-TYPE  66 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11   17
  4P GAIN WILD-TYPE   66  184
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              11                66
  MALE                17               184
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       3                         0    19
  4P GAIN WILD-TYPE    28                        13   196
D7V11, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   3                28
  BLACK OR AFRICAN AMERICAN               0                13
  WHITE                                  19               196
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  22
  4P GAIN WILD-TYPE   4 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   22
  4P GAIN WILD-TYPE    4  236
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              22               236
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    13   4
  4Q GAIN WILD-TYPE 169  84
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               253 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4                84 
$`4Q GAIN MUTATED`
TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A3X1 TCGA-DK-A6B1 
       23.01         0.10         5.46         2.14        48.00        67.36 
TCGA-E5-A4U1 TCGA-FD-A3NA TCGA-FD-A5BV TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-G2-A2EF 
       26.17        45.93         5.36         6.87         4.11        61.94 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-YF-AA3L 
        7.36         6.41        11.54         9.01         7.96 

$`4Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       15.42        28.70         9.99        28.41         8.98         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
        0.07         0.10        12.92         4.90         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         1.84         9.34         2.53        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20         3.98         7.82         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
       17.98        64.18        41.56        76.60        15.68        41.06 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       30.67        43.59        15.35        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.53         0.59         0.56         0.66         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.99        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79         1.97        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93         3.62        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N 
        6.87         5.69         6.84        27.45        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        4.83         6.28         6.38        50.66        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        6.71         2.07         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
       15.19         7.13         3.48         4.08         3.25         6.48 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12         0.85        52.67         6.94        19.46         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        1.12         2.66         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        2.20         7.59        11.31         2.04        27.09         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65         4.41         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        7.63         7.79         4.14         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51         6.74        38.60         3.06         8.22         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        3.45         4.67         2.50         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81         4.27         6.38         6.35         3.45        11.80 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         0.85         3.75 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       45.04         6.58        88.93        97.45        56.19        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        92.98        10.82        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
       91.73         2.96         8.32         6.77        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3M 
        9.04 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.10              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            67.36            140.81 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             7.96              9.34 
[1] "0.1 - 67.4 (8.0)"  "0.1 - 140.8 (9.3)"
[1] "hr=" "1.5"
D8V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED          1       0        8         4        4
  4Q GAIN WILD-TYPE        0       2       78        89       88
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II                8                78
  STAGE III               4                89
  STAGE IV                4                88
[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"
                   vv
clus                T0+T1+T2  T3  T4
  4Q GAIN MUTATED          8   8   0
  4Q GAIN WILD-TYPE       74 128  39
D8V4, multiclass
          clus
vv         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1+T2               8                74
  T3                     8               128
  T4                     0                39
[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"
                   vv
clus                 N0  N1  N2  N3
  4Q GAIN MUTATED    13   2   2   0
  4Q GAIN WILD-TYPE 153  26  53   7
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              13               153
  N1               2                26
  N2               2                53
  N3               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  4Q GAIN MUTATED    10   0   7
  4Q GAIN WILD-TYPE 119   7 134
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0              10               119
  M1               0                 7
  MX               7               134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5  12
  4Q GAIN WILD-TYPE  72 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5   12
  4Q GAIN WILD-TYPE   72  189
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               5                72
  MALE                12               189
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         0    12
  4Q GAIN WILD-TYPE    30                        13   203
D8V11, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                30
  BLACK OR AFRICAN AMERICAN               0                13
  WHITE                                  12               203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  14
  4Q GAIN WILD-TYPE   4 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   14
  4Q GAIN WILD-TYPE    4  244
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              14               244
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    67  31
  5P GAIN WILD-TYPE 115  57
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               98               172 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               31                57 
$`5P GAIN MUTATED`
TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
       98.33        40.08         6.74        12.39        32.84        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
        5.06         8.35        17.16        12.82         2.07        28.70 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A3 
        0.43         0.13        12.92         7.20         5.19         2.53 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX 
      123.85        87.32         8.22        20.02         9.67        10.55 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       67.36        41.06        30.67        15.35        26.17        24.66 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.49         0.59         1.22        12.89        15.68         8.94 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43Y 
       11.93        45.93         5.52        13.18        19.79        12.13 
TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N 
       13.38         6.87         5.36         6.84        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        4.83         6.28         6.38        18.81         9.30         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        2.66         2.20        10.85         4.08         3.25         6.48 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 
       35.24         7.04        20.12        52.67        19.46         2.24 
TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
       15.81         1.12         2.10        20.98         7.36         6.41 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF 
        2.04         5.62        10.65         4.41         6.15         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A5NE 
        7.79         4.14         6.41        19.07         6.74         8.22 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-A6DX 
        6.48         1.81         6.35        13.48        16.67         0.85 
TCGA-XF-A8HF TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML 
       56.19         2.24        66.64        92.98        54.90         7.63 
TCGA-XF-AAMT TCGA-YF-AA3M 
        2.96         9.04 

$`5P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A13I 
       22.29        11.97        84.00       103.50         4.83         7.33 
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.58        11.93        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       19.50         5.06        14.96         8.25         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        4.67        15.42         9.99        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.46         0.69         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
        0.10         0.10         4.90         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.14        66.41        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ 
       10.59         7.79         2.20         3.98         7.82        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30         8.28       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E7-A3Y1 
       64.18        41.56        76.60        15.68        43.59         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.53         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.33         0.46         6.87         4.01        12.43        15.88 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS 
       24.30        22.45         6.12        12.82        46.78         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS 
       22.98        14.93        14.96        14.93         3.62        37.15 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TD 
       11.01         5.69        27.45         6.87        50.66         6.71 
TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EF 
        2.07         4.01        15.19         7.13         3.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3C 
       30.61         5.69        26.93        17.26         0.85         6.94 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 
        2.89         4.50        15.91        14.07        17.75         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 
        7.73         3.12         2.20         7.59        11.31        27.09 
TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.73         6.41         5.69         6.67        11.54         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         9.01         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 
        2.50        10.52         1.74         4.27         6.38         3.45 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       11.80        12.23        14.24         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       88.93        97.45        15.35         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       79.66        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMW 
       18.90        16.27         2.10        10.82        91.73         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        6.77        56.48        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       10.36         4.83         0.66         7.96 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.13              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           123.85            140.81 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            8.285            10.425 
[1] "0.1 - 123.8 (8.3)"  "0.1 - 140.8 (10.4)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED          0       1       35        35       30
  5P GAIN WILD-TYPE        1       1       51        58       62
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 1                 1
  STAGE II               35                51
  STAGE III              35                58
  STAGE IV               30                62
[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"
                   vv
clus                T0+T1+T2 T3 T4
  5P GAIN MUTATED         32 44 16
  5P GAIN WILD-TYPE       50 92 23
D9V4, multiclass
          clus
vv         5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1+T2              32                50
  T3                    44                92
  T4                    16                23
[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"
                   vv
clus                 N0  N1  N2  N3
  5P GAIN MUTATED    59  10  19   2
  5P GAIN WILD-TYPE 107  18  36   5
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              59               107
  N1              10                18
  N2              19                36
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED   41  1 60
  5P GAIN WILD-TYPE 88  6 81
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              41                88
  M1               1                 6
  MX              60                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    24  78
  5P GAIN WILD-TYPE  53 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     24   78
  5P GAIN WILD-TYPE   53  123
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              24                53
  MALE                78               123
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       9                         8    80
  5P GAIN WILD-TYPE    22                         5   135
D9V11, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   9                22
  BLACK OR AFRICAN AMERICAN               8                 5
  WHITE                                  80               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"
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  99
  5P GAIN WILD-TYPE   4 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   99
  5P GAIN WILD-TYPE    4  159
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              99               159
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    22  10
  5Q GAIN WILD-TYPE 160  78
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               32               238 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               10                78 
$`5Q GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A42C TCGA-CF-A1HS 
       40.08         6.74        32.84        14.89        28.70         0.43 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A6B6 TCGA-E7-A541 TCGA-FD-A5BU TCGA-FD-A5C1 
      123.85        87.32        30.67         0.59         6.87        49.68 
TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-AA3F 
        6.28         4.11         2.20         3.25        35.24        19.46 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GD-A76B TCGA-GU-A762 TCGA-GV-A3JV 
        2.24        15.81         1.12         7.36         2.04         4.41 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-K4-A6FZ TCGA-LC-A66R TCGA-MV-A51V 
        7.79         4.14         6.41         1.81         6.35        13.48 
TCGA-S5-A6DX TCGA-XF-A9T5 
        0.85        66.64 

$`5Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66        12.39         6.58        11.93        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         2.07        15.42         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94        23.01         0.46         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.10         0.07         0.10         0.10        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        2.53         2.14        66.41        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
       10.59         7.79         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       10.49        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ 
       76.60        67.36        15.68        41.06        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE 
       26.17        24.66         0.10         0.49         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV 
        0.66         1.38         0.82        12.99        14.33         1.22 
TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        0.46        12.89        15.68         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.43        11.93        15.88        45.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
        6.12        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        1.97        22.98        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX 
       12.13        13.38        37.15        11.01         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
        6.84        27.45         6.87         2.66         4.83         6.38 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG 
       50.66        18.81         9.30         6.71         2.07         2.66 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.01        10.85        15.19         7.13         3.48         4.08 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        6.48        61.94        30.61         5.69        26.93        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM 
        7.04        20.12         0.85        52.67         6.94         2.89 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        14.07        17.75         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
        2.10         3.12        20.98         2.20         6.41         7.59 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW 
       11.31        27.09         5.62         4.73        10.65         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
        6.15         5.69         7.63         6.67        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51         6.74        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.75         3.45         4.67         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
        1.74         4.27         6.38         3.45        11.80        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       16.67        14.24         3.75        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       97.45        56.19        15.35         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       79.66        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        16.27         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        91.73         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.43              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           123.85            140.81 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            6.805             9.830 
[1] "0.4 - 123.8 (6.8)" "0.1 - 140.8 (9.8)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED          0       1       10        11       11
  5Q GAIN WILD-TYPE        1       1       76        82       81
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 1                 1
  STAGE II               10                76
  STAGE III              11                82
  STAGE IV               11                81
[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"
                   vv
clus                T0+T1+T2  T3  T4
  5Q GAIN MUTATED          8  18   4
  5Q GAIN WILD-TYPE       74 118  35
D10V4, multiclass
          clus
vv         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1+T2               8                74
  T3                    18               118
  T4                     4                35
[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"
                   vv
clus                 N0  N1  N2  N3
  5Q GAIN MUTATED    19   6   5   0
  5Q GAIN WILD-TYPE 147  22  50   7
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              19               147
  N1               6                22
  N2               5                50
  N3               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  5Q GAIN MUTATED    14   0  20
  5Q GAIN WILD-TYPE 115   7 121
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              14               115
  M1               0                 7
  MX              20               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7  27
  5Q GAIN WILD-TYPE  70 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   27
  5Q GAIN WILD-TYPE   70  174
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               7                70
  MALE                27               174
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       3                         1    29
  5Q GAIN WILD-TYPE    28                        12   186
D10V11, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   3                28
  BLACK OR AFRICAN AMERICAN               1                12
  WHITE                                  29               186
[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"
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  33
  5Q GAIN WILD-TYPE   5 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   33
  5Q GAIN WILD-TYPE    5  225
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              33               225
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    28  12
  6P GAIN WILD-TYPE 154  76
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               40               230 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               12                76 
$`6P GAIN MUTATED`
TCGA-BT-A0S7 TCGA-CF-A47V TCGA-CF-A47X TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IM 
        6.58         0.10         0.10       130.88        87.32         7.82 
TCGA-DK-A3WX TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A541 TCGA-FD-A3B7 
       10.55        64.18        67.36        15.68         0.59         4.01 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A5BU TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TF 
       19.79         1.97         6.87        49.68         9.30         2.07 
TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-AA3B TCGA-GC-A3BM 
        2.66         3.48         3.25         6.48        52.67         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GU-A42P 
        2.24        15.81        15.91         1.12         7.73         6.41 
TCGA-GU-A762 TCGA-GU-AATO TCGA-GV-A6ZA TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-LC-A66R 
        2.04        10.65        11.54         8.22         6.48         6.35 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A9T5 TCGA-XF-AAML 
        6.58        88.93        66.64         7.63 

$`6P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        5.59         3.65         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70         9.99        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
        0.46         0.43         0.69         0.13         0.07         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.10        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84         9.34         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00         8.91       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        3.98         8.22        10.49        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
        9.67         8.28       140.81        48.00        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       76.60        41.06        30.67        43.59        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         0.49         0.53         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        1.38         0.82        12.99        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
       12.89        15.68         8.94         6.87        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       15.88        45.93        24.30        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
        5.52        13.18        46.78        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93         3.62        12.13        13.38        37.15        11.01 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
        5.36         5.69         6.84        27.45         6.87         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        4.83         6.28         6.38        50.66        18.81         6.71 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        4.11         2.20         4.01        10.85        15.19         7.13 
TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        4.08        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F 
       17.26         7.04        20.12         0.85         6.94        19.46 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
        4.50        14.07        17.75         2.66         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 
       20.98         2.20         7.36         7.59        11.31        27.09 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        5.62         4.73         4.41         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        7.63         7.79         4.14         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS 
        1.51         6.74        38.60         3.06         9.01         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        3.45         4.67         2.50        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        4.27         6.38         3.45        11.80        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HE 
       16.67        14.24         0.85         3.75        45.04        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       56.19        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
        2.24        16.27         2.10        92.98        10.82        54.90 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
       91.73         2.96         8.32         6.77        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.10              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           130.88            140.81 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            7.250            10.425 
[1] "0.1 - 130.9 (7.2)"  "0.1 - 140.8 (10.4)"
[1] "hr=" "1"  
D11V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED          1       0       13        11       16
  6P GAIN WILD-TYPE        0       2       73        82       76
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               13                73
  STAGE III              11                82
  STAGE IV               16                76
[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"
                   vv
clus                T0+T1+T2  T3  T4
  6P GAIN MUTATED         15  17   8
  6P GAIN WILD-TYPE       67 119  31
D11V4, multiclass
          clus
vv         6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1+T2              15                67
  T3                    17               119
  T4                     8                31
[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"
                   vv
clus                 N0  N1  N2  N3
  6P GAIN MUTATED    25   5   9   2
  6P GAIN WILD-TYPE 141  23  46   5
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              25               141
  N1               5                23
  N2               9                46
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  6P GAIN MUTATED    17   2  22
  6P GAIN WILD-TYPE 112   5 119
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              17               112
  M1               2                 5
  MX              22               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"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    10  31
  6P GAIN WILD-TYPE  67 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     10   31
  6P GAIN WILD-TYPE   67  170
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              10                67
  MALE                31               170
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
D11V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       5                         2    32
  6P GAIN WILD-TYPE    26                        11   183
D11V11, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   5                26
  BLACK OR AFRICAN AMERICAN               2                11
  WHITE                                  32               183
[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"
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0  39
  6P GAIN WILD-TYPE   5 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   39
  6P GAIN WILD-TYPE    5  219
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              39               219
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    16   6
  6Q GAIN WILD-TYPE 166  82
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               22               248 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6                82 
$`6Q GAIN MUTATED`
TCGA-BT-A0S7 TCGA-BT-A2LA TCGA-CF-A47V TCGA-CF-A47X TCGA-DK-A1AC TCGA-DK-A2I6 
        6.58        17.16         0.10         0.10       130.88        87.32 
TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A6B1 TCGA-FD-A3SS TCGA-FD-A5C1 TCGA-FJ-A3ZE 
        7.82        10.55        67.36         1.97        49.68         3.48 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATO TCGA-K4-A4AC 
        2.89        15.81         1.12         6.41        10.65         6.48 
TCGA-LC-A66R TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A9T5 
        6.35         6.58        88.93        66.64 

$`6Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB 
       14.89        14.96         5.06         8.35         8.25         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        3.65         4.67        12.82         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        9.99        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y 
        0.43         0.69         0.13         0.07         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84         9.34         2.53         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00         8.91       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59         7.79       123.85         2.20         3.98 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
        8.28       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       76.60        15.68        41.06        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       26.17        24.66         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66         1.38         0.82        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22         0.46        12.89        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        22.98        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       12.13        13.38        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O 
        5.69         6.84        27.45         6.87         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28         6.38        50.66        18.81         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        4.11         2.07         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       15.19         7.13         4.08         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
       20.12         0.85        52.67         6.94        19.46         2.24 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        14.07        17.75         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
        2.10         3.12        20.98         2.20         7.36         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV 
       11.31         2.04        27.09         5.62         4.73         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        6.41         6.15         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.67         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        4.67         2.50        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38         3.45        11.80        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF 
       14.24         0.85         3.75        45.04        97.45        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW 
       15.35         1.87        17.88        64.80        79.66        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       16.27         2.10        92.98        10.82        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
       91.73         2.96         8.32         6.77        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.10              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           130.88            140.81 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             7.20              9.32 
[1] "0.1 - 130.9 (7.2)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED          0       0        7         7        9
  6Q GAIN WILD-TYPE        1       2       79        86       83
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                7                79
  STAGE III               7                86
  STAGE IV                9                83
[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"
                   vv
clus                T0+T1+T2  T3  T4
  6Q GAIN MUTATED          8  10   4
  6Q GAIN WILD-TYPE       74 126  35
D12V4, multiclass
          clus
vv         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1+T2               8                74
  T3                    10               126
  T4                     4                35
[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"
                   vv
clus                 N0  N1  N2  N3
  6Q GAIN MUTATED    14   4   3   2
  6Q GAIN WILD-TYPE 152  24  52   5
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              14               152
  N1               4                24
  N2               3                52
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  6Q GAIN MUTATED    12   1  10
  6Q GAIN WILD-TYPE 117   6 131
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              12               117
  M1               1                 6
  MX              10               131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3  20
  6Q GAIN WILD-TYPE  74 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   20
  6Q GAIN WILD-TYPE   74  181
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               3                74
  MALE                20               181
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       4                         0    19
  6Q GAIN WILD-TYPE    27                        13   196
D12V11, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   4                27
  BLACK OR AFRICAN AMERICAN               0                13
  WHITE                                  19               196
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  22
  6Q GAIN WILD-TYPE   5 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   22
  6Q GAIN WILD-TYPE    5  236
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              22               236
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    76  33
  7P GAIN WILD-TYPE 106  55
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              109               161 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               33                55 
$`7P GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O 
       40.08         2.66        12.39         6.58        32.84        12.16 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
        8.25        17.16         5.59         3.65        12.82        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CU-A0YN TCGA-CU-A0YO 
        9.99        28.41        23.01         0.46        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I2 
        5.46         9.34         2.53       130.88        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
       50.27        20.02        48.00        17.98        64.18        67.36 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME 
       30.67        43.59        15.35         0.49         0.59        12.99 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SQ 
        1.22        12.89         8.94         4.01        11.93        46.78 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
        1.97        22.98        14.93        14.93         3.62        13.38 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC 
        5.36        27.45        49.68         4.83         6.28         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
        6.71         4.11         2.07         2.66         4.01        15.19 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY 
        3.48         4.08         3.25         6.48        35.24         0.85 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
       52.67        19.46         2.89         2.24        15.91        14.07 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A766 
        7.73        20.98         2.20         6.41         7.59         5.62 
TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
        5.69         6.67         6.41        11.54         6.74        38.60 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V 
        9.01         8.22         1.81         6.38         6.35        13.48 
TCGA-S5-A6DX TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SY 
        0.85        88.93        56.19        15.35        79.66        21.04 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
        2.24        66.64         2.96         6.77        56.48        75.39 
TCGA-YF-AA3M 
        9.04 

$`7P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q 
        7.33         6.74        11.93        19.04        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A3PH 
        5.06        14.89        14.96         5.06         8.35         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C 
        2.07        15.42         8.98         1.94         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.13         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 
        7.20         5.19        16.31         1.84         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00         8.91       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
       15.62         1.81        10.49        21.30         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
       10.55       140.81        41.56        76.60        15.68        41.06 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF 
       26.17        24.66         0.10         0.53         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B6 
        1.38         0.82        14.33         0.46        15.68         6.87 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        15.88        45.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y 
       12.82         5.52        13.18        19.79        14.96        12.13 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       37.15        11.01         6.87         5.69         6.84         6.87 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TH TCGA-FD-A6TK 
        2.66         6.38        50.66        18.81         2.20        10.85 
TCGA-FJ-A3Z9 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        7.13        61.94        30.61         5.69        26.93        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC 
        7.04        20.12         6.94        15.81         4.50        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42R 
        1.12         2.66         2.10         3.12         7.36        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
        2.04        27.09         4.73        10.65         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HO 
        6.15         7.63         7.79         4.14        19.07         1.51 
TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        3.06         8.75         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
       10.52         1.74         4.27         3.45        11.80        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE 
       16.67        14.24         3.75        45.04         6.58        97.45 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
        1.87        17.88        64.80        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       26.27        18.90        16.27         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 
       54.90         7.63        91.73         8.32        30.94        27.06 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.46              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           130.88            140.81 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             9.04              9.67 
[1] "0.5 - 130.9 (9.0)" "0.1 - 140.8 (9.7)"
[1] "hr=" "1.2"
D13V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED          1       1       27        39       42
  7P GAIN WILD-TYPE        0       1       59        54       50
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 1                 1
  STAGE II               27                59
  STAGE III              39                54
  STAGE IV               42                50
[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"
                   vv
clus                T0+T1+T2 T3 T4
  7P GAIN MUTATED         28 56 20
  7P GAIN WILD-TYPE       54 80 19
D13V4, multiclass
          clus
vv         7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1+T2              28                54
  T3                    56                80
  T4                    20                19
[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"
                   vv
clus                 N0  N1  N2  N3
  7P GAIN MUTATED    59  12  26   6
  7P GAIN WILD-TYPE 107  16  29   1
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              59               107
  N1              12                16
  N2              26                29
  N3               6                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   51  3 57
  7P GAIN WILD-TYPE 78  4 84
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              51                78
  M1               3                 4
  MX              57                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    31  81
  7P GAIN WILD-TYPE  46 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     31   81
  7P GAIN WILD-TYPE   46  120
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              31                46
  MALE                81               120
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       9                         6    90
  7P GAIN WILD-TYPE    22                         7   125
D13V11, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   9                22
  BLACK OR AFRICAN AMERICAN               6                 7
  WHITE                                  90               125
[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"
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     1 105
  7P GAIN WILD-TYPE   4 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1  105
  7P GAIN WILD-TYPE    4  153
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO             105               153
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    64  31
  7Q GAIN WILD-TYPE 118  57
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               95               175 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               31                57 
$`7Q GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20X 
       40.08         2.66        12.39         6.58        32.84         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42E TCGA-BT-A42F 
       17.16         5.59         3.65        12.82         9.99        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E 
       23.01         0.46        12.92         4.90         5.46         9.34 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IL 
      112.44         1.81        10.59         7.79        87.32         3.98 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 
        8.22        50.27        20.02        17.98        67.36        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B4 
       43.59        15.35         0.49         0.59         1.22        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
        8.94         4.01        11.93        46.78         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ 
       14.93        14.93         3.62        13.38         5.36        27.45 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF 
       49.68         4.83         6.28         9.30         6.71         2.07 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        2.20         4.01         3.48         4.08         3.25         6.48 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       35.24         0.85        52.67        19.46         2.89         2.24 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GV-A3JZ TCGA-GV-A3QF 
       15.91        14.07         7.73        20.98         5.69         7.63 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.67         6.41        19.07        11.54         6.74        38.60 
TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V 
        9.01         4.67         1.81         6.38         6.35        13.48 
TCGA-S5-A6DX TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        0.85         6.58        88.93        97.45        56.19        15.35 
TCGA-XF-A9SI TCGA-XF-A9T5 TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
       79.66        66.64         6.77        56.48        75.39 

$`7Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        7.33         6.74        11.93        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 
        4.67         2.07        15.42        28.70         8.98         1.94 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        0.10         0.10         7.20         5.19        16.31         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        2.53         2.14        66.41        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IK 
      130.88        16.14        17.62        15.62       123.85         2.20 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        7.82        10.49        21.30         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
      140.81        48.00        64.18        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE 
       41.06        26.17        24.66         0.10         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        0.66         1.38         0.82        12.99        14.33         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       12.89         6.87        12.43        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR 
       22.45         6.12        12.82         5.52        13.18        19.79 
TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       14.96        12.13        37.15        11.01         6.87         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        6.84         6.87         2.66         6.38        50.66        18.81 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-G2-A2EF 
        4.11         2.66        10.85        15.19         7.13        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61         5.69        26.93        17.26         7.04        20.12 
TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        6.94        15.81         4.50        17.75         1.12         2.66 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        2.10         3.12         2.20         7.36         6.41         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       11.31         2.04        27.09         5.62         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
        4.41         6.41         6.15         7.79         4.14         1.51 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
        3.06         8.22         8.75         3.45         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
       10.52         1.74         4.27         3.45        11.80        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI 
       16.67        14.24         3.75        45.04         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       64.80        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        16.27         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 
       54.90         7.63        91.73         2.96         8.32        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       27.06         3.88        10.36         4.83         0.66         7.96 
TCGA-YF-AA3M 
        9.04 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.46              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           112.44            140.81 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             9.30              9.04 
[1] "0.5 - 112.4 (9.3)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED          1       1       23        32       39
  7Q GAIN WILD-TYPE        0       1       63        61       53
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 1                 1
  STAGE II               23                63
  STAGE III              32                61
  STAGE IV               39                53
[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"
                   vv
clus                T0+T1+T2 T3 T4
  7Q GAIN MUTATED         25 46 20
  7Q GAIN WILD-TYPE       57 90 19
D14V4, multiclass
          clus
vv         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1+T2              25                57
  T3                    46                90
  T4                    20                19
[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"
                   vv
clus                 N0  N1  N2  N3
  7Q GAIN MUTATED    50  11  23   7
  7Q GAIN WILD-TYPE 116  17  32   0
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              50               116
  N1              11                17
  N2              23                32
  N3               7                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   40  3 54
  7Q GAIN WILD-TYPE 89  4 87
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              40                89
  M1               3                 4
  MX              54                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    28  70
  7Q GAIN WILD-TYPE  49 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     28   70
  7Q GAIN WILD-TYPE   49  131
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              28                49
  MALE                70               131
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
D14V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       7                         7    78
  7Q GAIN WILD-TYPE    24                         6   137
D14V11, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   7                24
  BLACK OR AFRICAN AMERICAN               7                 6
  WHITE                                  78               137
[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"
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     0  92
  7Q GAIN WILD-TYPE   5 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0   92
  7Q GAIN WILD-TYPE    5  166
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              92               166
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    40  13
  8P GAIN WILD-TYPE 142  75
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               53               217 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               13                75 
$`8P GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V 
       40.08         6.74        12.39        19.04        32.84         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C 
        8.35        17.16         9.99         1.94        23.01         0.69 
TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3WX 
        9.34        66.41        16.14        10.49        50.27        10.55 
TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A6ME 
       17.98        15.68        30.67        43.59         0.49        12.99 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5C1 TCGA-FD-A62O 
       15.88        45.93        14.93        37.15        49.68         4.83 
TCGA-FD-A62S TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3B 
        6.38         4.01         3.48        17.26         0.85        52.67 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OE 
        2.89         2.24         4.41         4.14        11.54        38.60 
TCGA-HQ-A2OF TCGA-K4-A83P TCGA-MV-A51V TCGA-S5-A6DX TCGA-XF-A8HD TCGA-XF-A8HF 
        3.06         6.38        13.48         0.85        88.93        56.19 
TCGA-XF-A8HG TCGA-XF-A9SH TCGA-XF-A9SY TCGA-XF-A9T6 TCGA-YF-AA3M 
       15.35        64.80        21.04         2.10         9.04 

$`8P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        7.33         2.66         6.58        11.93        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB 
       19.50         5.06        14.89        14.96         8.25         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        3.65         4.67        12.82         2.07        15.42        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T 
       28.41         8.98         0.46         0.43         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.10         0.07         0.10         0.10        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
        7.20         5.46         5.19        16.31         1.84         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT 
       87.32         2.20         3.98         7.82         8.22        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV 
       20.02         9.67         8.28       140.81        48.00        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 
       41.56        76.60        67.36        41.06        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         0.53         0.59         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        1.38         0.82        14.33         1.22         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.68         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79         1.97        22.98        14.93        14.96 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        12.13        13.38        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P 
        5.69         6.84        27.45         6.87         2.66         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       50.66        18.81         9.30         6.71         4.11         2.07 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        2.66         2.20        10.85        15.19         7.13         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61         5.69        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
       35.24         7.04        20.12         6.94        19.46        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        6.41         7.59        11.31         2.04        27.09         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        4.73        10.65         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.79         6.67         6.41        19.07         1.51         6.74 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22         8.75         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R 
        6.48        10.52         1.74         1.81         4.27         6.35 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
        3.45        11.80        12.23        16.67        14.24         3.75 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI 
       45.04         6.58        97.45         1.87        17.88        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       16.27        66.64        92.98        10.82        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
       91.73         2.96         8.32         6.77        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L 
        7.96 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.49              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            88.93            140.81 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            12.99              8.28 
[1] "0.5 - 88.9 (13.0)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.7"
D15V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED          1       1       17        21       13
  8P GAIN WILD-TYPE        0       1       69        72       79
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 1                 1
  STAGE II               17                69
  STAGE III              21                72
  STAGE IV               13                79
[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"
                   vv
clus                T0+T1+T2  T3  T4
  8P GAIN MUTATED         19  27   6
  8P GAIN WILD-TYPE       63 109  33
D15V4, multiclass
          clus
vv         8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1+T2              19                63
  T3                    27               109
  T4                     6                33
[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"
                   vv
clus                 N0  N1  N2  N3
  8P GAIN MUTATED    34   6   8   1
  8P GAIN WILD-TYPE 132  22  47   6
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              34               132
  N1               6                22
  N2               8                47
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  8P GAIN MUTATED    29   1  24
  8P GAIN WILD-TYPE 100   6 117
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              29               100
  M1               1                 6
  MX              24               117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    13  42
  8P GAIN WILD-TYPE  64 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     13   42
  8P GAIN WILD-TYPE   64  159
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              13                64
  MALE                42               159
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       7                         3    39
  8P GAIN WILD-TYPE    24                        10   176
D15V11, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   7                24
  BLACK OR AFRICAN AMERICAN               3                10
  WHITE                                  39               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1  48
  8P GAIN WILD-TYPE   4 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   48
  8P GAIN WILD-TYPE    4  210
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              48               210
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   91 35
  8Q GAIN WILD-TYPE 91 53
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              126               144 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               35                53 
$`8Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BL-A5ZZ 
       22.29        11.97       103.50        40.08         6.74        12.39 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       19.04        32.84         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
        5.59         9.99        28.41         8.98         1.94        23.01 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.69         0.13         0.10        12.92         5.46         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
        1.84         9.34         2.53        66.41        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IN 
      112.44        16.14        10.59       123.85        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
       10.49        50.27        20.02        10.55        48.00        17.98 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 
       15.68        30.67        43.59        26.17         0.49         0.59 
TCGA-E7-A6ME TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SQ 
       12.99         6.87         4.01        15.88        45.93        46.78 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV 
       22.98        14.93        13.38        37.15        11.01         5.36 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        5.69         6.87        49.68         4.83         6.28         6.38 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.71         4.11         2.20         4.01         7.13         3.48 
TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM 
        3.25         5.69        17.26         0.85        52.67         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        2.24         4.50        17.75         2.10         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        7.36         6.41         4.41         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF 
        7.63         7.79         4.14        11.54        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.01         8.22         2.50         1.81         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        6.35        11.80        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SH 
        0.85        45.04        88.93        56.19        15.35        64.80 
TCGA-XF-A9SI TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMJ 
       79.66        21.04        26.27         2.24         2.10        54.90 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YF-AA3M 
        7.63         2.96         8.32        75.39        10.36         9.04 

$`8Q GAIN WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 
       84.00        98.33         4.83         7.33         2.66         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       11.93        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       14.96         3.65         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       28.70         0.46         0.43         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1AA 
        0.10         4.90         7.20        16.31         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IK 
        8.91        17.62        15.62         1.81         7.79         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        3.98         7.82        21.30         9.67         8.28       140.81 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A4TZ 
       64.18        41.56        76.60        67.36        41.06        15.35 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       24.66         0.10         0.53         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.82        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        8.94        12.43        11.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       12.82         5.52        13.18        19.79         1.97        14.93 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5BZ 
       14.96         3.62        12.13         6.87         6.84        27.45 
TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG 
        2.66        50.66        18.81         9.30         2.07         2.66 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.85        15.19         4.08         6.48        61.94        30.61 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F 
       26.93        35.24         7.04        20.12         6.94        19.46 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.81        15.91        14.07         1.12         2.66         7.73 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        2.20         7.59        11.31         2.04        27.09         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        4.73        10.65         6.67         6.41        19.07         1.51 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R 
        6.74         8.75         3.45         4.67         6.48        10.52 
TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH 
        1.74         3.45         3.75         6.58        97.45         1.87 
TCGA-XF-A8HI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 
       17.88        11.90        23.64        28.24        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN0 
       66.64        92.98        10.82        91.73         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       30.94        27.06         3.88         4.83         0.66         7.96 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           130.88            140.81 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             9.19              9.12 
[1] "0.1 - 130.9 (9.2)" "0.1 - 140.8 (9.1)"
[1] "hr=" "1.4"
D16V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED          1       2       38        47       39
  8Q GAIN WILD-TYPE        0       0       48        46       53
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 2                 0
  STAGE II               38                48
  STAGE III              47                46
  STAGE IV               39                53
[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"
                   vv
clus                T0+T1+T2 T3 T4
  8Q GAIN MUTATED         40 66 16
  8Q GAIN WILD-TYPE       42 70 23
D16V4, multiclass
          clus
vv         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1+T2              40                42
  T3                    66                70
  T4                    16                23
[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"
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   79 16 22  2
  8Q GAIN WILD-TYPE 87 12 33  5
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              79                87
  N1              16                12
  N2              22                33
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED   60  2 66
  8Q GAIN WILD-TYPE 69  5 75
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              60                69
  M1               2                 5
  MX              66                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    35  94
  8Q GAIN WILD-TYPE  42 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     35   94
  8Q GAIN WILD-TYPE   42  107
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              35                42
  MALE                94               107
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
D16V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED      12                         4   101
  8Q GAIN WILD-TYPE    19                         9   114
D16V11, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                  12                19
  BLACK OR AFRICAN AMERICAN               4                 9
  WHITE                                 101               114
[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"
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     2 115
  8Q GAIN WILD-TYPE   3 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2  115
  8Q GAIN WILD-TYPE    3  143
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             115               143
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    38   8
  9P GAIN WILD-TYPE 144  80
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               46               224 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8                80 
$`9P GAIN MUTATED`
TCGA-2F-A9KO TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-C4-A0F0 
       22.29        40.08         6.74        17.16        12.82         1.94 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 
       12.92         7.20         5.19       130.88       112.44        10.59 
TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A6B6 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3N5 
       87.32         7.82        30.67        12.89         6.87        11.93 
TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A5BT TCGA-FD-A62N TCGA-FD-A6TF TCGA-FD-A6TH 
       22.45        14.93        11.01         2.66         2.07         2.20 
TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GD-A2C5 
        3.48        61.94        30.61         2.24        15.91         7.73 
TCGA-GD-A3OP TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40G TCGA-HQ-A5NE 
        2.10        27.09         5.69         4.14        19.07         8.22 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9SY 
        1.81         6.35         6.58        88.93        15.35        21.04 
TCGA-XF-A9T3 TCGA-XF-AAML TCGA-XF-AAN5 TCGA-YF-AA3M 
        2.24         7.63        75.39         9.04 

$`9P GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I 
       11.97        84.00       103.50        98.33         4.83         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66        12.39         6.58        11.93        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25         5.59         3.65         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        2.07        15.42        28.70         9.99        28.41         8.98 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       23.01         0.46         0.43         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A3KJ 
        0.10         0.07         0.10         0.10         4.90         5.46 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84         9.34         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       18.41        19.00         8.91        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN 
        1.81         7.79       123.85         2.20         3.98         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       10.49        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ 
       76.60        67.36        15.68        41.06        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       26.17        24.66         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66         1.38         0.82        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
        1.22         0.46        15.68         8.94         4.01        12.43 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        45.93        24.30         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S 
       13.18        46.78        19.79         1.97        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU 
       14.93         3.62        12.13        13.38        37.15         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         6.84        27.45         6.87        49.68 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        4.83         6.28         6.38        50.66        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        6.71         4.11         2.66         4.01        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL 
        7.13         4.08         3.25         6.48         5.69        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        17.26         7.04        20.12         0.85        52.67 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
        6.94        19.46         2.89        15.81         4.50        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       17.75         1.12         2.66         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 
        7.36         6.41         7.59        11.31         2.04         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF 
        4.73        10.65         4.41         6.41         6.15         7.63 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.79         6.67         6.41        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         9.01         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        2.50         6.48        10.52         1.74         4.27         6.38 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        3.45        11.80        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
        0.85         3.75        45.04        97.45        56.19         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
       17.88        64.80        79.66        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       26.27        18.90        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       10.82        54.90        91.73         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       56.48        30.94        27.06         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L 
        0.66         7.96 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.81              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           130.88            140.81 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           10.800             8.995 
[1] "1.8 - 130.9 (10.8)" "0.1 - 140.8 (9.0)" 
[1] "hr=" "2.3"
D17V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED          0       1       12        17       16
  9P GAIN WILD-TYPE        1       1       74        76       76
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 1                 1
  STAGE II               12                74
  STAGE III              17                76
  STAGE IV               16                76
[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"
                   vv
clus                T0+T1+T2  T3  T4
  9P GAIN MUTATED         13  24   5
  9P GAIN WILD-TYPE       69 112  34
D17V4, multiclass
          clus
vv         9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1+T2              13                69
  T3                    24               112
  T4                     5                34
[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"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    26   3  11   3
  9P GAIN WILD-TYPE 140  25  44   4
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              26               140
  N1               3                25
  N2              11                44
  N3               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED    20   3  23
  9P GAIN WILD-TYPE 109   4 118
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              20               109
  M1               3                 4
  MX              23               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    10  36
  9P GAIN WILD-TYPE  67 165
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     10   36
  9P GAIN WILD-TYPE   67  165
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              10                67
  MALE                36               165
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       2                         2    39
  9P GAIN WILD-TYPE    29                        11   176
D17V11, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   2                29
  BLACK OR AFRICAN AMERICAN               2                11
  WHITE                                  39               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  41
  9P GAIN WILD-TYPE   4 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   41
  9P GAIN WILD-TYPE    4  217
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              41               217
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    29   7
  9Q GAIN WILD-TYPE 153  81
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               36               234 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7                81 
$`9Q GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CU-A0YN TCGA-DK-A1AC 
       40.08         6.74        17.16         1.94        12.92       130.88 
TCGA-DK-A2I1 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A6B6 TCGA-FD-A3B3 TCGA-FD-A3B4 
       10.59         7.82         8.22        30.67        12.89        15.68 
TCGA-FD-A3SL TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A6TD TCGA-FD-A6TH 
       22.45        11.01         5.36         2.66         6.71         2.20 
TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-GC-A3I6 TCGA-GC-A3RC 
       10.85         3.48        61.94        30.61         2.24        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A76B TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A6FZ 
       17.75         1.12         7.36         6.74         8.22         1.81 
TCGA-LC-A66R TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9T3 TCGA-XF-AAN5 
        6.35         6.58        88.93        15.35         2.24        75.39 

$`9Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66        12.39         6.58        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         2.07        15.42        28.70         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         8.98        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.13         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        9.34         2.53         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
        8.91       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ 
        7.79       123.85        87.32         2.20         3.98        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       67.36        15.68        41.06        43.59        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.10         0.49         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV 
        0.66         1.38         0.82        12.99        14.33         1.22 
TCGA-E7-A7XN TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        0.46         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        45.93        24.30         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       13.18        46.78        19.79         1.97        22.98        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        14.93         3.62        12.13        13.38        37.15 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        6.87         5.69         6.84        27.45         6.87        49.68 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        4.83         6.28         6.38        50.66        18.81         9.30 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        4.11         2.07         2.66         4.01        15.19         7.13 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        4.08         3.25         6.48         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       17.26         7.04        20.12         0.85        52.67         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I1 
       19.46         2.89        15.81         4.50        14.07         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         2.20         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.59        11.31         2.04        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        7.79         4.14         6.67         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        1.51        38.60         3.06         9.01         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB 
        4.67         2.50         6.48        10.52         1.74         4.27 
TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38         3.45        11.80        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF 
       14.24         0.85         3.75        45.04        97.45        56.19 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       21.04        28.24        26.27        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
        2.10        92.98        10.82        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
        2.96         8.32         6.77        56.48        30.94        27.06 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         7.96         9.04 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.12              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           130.88            140.81 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            9.405             9.170 
[1] "1.1 - 130.9 (9.4)" "0.1 - 140.8 (9.2)"
[1] "hr=" "1.8"
D18V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED          0       1        7        20        8
  9Q GAIN WILD-TYPE        1       1       79        73       84
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 1                 1
  STAGE II                7                79
  STAGE III              20                73
  STAGE IV                8                84
[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"
                   vv
clus                T0+T1+T2  T3  T4
  9Q GAIN MUTATED          5  22   4
  9Q GAIN WILD-TYPE       77 114  35
D18V4, multiclass
          clus
vv         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1+T2               5                77
  T3                    22               114
  T4                     4                35
[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"
                   vv
clus                 N0  N1  N2  N3
  9Q GAIN MUTATED    26   1   5   1
  9Q GAIN WILD-TYPE 140  27  50   6
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              26               140
  N1               1                27
  N2               5                50
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  9Q GAIN MUTATED    14   3  19
  9Q GAIN WILD-TYPE 115   4 122
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              14               115
  M1               3                 4
  MX              19               122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    11  25
  9Q GAIN WILD-TYPE  66 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11   25
  9Q GAIN WILD-TYPE   66  176
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              11                66
  MALE                25               176
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       2                         2    30
  9Q GAIN WILD-TYPE    29                        11   185
D18V11, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   2                29
  BLACK OR AFRICAN AMERICAN               2                11
  WHITE                                  30               185
[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"
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  33
  9Q GAIN WILD-TYPE   5 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   33
  9Q GAIN WILD-TYPE    5  225
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              33               225
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    43  29
  10P GAIN WILD-TYPE 139  59
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                72                198 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                29                 59 
$`10P GAIN MUTATED`
TCGA-2F-A9KO TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20R 
       22.29        40.08         2.66         6.58        32.84         5.06 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42E TCGA-CF-A1HS 
        5.06         8.35         5.59        12.82         9.99         0.43 
TCGA-CU-A0YN TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I6 
       12.92         2.53         2.14        66.41       112.44        87.32 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4U1 
        3.98         8.22        48.00        15.68        30.67        26.17 
TCGA-E7-A6ME TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SS TCGA-FD-A5BR 
       12.99         6.87        45.93        24.30         1.97        13.38 
TCGA-FD-A5BS TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FD-A6TF 
       37.15        27.45         6.87        49.68         4.11         2.07 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE 
        2.66         4.01         3.25         6.48        17.26        20.12 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 
       52.67        19.46         4.50         7.73        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
        6.41         4.73        10.65         6.41         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        7.79         6.41        11.54        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        8.22         8.75         6.48        10.52         1.74         1.81 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SH TCGA-XF-AAML TCGA-XF-AAMT TCGA-YF-AA3M 
       56.19        15.35        64.80         7.63         2.96         9.04 

$`10P GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I 
       11.97        84.00       103.50        98.33         4.83         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74        12.39        11.93        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       19.50        14.89        14.96         8.25        17.16         3.65 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ 
        4.67         2.07        15.42        28.70        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94        23.01         0.46         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR 
        0.10         0.07         0.10         0.10         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A7 
        5.46         5.19        16.31         1.84         9.34        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00         8.91       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
        1.81        10.59         7.79       123.85         2.20         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       10.49        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       67.36        41.06        43.59        15.35        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.82        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL 
        8.94         4.01        12.43        11.93        15.88        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
        6.12        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        14.93        14.96        14.93         3.62        12.13 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N 
       11.01         6.87         5.36         5.69         6.84         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        4.83         6.28         6.38        50.66        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.71         2.20        10.85        15.19         7.13         3.48 
TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        4.08        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.04         0.85         6.94         2.89         2.24        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP 
       15.91        14.07        17.75         1.12         2.66         2.10 
TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        3.12         7.36         7.59        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
        5.62         4.41         6.15         4.14         6.67        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB 
        1.51         6.74         3.45         4.67         2.50         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38         6.35         3.45        11.80        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       16.67        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SW 
       88.93        97.45         1.87        17.88        79.66        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        10.82        54.90 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
       91.73         8.32         6.77        56.48        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.43               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            112.44             140.81 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             8.285             10.425 
[1] "0.4 - 112.4 (8.3)"  "0.1 - 140.8 (10.4)"
[1] "hr=" "1.3"
D19V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED          1       1       24        20       28
  10P GAIN WILD-TYPE        0       1       62        73       64
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  1                  1
  STAGE II                24                 62
  STAGE III               20                 73
  STAGE IV                28                 64
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  10P GAIN MUTATED         24 38  9
  10P GAIN WILD-TYPE       58 98 30
D19V4, multiclass
          clus
vv         10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1+T2               24                 58
  T3                     38                 98
  T4                      9                 30
[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"
                    vv
clus                  N0  N1  N2  N3
  10P GAIN MUTATED    37  10  17   3
  10P GAIN WILD-TYPE 129  18  38   4
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               37                129
  N1               10                 18
  N2               17                 38
  N3                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  10P GAIN MUTATED    36   1  39
  10P GAIN WILD-TYPE  93   6 102
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               36                 93
  M1                1                  6
  MX               39                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    17  59
  10P GAIN WILD-TYPE  60 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     17   59
  10P GAIN WILD-TYPE   60  142
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               17                 60
  MALE                 59                142
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       7                         1    60
  10P GAIN WILD-TYPE    24                        12   155
D19V11, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    7                 24
  BLACK OR AFRICAN AMERICAN                1                 12
  WHITE                                   60                155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1  67
  10P GAIN WILD-TYPE   4 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   67
  10P GAIN WILD-TYPE    4  191
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               67                191
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    12  11
  10Q GAIN WILD-TYPE 170  77
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                23                247 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                 77 
$`10Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W TCGA-DK-A1A3 
       22.29         6.58         5.06         5.06         8.35         2.53 
TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A3IN TCGA-DK-A6B2 TCGA-E5-A4U1 TCGA-FD-A3B6 
       66.41       112.44         8.22        15.68        26.17         6.87 
TCGA-FD-A3SS TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FD-A6TI TCGA-G2-AA3B TCGA-GC-A3RB 
        1.97        13.38        27.45         4.01        52.67         4.50 
TCGA-GU-A767 TCGA-GU-AATO TCGA-HQ-A2OE TCGA-XF-A8HG TCGA-XF-AAMT 
        4.73        10.65        38.60        15.35         2.96 

$`10Q GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74        12.39        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       32.84        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        2.07        15.42        28.70         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        1.94        23.01         0.46         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        9.34         2.14        18.41        19.00         8.91       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ 
      123.85        87.32         2.20         3.98         7.82        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       67.36        41.06        30.67        43.59        15.35        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         0.53         0.59         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        1.38         0.82        12.99        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       12.89        15.68         8.94         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       15.88        45.93        24.30        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P 
        5.52        13.18        46.78        19.79        22.98        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        14.93         3.62        12.13        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
        6.87         5.36         5.69         6.84         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.66         4.83         6.28         6.38        50.66        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        9.30         6.71         4.11         2.07         2.66         2.20 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
       10.85        15.19         7.13         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F 
       17.26         7.04        20.12         0.85         6.94        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.89         2.24        15.81        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        1.12         2.66         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36         6.41         7.59        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       27.09         5.62         4.41         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        7.63         7.79         4.14         6.67         6.41        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       11.54         1.51         6.74         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.75         3.45         4.67         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        1.74         1.81         4.27         6.38         6.35         3.45 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       11.80        13.48        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.75        45.04         6.58        88.93        97.45        56.19 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        92.98        10.82        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
       91.73         8.32         6.77        56.48        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 
TCGA-YF-AA3M 
        9.04 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.97               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            112.44             140.81 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              8.35               9.30 
[1] "2.0 - 112.4 (8.3)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.4"
D20V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED          0       0        6         5       13
  10Q GAIN WILD-TYPE        1       2       80        88       79
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 6                 80
  STAGE III                5                 88
  STAGE IV                13                 79
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  10Q GAIN MUTATED          8  11   6
  10Q GAIN WILD-TYPE       74 125  33
D20V4, multiclass
          clus
vv         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1+T2                8                 74
  T3                     11                125
  T4                      6                 33
[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"
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED    11   6   7   1
  10Q GAIN WILD-TYPE 155  22  48   6
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               11                155
  N1                6                 22
  N2                7                 48
  N3                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  10Q GAIN MUTATED    14   0  11
  10Q GAIN WILD-TYPE 115   7 130
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0               14                115
  M1                0                  7
  MX               11                130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5  20
  10Q GAIN WILD-TYPE  72 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5   20
  10Q GAIN WILD-TYPE   72  181
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                5                 72
  MALE                 20                181
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       2                         1    20
  10Q GAIN WILD-TYPE    29                        12   195
D20V11, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    2                 29
  BLACK OR AFRICAN AMERICAN                1                 12
  WHITE                                   20                195
[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"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0  22
  10Q GAIN WILD-TYPE   5 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   22
  10Q GAIN WILD-TYPE    5  236
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               22                236
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    16   9
  11P GAIN WILD-TYPE 166  79
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                25                245 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                 79 
$`11P GAIN MUTATED`
TCGA-BL-A13J TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-DK-A3IV TCGA-DK-A3WX 
        2.66        12.82        12.92         4.90         9.67        10.55 
TCGA-E7-A5KF TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A5BT TCGA-FD-A62P TCGA-FD-A6TI 
        0.66         1.22         6.87        11.01         6.28         4.01 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3JZ TCGA-GV-A3QI 
        2.24        15.91         2.04         5.62         5.69         4.14 
TCGA-GV-A40E TCGA-K4-A4AC TCGA-LC-A66R TCGA-PQ-A6FI TCGA-XF-A8HF TCGA-XF-A9SY 
        6.41         6.48         6.35        12.23        56.19        21.04 
TCGA-YF-AA3M 
        9.04 

$`11P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        5.59         3.65         4.67         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        9.99        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
        0.10         0.10         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84         9.34         2.53         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20         3.98         7.82         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       21.30        20.02         8.28       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       30.67        43.59        15.35        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 
        0.49         0.53         0.59         0.56         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.99        14.33         0.46        12.89        15.68         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79         1.97        22.98        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        12.13        13.38        37.15         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         6.84        27.45         6.87        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        4.83         6.38        50.66        18.81         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
        4.11         2.07         2.66         2.20        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        7.13         3.48         4.08         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12         0.85        52.67         6.94        19.46         2.89 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81         4.50        14.07        17.75         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO 
        6.41         7.59        11.31        27.09         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        4.41         6.41         6.15         7.63         7.79         6.67 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        11.54         1.51         6.74        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22         8.75         3.45         4.67         2.50 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 
       10.52         1.74         1.81         4.27         6.38         3.45 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       11.80        13.48        16.67        14.24         0.85         3.75 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58        88.93        97.45        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
       17.88        64.80        79.66        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT 
       92.98        10.82        54.90         7.63        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        8.32         6.77        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.66               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             56.19             140.81 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              6.41              10.36 
[1] "0.7 - 56.2 (6.4)"   "0.1 - 140.8 (10.4)"
[1] "hr=" "1.8"
D21V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED          0       0       10         7        8
  11P GAIN WILD-TYPE        1       2       76        86       84
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                10                 76
  STAGE III                7                 86
  STAGE IV                 8                 84
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  11P GAIN MUTATED          8   9   6
  11P GAIN WILD-TYPE       74 127  33
D21V4, multiclass
          clus
vv         11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1+T2                8                 74
  T3                      9                127
  T4                      6                 33
[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"
                    vv
clus                  N0  N1  N2  N3
  11P GAIN MUTATED    13   1   5   3
  11P GAIN WILD-TYPE 153  27  50   4
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               13                153
  N1                1                 27
  N2                5                 50
  N3                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  11P GAIN MUTATED     9   0  16
  11P GAIN WILD-TYPE 120   7 125
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                9                120
  M1                0                  7
  MX               16                125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  23
  11P GAIN WILD-TYPE  75 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   23
  11P GAIN WILD-TYPE   75  178
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 75
  MALE                 23                178
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       1                         0    23
  11P GAIN WILD-TYPE    30                        13   192
D21V11, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                 30
  BLACK OR AFRICAN AMERICAN                0                 13
  WHITE                                   23                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  24
  11P GAIN WILD-TYPE   4 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   24
  11P GAIN WILD-TYPE    4  234
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               24                234
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    24  13
  11Q GAIN WILD-TYPE 158  75
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                37                233 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 75 
$`11Q GAIN MUTATED`
TCGA-BL-A13J TCGA-BT-A3PJ TCGA-C4-A0F6 TCGA-CU-A0YN TCGA-CU-A0YO TCGA-DK-A1A3 
        2.66        12.82        23.01        12.92         4.90         2.53 
TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-E7-A5KF TCGA-E7-A7DV TCGA-FD-A3B6 
        7.82        10.55        17.98         0.66         1.22         6.87 
TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A62P TCGA-FD-A6TG 
       45.93        14.93        13.38        11.01         6.28         2.66 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GU-A762 
        4.01        15.19        19.46         2.24        15.91         2.04 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-K4-A4AC 
        5.62         4.73         5.69         7.63         6.41         6.48 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-XF-A8HF TCGA-XF-A9SY TCGA-XF-AAMX 
        6.35        12.23         0.85        56.19        21.04         6.77 
TCGA-YF-AA3M 
        9.04 

$`11Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        5.59         3.65         4.67         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
        9.99        28.41         8.98         1.94         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        0.10         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.14        66.41        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20         3.98 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28       140.81        48.00        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       67.36        15.68        41.06        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       26.17        24.66         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        0.56         1.38         0.82        12.99        14.33         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       12.89        15.68         8.94         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        24.30        22.45         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S 
       13.18        46.78        19.79         1.97        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV 
       14.93         3.62        12.13        37.15         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         6.84        27.45         6.87        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        4.83         6.38        50.66        18.81         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.11         2.07         2.20        10.85         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.08         3.25         6.48        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        17.26         7.04        20.12         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
       52.67         6.94         2.89        15.81         4.50        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75         1.12         2.66         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36         6.41         7.59        11.31 
TCGA-GU-A763 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       27.09        10.65         4.41         6.41         6.15         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.67        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        4.67         2.50        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
        6.38         3.45        11.80        13.48        16.67        14.24 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        3.75        45.04         6.58        88.93        97.45        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        11.90        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
        2.10        92.98        10.82        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.66               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             56.19             140.81 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              6.87               9.99 
[1] "0.7 - 56.2 (6.9)"   "0.1 - 140.8 (10.0)"
[1] "hr=" "1.5"
D22V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED          0       0       12         9       16
  11Q GAIN WILD-TYPE        1       2       74        84       76
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                12                 74
  STAGE III                9                 84
  STAGE IV                16                 76
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  11Q GAIN MUTATED         11  17   8
  11Q GAIN WILD-TYPE       71 119  31
D22V4, multiclass
          clus
vv         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1+T2               11                 71
  T3                     17                119
  T4                      8                 31
[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"
                    vv
clus                  N0  N1  N2  N3
  11Q GAIN MUTATED    18   2  12   3
  11Q GAIN WILD-TYPE 148  26  43   4
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               18                148
  N1                2                 26
  N2               12                 43
  N3                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  11Q GAIN MUTATED    13   0  24
  11Q GAIN WILD-TYPE 116   7 117
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0               13                116
  M1                0                  7
  MX               24                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  33
  11Q GAIN WILD-TYPE  73 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   33
  11Q GAIN WILD-TYPE   73  168
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                4                 73
  MALE                 33                168
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
D22V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       1                         2    32
  11Q GAIN WILD-TYPE    30                        11   183
D22V11, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    1                 30
  BLACK OR AFRICAN AMERICAN                2                 11
  WHITE                                   32                183
[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"
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  35
  11Q GAIN WILD-TYPE   4 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   35
  11Q GAIN WILD-TYPE    4  223
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               35                223
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    49  25
  12P GAIN WILD-TYPE 133  63
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                74                196 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                25                 63 
$`12P GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N 
       22.29        11.97        40.08         6.74        19.04        32.84 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       17.88         5.06         5.06         8.25         5.59         3.65 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.82         2.07         9.99        12.92         4.90         7.20 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 
        2.53        66.41         7.82        50.27        10.55        48.00 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E7-A4IJ TCGA-E7-A5KE 
       64.18        67.36        15.68        30.67         0.49         0.56 
TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A43P 
       12.99        12.89         6.87        45.93         1.97        14.93 
TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB 
       37.15         5.36        27.45         6.28         6.38        18.81 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM 
       15.19         6.48        35.24         0.85        52.67         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GU-A762 TCGA-GU-AATO TCGA-GV-A3JZ 
        2.24        15.81        14.07         2.04        10.65         5.69 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A2OE 
        7.79         4.14         6.67         6.41        19.07        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
        3.06         9.01         8.22         3.45         4.67         6.48 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-MV-A51V TCGA-XF-A9SI TCGA-XF-AAML TCGA-XF-AAMT 
        1.81         6.38        13.48        79.66         7.63         2.96 
TCGA-XF-AAN5 TCGA-YF-AA3M 
       75.39         9.04 

$`12P GAIN WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A13J 
       84.00       103.50        98.33         4.83         7.33         2.66 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T 
       12.39         6.58        11.93        12.16        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
       14.96         8.35        17.16         4.67        15.42        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        0.10         5.46         5.19        16.31         1.84         9.34 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ 
      123.85        87.32         2.20         3.98         8.22        10.49 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X2 
       21.30        20.02         9.67         8.28       140.81        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       41.56        76.60        41.06        43.59        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
       24.66         0.10         0.53         0.59         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.82        14.33         1.22         0.46        15.68         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.43        11.93        15.88        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
        6.12        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       22.98        14.96        14.93         3.62        12.13        13.38 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       11.01         6.87         5.69         6.84         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        2.66         4.83        50.66         9.30         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.07         2.66         2.20         4.01        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         4.08         3.25        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F 
       26.93        17.26         7.04        20.12         6.94        19.46 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        17.75         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV 
        7.59        11.31        27.09         5.62         4.73         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.41         6.15         7.63        11.54         1.51         6.74 
TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LC-A66R 
        8.75         2.50        10.52         1.74         4.27         6.35 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        3.45        11.80        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.75        45.04         6.58        88.93        97.45        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX 
       15.35         1.87        17.88        64.80        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR 
       66.64         2.10        92.98        10.82        54.90        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 
        8.32         6.77        56.48        30.94        27.06         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       10.36         4.83         0.66         7.96 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.49               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             79.66             140.81 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             8.630              9.505 
[1] "0.5 - 79.7 (8.6)"  "0.1 - 140.8 (9.5)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED          0       1       28        25       22
  12P GAIN WILD-TYPE        1       1       58        68       70
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                28                 58
  STAGE III               25                 68
  STAGE IV                22                 70
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  12P GAIN MUTATED         28  35  10
  12P GAIN WILD-TYPE       54 101  29
D23V4, multiclass
          clus
vv         12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1+T2               28                 54
  T3                     35                101
  T4                     10                 29
[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"
                    vv
clus                  N0  N1  N2  N3
  12P GAIN MUTATED    45   8  13   3
  12P GAIN WILD-TYPE 121  20  42   4
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               45                121
  N1                8                 20
  N2               13                 42
  N3                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  12P GAIN MUTATED    39   0  37
  12P GAIN WILD-TYPE  90   7 104
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               39                 90
  M1                0                  7
  MX               37                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    22  55
  12P GAIN WILD-TYPE  55 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     22   55
  12P GAIN WILD-TYPE   55  146
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               22                 55
  MALE                 55                146
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       9                         3    57
  12P GAIN WILD-TYPE    22                        10   158
D23V11, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    9                 22
  BLACK OR AFRICAN AMERICAN                3                 10
  WHITE                                   57                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"
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1  68
  12P GAIN WILD-TYPE   4 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   68
  12P GAIN WILD-TYPE    4  190
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               68                190
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    34  20
  12Q GAIN WILD-TYPE 148  68
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                54                216 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                20                 68 
$`12Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20P 
       22.29        11.97        40.08         6.74        19.04        17.88 
TCGA-BT-A20R TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42E TCGA-CU-A0YO 
        5.06         8.25         5.59         2.07         9.99         4.90 
TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AC 
        7.20         1.84         2.53         2.14        66.41       130.88 
TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-E7-A5KE 
       50.27        10.55        48.00        64.18        67.36         0.56 
TCGA-E7-A6ME TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BZ 
       12.99        45.93        14.93        12.13         5.36        27.45 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3VY 
        6.28         6.38        15.19        61.94        35.24         0.85 
TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GU-AATO TCGA-GV-A3QH TCGA-GV-A3QI 
       52.67         2.89         2.24        10.65         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A6FZ 
        6.67         6.41        38.60         3.06         3.45         1.81 
TCGA-K4-A83P TCGA-MV-A51V TCGA-XF-A9SI TCGA-XF-AAML TCGA-XF-AAMT TCGA-YF-AA3M 
        6.38        13.48        79.66         7.63         2.96         9.04 

$`12Q GAIN WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A13J 
       84.00       103.50        98.33         4.83         7.33         2.66 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q 
       12.39         6.58        11.93        32.84        12.16        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD 
       14.89        14.96         5.06         8.35        17.16         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ 
        4.67        12.82        15.42        28.70        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        1.94        23.01         0.46         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.46         5.19        16.31         9.34        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
        8.91       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        10.49        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
        8.28       140.81        17.98        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       41.06        30.67        43.59        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
        0.10         0.49         0.53         0.59         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.82        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79         1.97        22.98        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        13.38        37.15        11.01         6.87         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA 
        6.84         6.87        49.68         2.66         4.83        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         9.30         6.71         4.11         2.07         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.20         4.01        10.85         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        3.25         6.48        30.61         5.69        26.93        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB 
        7.04        20.12         6.94        19.46        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.91        14.07        17.75         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.59        11.31         2.04        27.09         5.62         4.73 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40G 
        4.41         6.41         6.15         5.69         7.63        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       11.54         1.51         6.74         9.01         8.22         8.75 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB 
        4.67         2.50         6.48        10.52         1.74         4.27 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        6.35         3.45        11.80        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        0.85         3.75        45.04         6.58        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW 
       56.19        15.35         1.87        17.88        64.80        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        10.82        54.90 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
       91.73         8.32         6.77        56.48        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.56               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            130.88             140.81 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             8.645              9.320 
[1] "0.6 - 130.9 (8.6)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED          0       1       23        19       14
  12Q GAIN WILD-TYPE        1       1       63        74       78
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                23                 63
  STAGE III               19                 74
  STAGE IV                14                 78
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  12Q GAIN MUTATED         23  23   8
  12Q GAIN WILD-TYPE       59 113  31
D24V4, multiclass
          clus
vv         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1+T2               23                 59
  T3                     23                113
  T4                      8                 31
[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"
                    vv
clus                  N0  N1  N2  N3
  12Q GAIN MUTATED    37   5  10   0
  12Q GAIN WILD-TYPE 129  23  45   7
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               37                129
  N1                5                 23
  N2               10                 45
  N3                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  12Q GAIN MUTATED    33   0  24
  12Q GAIN WILD-TYPE  96   7 117
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               33                 96
  M1                0                  7
  MX               24                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    16  42
  12Q GAIN WILD-TYPE  61 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     16   42
  12Q GAIN WILD-TYPE   61  159
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               16                 61
  MALE                 42                159
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       9                         2    43
  12Q GAIN WILD-TYPE    22                        11   172
D24V11, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    9                 22
  BLACK OR AFRICAN AMERICAN                2                 11
  WHITE                                   43                172
[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"
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1  52
  12Q GAIN WILD-TYPE   4 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   52
  12Q GAIN WILD-TYPE    4  206
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               52                206
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    42  20
  13Q GAIN WILD-TYPE 140  68
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                62                208 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                20                 68 
$`13Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20Q 
       22.29        98.33         6.74         6.58        19.04        19.50 
TCGA-BT-A20U TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CU-A0YN 
       14.96         3.65        12.82         8.98         0.43        12.92 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A2HX TCGA-DK-A3IL TCGA-DK-A3IS 
        7.20         5.19        16.31         1.81         3.98        50.27 
TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-E5-A2PC TCGA-E7-A541 
       20.02        48.00        17.98        67.36        43.59         0.59 
TCGA-E7-A6ME TCGA-FD-A3B6 TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A43X TCGA-FD-A5BT 
       12.99         6.87         6.12        46.78         3.62        11.01 
TCGA-FD-A62O TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZE TCGA-FT-A61P 
        4.83         4.11         2.66         2.20         3.48         6.48 
TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A3OP 
       61.94         5.69        52.67        15.81        17.75         2.10 
TCGA-GD-A3OS TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       20.98         4.73        10.65         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A54R TCGA-LC-A66R 
        7.79         6.67         6.74         8.22        10.52         6.35 
TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        14.24         0.85        88.93        56.19        15.35 
TCGA-XF-AAMR TCGA-XF-AAN0 
       91.73        56.48 

$`13Q GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I 
       11.97        84.00       103.50         4.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        2.66        12.39        11.93        32.84        12.16        17.88 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.89         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        5.59         4.67         2.07        15.42        28.70         9.99 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
       28.41         1.94        23.01         0.46         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO 
        0.07         0.10         0.07         0.10         0.10         4.90 
TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.46         1.84         9.34         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV 
        2.20         7.82         8.22        10.49        21.30         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        64.18        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       15.68        41.06        30.67        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         0.49         0.53         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.82        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        8.94         4.01        12.43        11.93        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR 
       24.30        22.45        12.82         5.52        13.18        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y 
        1.97        22.98        14.93        14.96        14.93        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       13.38        37.15         6.87         5.36         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
       27.45         6.87        49.68         2.66         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI 
       50.66        18.81         9.30         6.71         2.07         4.01 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EJ 
       10.85        15.19         7.13         4.08         3.25        30.61 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        17.26         7.04        20.12         0.85 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC 
        6.94        19.46         2.89         2.24         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 
       14.07         1.12         2.66         7.73         3.12         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36         6.41         7.59        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G 
        5.62         4.41         6.41         4.14         6.41        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS 
       11.54         1.51        38.60         3.06         9.01         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ 
        3.45         4.67         2.50         6.48         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        4.27         6.38         3.45        11.80        12.23        16.67 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
        3.75        45.04         6.58        97.45         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       64.80        79.66        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW 
       92.98        10.82        54.90         7.63         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
        6.77        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.43               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             98.33             140.81 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              9.75               9.17 
[1] "0.4 - 98.3 (9.8)"  "0.1 - 140.8 (9.2)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED          0       0       18        18       28
  13Q GAIN WILD-TYPE        1       2       68        75       64
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                18                 68
  STAGE III               18                 75
  STAGE IV                28                 64
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  13Q GAIN MUTATED         17  33   9
  13Q GAIN WILD-TYPE       65 103  30
D25V4, multiclass
          clus
vv         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1+T2               17                 65
  T3                     33                103
  T4                      9                 30
[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"
                    vv
clus                  N0  N1  N2  N3
  13Q GAIN MUTATED    32   5  20   4
  13Q GAIN WILD-TYPE 134  23  35   3
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               32                134
  N1                5                 23
  N2               20                 35
  N3                4                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  13Q GAIN MUTATED    32   4  29
  13Q GAIN WILD-TYPE  97   3 112
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               32                 97
  M1                4                  3
  MX               29                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    14  51
  13Q GAIN WILD-TYPE  63 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     14   51
  13Q GAIN WILD-TYPE   63  150
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               14                 63
  MALE                 51                150
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       4                         1    58
  13Q GAIN WILD-TYPE    27                        12   157
D25V11, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    4                 27
  BLACK OR AFRICAN AMERICAN                1                 12
  WHITE                                   58                157
[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"
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  63
  13Q GAIN WILD-TYPE   5 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   63
  13Q GAIN WILD-TYPE    5  195
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               63                195
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    26  18
  14Q GAIN WILD-TYPE 156  70
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                44                226 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                18                 70 
$`14Q GAIN MUTATED`
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-C4-A0EZ TCGA-C4-A0F0 
        2.66        12.39         6.58        32.84         8.98         1.94 
TCGA-C4-A0F6 TCGA-CU-A0YN TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3WX 
       23.01        12.92         2.20         8.22        21.30        10.55 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A5BT 
       30.67        43.59        12.89         4.01        11.93        11.01 
TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3ZE 
       27.45         4.83         6.38         6.71         4.11         3.48 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3YS TCGA-GD-A3OS 
       26.93        35.24         2.89         2.24         1.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-AATO TCGA-GV-A3QH TCGA-K4-A3WV TCGA-K4-A4AC 
        2.20         6.41        10.65         7.79         4.67         6.48 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-XF-A8HB TCGA-XF-A8HG TCGA-XF-A9T3 
        1.81         3.45        16.67        45.04        15.35         2.24 
TCGA-XF-AAMF TCGA-XF-AAMT 
       10.82         2.96 

$`14Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
       40.08         7.33         6.74        11.93        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         2.07        15.42        28.70         9.99        28.41 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.07         0.10         0.10         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84         9.34         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS 
      123.85        87.32         3.98         7.82        10.49        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       20.02         9.67         8.28       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        26.17        24.66         0.10         0.49         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.59         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.33         1.22         0.46        15.68         8.94         6.87 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        15.88        45.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       12.82         5.52        13.18        46.78        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        14.93        14.96        14.93         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       13.38        37.15         6.87         5.36         5.69         6.84 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        6.87        49.68         2.66         6.28        50.66        18.81 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        9.30         2.07         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       15.19         7.13         4.08         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       30.61         5.69        17.26         7.04        20.12         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       52.67         6.94        19.46        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        17.75         2.66         7.73         2.10         3.12 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        7.36         7.59        11.31         2.04        27.09         5.62 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        4.73         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.14         6.67         6.41        19.07        11.54         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        6.74        38.60         3.06         9.01         8.22         8.75 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        3.45         2.50        10.52         1.74         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
        6.35        11.80        13.48        12.23        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
        3.75         6.58        88.93        97.45        56.19         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       17.88        64.80        79.66        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       92.98        54.90         7.63        91.73         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.12               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             45.04             140.81 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             8.005              9.505 
[1] "1.1 - 45.0 (8.0)"  "0.1 - 140.8 (9.5)"
[1] "hr=" "1.6"
D26V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED          0       0       11        20       13
  14Q GAIN WILD-TYPE        1       2       75        73       79
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                11                 75
  STAGE III               20                 73
  STAGE IV                13                 79
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  14Q GAIN MUTATED          7  25   6
  14Q GAIN WILD-TYPE       75 111  33
D26V4, multiclass
          clus
vv         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1+T2                7                 75
  T3                     25                111
  T4                      6                 33
[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"
                    vv
clus                  N0  N1  N2  N3
  14Q GAIN MUTATED    26   5   8   1
  14Q GAIN WILD-TYPE 140  23  47   6
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               26                140
  N1                5                 23
  N2                8                 47
  N3                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  14Q GAIN MUTATED    13   2  29
  14Q GAIN WILD-TYPE 116   5 112
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0               13                116
  M1                2                  5
  MX               29                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    15  29
  14Q GAIN WILD-TYPE  62 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15   29
  14Q GAIN WILD-TYPE   62  172
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               15                 62
  MALE                 29                172
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
D26V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         3    35
  14Q GAIN WILD-TYPE    31                        10   180
D26V11, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                 31
  BLACK OR AFRICAN AMERICAN                3                 10
  WHITE                                   35                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"
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  38
  14Q GAIN WILD-TYPE   4 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   38
  14Q GAIN WILD-TYPE    4  220
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               38                220
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    13   7
  15Q GAIN WILD-TYPE 169  81
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                20                250 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                 81 
$`15Q GAIN MUTATED`
TCGA-BT-A20Q TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 
       19.50        28.41        23.01        16.31         1.84         2.14 
TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A6B1 TCGA-E5-A4TZ TCGA-FD-A43U 
        1.81        50.27        10.55        67.36        15.35        14.93 
TCGA-FD-A43X TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GC-A3I6 
        3.62         2.66         3.48        35.24         2.89         2.24 
TCGA-S5-A6DX TCGA-XF-AAN1 
        0.85        30.94 

$`15Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R 
       11.93        19.04        32.84        12.16        17.88         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        5.59         3.65         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.70         9.99         8.98         1.94         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.10        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.53        66.41        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
      130.88       112.44        16.14        17.62        15.62        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        10.49        21.30        20.02         9.67         8.28 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       15.68        41.06        30.67        43.59        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         0.53         0.59         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        1.38         0.82        12.99        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       12.89        15.68         8.94         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       11.93        15.88        45.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       12.82         5.52        13.18        46.78        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       22.98        14.93        14.96        12.13        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01         6.87         5.36         5.69         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        6.87        49.68         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       50.66        18.81         9.30         6.71         4.11         2.07 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        2.20         4.01        10.85        15.19         7.13         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61         5.69        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       17.26         7.04        20.12         0.85        52.67         6.94 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       19.46        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        1.12         2.66         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36         6.41         7.59        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
       27.09         5.62         4.73        10.65         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.15         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.41        19.07        11.54         1.51         6.74        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.50         6.48        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38         6.35         3.45        11.80        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       16.67        14.24         3.75        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       97.45        56.19        15.35         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       79.66        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       10.82        54.90         7.63        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
        6.77        56.48        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.85               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             67.36             140.81 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            12.740              9.025 
[1] "0.8 - 67.4 (12.7)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED          0       0        6         7        9
  15Q GAIN WILD-TYPE        1       2       80        86       83
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 6                 80
  STAGE III                7                 86
  STAGE IV                 9                 83
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  15Q GAIN MUTATED          6   8   7
  15Q GAIN WILD-TYPE       76 128  32
D27V4, multiclass
          clus
vv         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1+T2                6                 76
  T3                      8                128
  T4                      7                 32
[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"
                    vv
clus                  N0  N1  N2  N3
  15Q GAIN MUTATED    13   1   6   2
  15Q GAIN WILD-TYPE 153  27  49   5
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               13                153
  N1                1                 27
  N2                6                 49
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  15Q GAIN MUTATED    14   1   7
  15Q GAIN WILD-TYPE 115   6 134
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               14                115
  M1                1                  6
  MX                7                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     4  18
  15Q GAIN WILD-TYPE  73 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4   18
  15Q GAIN WILD-TYPE   73  183
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                4                 73
  MALE                 18                183
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         0    19
  15Q GAIN WILD-TYPE    30                        13   196
D27V11, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                 30
  BLACK OR AFRICAN AMERICAN                0                 13
  WHITE                                   19                196
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  21
  15Q GAIN WILD-TYPE   5 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   21
  15Q GAIN WILD-TYPE    5  237
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               21                237
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    29  20
  16P GAIN WILD-TYPE 153  68
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                49                221 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                20                 68 
$`16P GAIN MUTATED`
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42C 
        2.66         6.58         5.06         8.25        17.16        28.70 
TCGA-C4-A0EZ TCGA-CF-A47X TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IS 
        8.98         0.10         7.79         3.98         8.22        50.27 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E7-A4IJ 
       21.30         9.67        48.00        15.68        43.59         0.49 
TCGA-E7-A6ME TCGA-FD-A3SJ TCGA-FD-A5BY TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       12.99        24.30         6.84         2.07         2.66         4.01 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 
        3.48         3.25        35.24        52.67         2.89         2.24 
TCGA-GD-A76B TCGA-GU-A762 TCGA-GV-A3JV TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
        7.36         2.04         4.41         6.74         3.06         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A83P TCGA-LC-A66R TCGA-R3-A69X 
        8.75         3.45         2.50         6.38         6.35        14.24 
TCGA-S5-A6DX TCGA-XF-A9SZ TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMR 
        0.85        28.24        66.64        10.82         7.63        91.73 
TCGA-XF-AAMX 
        6.77 

$`16P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         6.74        12.39        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         8.35         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        2.07        15.42         9.99        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.07         0.10        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84         9.34         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW 
       87.32         2.20         7.82        10.49        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        17.98        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       67.36        41.06        30.67        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.82        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       45.93        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79         1.97        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93         3.62        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        6.87         5.36         5.69        27.45         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.66         4.83         6.28         6.38        50.66        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
        9.30         6.71         4.11         2.20        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        7.13         4.08         6.48        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       26.93        17.26         7.04        20.12         0.85         6.94 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       19.46        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        1.12         2.66         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 
        2.20         6.41         7.59        11.31        27.09         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        4.73        10.65         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        7.79         4.14         6.67         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R 
        1.51        38.60         8.22         4.67         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        1.74         1.81         4.27         3.45        11.80        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       12.23        16.67         3.75        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       97.45        56.19        15.35         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       79.66        11.90        23.64        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAMT 
        2.24        16.27         2.10        92.98        54.90         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        8.32        56.48        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       10.36         4.83         0.66         7.96         9.04 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.10               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             91.73             140.81 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              7.36              10.59 
[1] "0.1 - 91.7 (7.4)"   "0.1 - 140.8 (10.6)"
[1] "hr=" "1.6"
D28V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED          0       0       10        16       23
  16P GAIN WILD-TYPE        1       2       76        77       69
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                10                 76
  STAGE III               16                 77
  STAGE IV                23                 69
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  16P GAIN MUTATED         10  21  14
  16P GAIN WILD-TYPE       72 115  25
D28V4, multiclass
          clus
vv         16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1+T2               10                 72
  T3                     21                115
  T4                     14                 25
[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"
                    vv
clus                  N0  N1  N2  N3
  16P GAIN MUTATED    23   8  12   2
  16P GAIN WILD-TYPE 143  20  43   5
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               23                143
  N1                8                 20
  N2               12                 43
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED    23   4  22
  16P GAIN WILD-TYPE 106   3 119
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               23                106
  M1                4                  3
  MX               22                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"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    15  34
  16P GAIN WILD-TYPE  62 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     15   34
  16P GAIN WILD-TYPE   62  167
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               15                 62
  MALE                 34                167
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       3                         3    38
  16P GAIN WILD-TYPE    28                        10   177
D28V11, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    3                 28
  BLACK OR AFRICAN AMERICAN                3                 10
  WHITE                                   38                177
[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"
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  44
  16P GAIN WILD-TYPE   5 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   44
  16P GAIN WILD-TYPE    5  214
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               44                214
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    38  16
  16Q GAIN WILD-TYPE 144  72
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                54                216 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                 72 
$`16Q GAIN MUTATED`
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        2.66         6.58         5.06         5.06         8.25        17.16 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A47X TCGA-DK-A2I2 TCGA-DK-A3IL 
       12.82        28.70         8.98         0.10         7.79         3.98 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-E5-A2PC 
        8.22        50.27        21.30        48.00        15.68        43.59 
TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A62P 
       12.99        12.89        14.93        12.13         6.84         6.28 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A3EE 
        2.07         2.66         4.01        10.85         3.48         3.25 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3YS 
       35.24         0.85        52.67         2.89         2.24         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A762 TCGA-GV-A3JW 
        2.66         7.73        20.98         7.36         2.04         6.41 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        6.74         3.06         9.01         8.75         3.45         2.50 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-AAMF TCGA-XF-AAMR 
        4.27         6.35        14.24         0.85        10.82        91.73 

$`16Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         6.74        12.39        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       32.84        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        8.35         5.59         3.65         4.67         2.07        15.42 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
        9.99        28.41         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84         9.34         2.53         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81        10.59       123.85        87.32         2.20 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        7.82        10.49        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       41.06        30.67        15.35        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.82        14.33         1.22         0.46        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        6.87         4.01        12.43        11.93        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79         1.97        22.98        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        13.38        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69        27.45         6.87        49.68         2.66         4.83 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.38        50.66        18.81         9.30         6.71         4.11 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        2.20        15.19         7.13         4.08         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61         5.69        26.93        17.26         7.04        20.12 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        19.46        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
       17.75         2.10         3.12         2.20         6.41         7.59 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
       11.31        27.09         5.62         4.73        10.65         4.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.15         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE 
        6.41        19.07        11.54         1.51        38.60         8.22 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        4.67         6.48        10.52         1.74         1.81         6.38 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
        3.45        11.80        13.48        12.23        16.67         3.75 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       45.04         6.58        88.93        97.45        56.19        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT 
       66.64         2.10        92.98        54.90         7.63         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        8.32         6.77        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         7.96         9.04 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.10               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             91.73             140.81 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              7.10              10.57 
[1] "0.1 - 91.7 (7.1)"   "0.1 - 140.8 (10.6)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED          0       0       13        19       22
  16Q GAIN WILD-TYPE        1       2       73        74       70
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                13                 73
  STAGE III               19                 74
  STAGE IV                22                 70
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  16Q GAIN MUTATED         11  24  14
  16Q GAIN WILD-TYPE       71 112  25
D29V4, multiclass
          clus
vv         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1+T2               11                 71
  T3                     24                112
  T4                     14                 25
[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"
                    vv
clus                  N0  N1  N2  N3
  16Q GAIN MUTATED    27   8  11   3
  16Q GAIN WILD-TYPE 139  20  44   4
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               27                139
  N1                8                 20
  N2               11                 44
  N3                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED    23   4  26
  16Q GAIN WILD-TYPE 106   3 115
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               23                106
  M1                4                  3
  MX               26                115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    18  36
  16Q GAIN WILD-TYPE  59 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     18   36
  16Q GAIN WILD-TYPE   59  165
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               18                 59
  MALE                 36                165
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       3                         3    43
  16Q GAIN WILD-TYPE    28                        10   172
D29V11, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    3                 28
  BLACK OR AFRICAN AMERICAN                3                 10
  WHITE                                   43                172
[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"
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  49
  16Q GAIN WILD-TYPE   5 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   49
  16Q GAIN WILD-TYPE    5  209
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               49                209
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    21  17
  17P GAIN WILD-TYPE 161  71
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                38                232 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                 71 
$`17P GAIN MUTATED`
TCGA-2F-A9KP TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20R 
       11.97        40.08         2.66         6.74         6.58         5.06 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ 
       14.96         8.35         3.65        12.82        28.70         8.98 
TCGA-CU-A0YR TCGA-DK-A3IM TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E7-A5KE TCGA-FD-A3B7 
        7.20         7.82        67.36        30.67         0.56         4.01 
TCGA-FD-A3SP TCGA-FD-A5BT TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       13.18        11.01        49.68         4.11         2.07         2.20 
TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-AA3F TCGA-GV-A3JV TCGA-GV-A3QH TCGA-HQ-A2OE 
       15.19         3.25        19.46         4.41         7.79        38.60 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-LC-A66R TCGA-MV-A51V TCGA-XF-A8HI 
        3.45         4.67         1.81         6.35        13.48        17.88 
TCGA-XF-A9T0 TCGA-XF-AAML 
       26.27         7.63 

$`17P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I 
       22.29        84.00       103.50        98.33         4.83         7.33 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39        11.93        19.04        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       19.50        14.89         5.06         8.25        17.16         5.59 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        4.67         2.07        15.42         9.99        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       23.01         0.46         0.43         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.10         0.07         0.10         0.10        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN 
        7.79       123.85        87.32         2.20         3.98         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       10.49        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       76.60        15.68        41.06        43.59        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF 
       24.66         0.10         0.49         0.53         0.59         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        1.38         0.82        12.99        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
       12.89        15.68         8.94         6.87        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       15.88        45.93        24.30        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        46.78        19.79         1.97        22.98        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        14.93         3.62        12.13        13.38        37.15 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
        6.87         5.36         5.69         6.84        27.45         6.87 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.66         4.83         6.28         6.38        50.66        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        9.30         6.71         2.66         4.01        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         4.08         6.48        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        17.26         7.04        20.12         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       52.67         6.94         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.91        14.07        17.75         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.59        11.31         2.04        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
       10.65         6.41         6.15         5.69         7.63         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.67         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC 
        3.06         9.01         8.22         8.75         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT 
       10.52         1.74         4.27         6.38         3.45        11.80 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB 
       12.23        16.67        14.24         0.85         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        88.93        97.45        56.19        15.35         1.87 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       64.80        79.66        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       10.82        54.90        91.73         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.56               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             67.36             140.81 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             7.805              9.830 
[1] "0.6 - 67.4 (7.8)"  "0.1 - 140.8 (9.8)"
[1] "hr=" "1.7"
D30V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED          0       1        8        15       14
  17P GAIN WILD-TYPE        1       1       78        78       78
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                 8                 78
  STAGE III               15                 78
  STAGE IV                14                 78
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  17P GAIN MUTATED          9  21   6
  17P GAIN WILD-TYPE       73 115  33
D30V4, multiclass
          clus
vv         17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1+T2                9                 73
  T3                     21                115
  T4                      6                 33
[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"
                    vv
clus                  N0  N1  N2  N3
  17P GAIN MUTATED    20   5  10   1
  17P GAIN WILD-TYPE 146  23  45   6
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               20                146
  N1                5                 23
  N2               10                 45
  N3                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  17P GAIN MUTATED    16   2  21
  17P GAIN WILD-TYPE 113   5 120
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               16                113
  M1                2                  5
  MX               21                120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    11  28
  17P GAIN WILD-TYPE  66 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     11   28
  17P GAIN WILD-TYPE   66  173
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               11                 66
  MALE                 28                173
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
D30V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       2                         1    32
  17P GAIN WILD-TYPE    29                        12   183
D30V11, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    2                 29
  BLACK OR AFRICAN AMERICAN                1                 12
  WHITE                                   32                183
[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"
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  35
  17P GAIN WILD-TYPE   5 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   35
  17P GAIN WILD-TYPE    5  223
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               35                223
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    52  38
  17Q GAIN WILD-TYPE 130  50
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                90                180 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                38                 50 
$`17Q GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O 
       40.08         2.66         6.74        12.39         6.58        12.16 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         8.35         8.25 
TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A47X TCGA-CU-A3YL TCGA-CU-A5W6 
        3.65        28.70         8.98         0.10        16.31         1.84 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IS 
       66.41        18.41       112.44         7.79         7.82        50.27 
TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A2PC 
       10.55        48.00        17.98        67.36        30.67        43.59 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6ME TCGA-FD-A3B5 
        0.49         0.59         0.56         1.38        12.99         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A5BR 
        6.87         4.01        24.30        13.18        46.78        13.38 
TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE 
        5.36        49.68         4.83        50.66        18.81         4.11 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-AA3F TCGA-GC-A3BM 
        2.07         2.20        15.19         3.25        19.46         2.89 
TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-AATO TCGA-GV-A3JV 
        2.10         7.36         6.41        11.31        10.65         4.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        5.69         7.63         7.79         6.67         6.41        19.07 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV 
        6.74        38.60         9.01         8.22         3.45         4.67 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HD 
        1.81         6.35        13.48        14.24         0.85        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9T0 TCGA-XF-AAML 
       56.19        15.35         1.87        17.88        26.27         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-YF-AA3M 
       91.73         2.96         8.32        56.48         7.96         9.04 

$`17Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20V 
        7.33        11.93        19.04        32.84        17.88         5.06 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       17.16         5.59         4.67        12.82         2.07        15.42 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
        9.99        28.41         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E 
       12.92         4.90         7.20         5.46         5.19         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
        2.53         2.14        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81        10.59       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         3.98         8.22        10.49        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67         8.28       140.81        64.18        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.68        41.06        15.35        26.17        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.53         0.66         0.82        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       12.89        15.68        12.43        11.93        15.88        45.93 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS 
       22.45         6.12        12.82         5.52        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        14.93        14.96        14.93         3.62        12.13 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       37.15        11.01         6.87         5.69         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD 
        6.87         2.66         6.28         6.38         9.30         6.71 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.66         4.01        10.85         7.13         3.48         4.08 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       17.26         7.04        20.12         0.85        52.67         6.94 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        1.12         2.66         7.73         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW 
        7.59         2.04        27.09         5.62         4.73         6.41 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WS 
        6.15         4.14        11.54         1.51         3.06         8.75 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        2.50         6.48        10.52         1.74         4.27         6.38 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HB 
        3.45        11.80        12.23        16.67         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
        6.58        97.45        64.80        79.66        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       21.04        28.24        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMX TCGA-XF-AAN1 
        2.10        92.98        10.82        54.90         6.77        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.10               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            112.44             140.81 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             8.645             10.175 
[1] "0.1 - 112.4 (8.6)"  "0.1 - 140.8 (10.2)"
[1] "hr=" "1.5"
D31V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED          0       1       24        28       38
  17Q GAIN WILD-TYPE        1       1       62        65       54
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                24                 62
  STAGE III               28                 65
  STAGE IV                38                 54
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  17Q GAIN MUTATED         27 43 16
  17Q GAIN WILD-TYPE       55 93 23
D31V4, multiclass
          clus
vv         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1+T2               27                 55
  T3                     43                 93
  T4                     16                 23
[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"
                    vv
clus                  N0  N1  N2  N3
  17Q GAIN MUTATED    45  11  25   2
  17Q GAIN WILD-TYPE 121  17  30   5
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               45                121
  N1               11                 17
  N2               25                 30
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED   41  3 48
  17Q GAIN WILD-TYPE 88  4 93
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               41                 88
  M1                3                  4
  MX               48                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    26  66
  17Q GAIN WILD-TYPE  51 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     26   66
  17Q GAIN WILD-TYPE   51  135
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               26                 51
  MALE                 66                135
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
D31V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       7                         3    73
  17Q GAIN WILD-TYPE    24                        10   142
D31V11, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    7                 24
  BLACK OR AFRICAN AMERICAN                3                 10
  WHITE                                   73                142
[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"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     2  82
  17Q GAIN WILD-TYPE   3 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   82
  17Q GAIN WILD-TYPE    3  176
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               82                176
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    48  30
  18P GAIN WILD-TYPE 134  58
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                78                192 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                30                 58 
$`18P GAIN MUTATED`
TCGA-BL-A3JM TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A42C TCGA-BT-A42E 
        6.74         5.06         8.35         5.59        28.70         9.99 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A2I2 
        8.98         1.94         0.43        12.92         5.46         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       87.32         7.82         8.22        48.00        30.67        15.35 
TCGA-E7-A6ME TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SR 
       12.99         8.94         6.87        11.93        45.93        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BV 
        1.97        14.93        12.13        13.38        11.01         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TF 
        6.84        27.45        49.68         6.28         4.11         2.07 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL 
        2.20        15.19         4.08         6.48        61.94        26.93 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GD-A2C5 
       35.24         0.85        19.46        15.91         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 
        2.10         2.20         7.36         6.41         7.59         2.04 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
        6.15         5.69         7.79         4.14         6.67        19.07 
TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 
        6.74         8.22         4.67         1.81         6.35         3.45 
TCGA-MV-A51V TCGA-R3-A69X TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9SX 
       13.48        14.24        45.04        88.93        15.35        23.64 
TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 
        2.24        54.90         7.63         2.96         6.77        56.48 

$`18P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.25        17.16         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
       12.82         2.07        15.42        28.41        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        0.10         4.90         7.20         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        9.34         2.53         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        8.91       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ 
        1.81        10.59       123.85         2.20         3.98        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.68        41.06        43.59        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.82        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.43        15.88        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43S 
       12.82         5.52        13.18        46.78        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C0 
       14.93         3.62        37.15         6.87         5.69         6.87 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.66         4.83         6.38        50.66        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.71         2.66         4.01        10.85         7.13         3.48 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        3.25        30.61         5.69        17.26         7.04        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       52.67         6.94         2.89         2.24        15.81         4.50 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R 
       14.07        17.75         1.12         3.12        20.98        11.31 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
       27.09         5.62         4.73        10.65         4.41         6.41 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF 
        7.63         6.41        11.54         1.51        38.60         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01         8.75         3.45         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.74         4.27         6.38        11.80        12.23        16.67 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
        0.85         3.75         6.58        97.45        56.19         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ 
       17.88        64.80        79.66        11.90        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       26.27        18.90        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       10.82        91.73         8.32        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         7.96         9.04 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.43               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             88.93             140.81 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              7.79              10.57 
[1] "0.4 - 88.9 (7.8)"   "0.1 - 140.8 (10.6)"
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED          0       0       23        27       27
  18P GAIN WILD-TYPE        1       2       63        66       65
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                23                 63
  STAGE III               27                 66
  STAGE IV                27                 65
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  18P GAIN MUTATED         18 38 13
  18P GAIN WILD-TYPE       64 98 26
D32V4, multiclass
          clus
vv         18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1+T2               18                 64
  T3                     38                 98
  T4                     13                 26
[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"
                    vv
clus                  N0  N1  N2  N3
  18P GAIN MUTATED    46   6  17   3
  18P GAIN WILD-TYPE 120  22  38   4
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               46                120
  N1                6                 22
  N2               17                 38
  N3                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  18P GAIN MUTATED   30  3 44
  18P GAIN WILD-TYPE 99  4 97
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               30                 99
  M1                3                  4
  MX               44                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    24  54
  18P GAIN WILD-TYPE  53 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     24   54
  18P GAIN WILD-TYPE   53  147
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               24                 53
  MALE                 54                147
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
D32V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       4                         6    63
  18P GAIN WILD-TYPE    27                         7   152
D32V11, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    4                 27
  BLACK OR AFRICAN AMERICAN                6                  7
  WHITE                                   63                152
[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"
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1  73
  18P GAIN WILD-TYPE   4 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   73
  18P GAIN WILD-TYPE    4  185
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               73                185
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    23  17
  18Q GAIN WILD-TYPE 159  71
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                40                230 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                17                 71 
$`18Q GAIN MUTATED`
TCGA-BL-A3JM TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
        6.74         5.06         5.59        28.70         9.99         8.98 
TCGA-C4-A0F0 TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3IN TCGA-DK-A6B6 TCGA-E5-A4TZ 
        1.94        16.14         7.79         8.22        30.67        15.35 
TCGA-FD-A3B6 TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV 
        6.87        19.79        14.93        12.13        13.38         5.36 
TCGA-FD-A5BZ TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P 
       27.45         9.30         4.11         2.20        15.19         6.48 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P 
       26.93        35.24         2.66         2.10         7.36         6.41 
TCGA-GU-A42Q TCGA-GV-A3QH TCGA-GV-A3QI TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-R3-A69X 
        7.59         7.79         4.14         1.81         3.45        14.24 
TCGA-XF-A8HB TCGA-XF-A8HG TCGA-XF-AAML TCGA-XF-AAN0 
       45.04        15.35         7.63        56.48 

$`18Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       14.89        14.96         8.35         8.25        17.16         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F6 
        4.67        12.82         2.07        15.42        28.41        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.07         0.10         0.10        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
      112.44        17.62        15.62         1.81        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS 
       87.32         2.20         3.98         7.82        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.68        41.06        43.59        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        0.82        12.99        14.33         1.22         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       15.68         8.94         4.01        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       45.93        24.30        22.45         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       13.18        46.78         1.97        22.98        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        37.15        11.01         6.87         5.69         6.84 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        6.87        49.68         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       50.66        18.81         6.71         2.07         2.66         4.01 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
       10.85         7.13         3.48         4.08         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       30.61         5.69        17.26         7.04        20.12         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       52.67         6.94        19.46         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 
        4.50        15.91        14.07        17.75         1.12         7.73 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        3.12        20.98         2.20        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        5.62         4.73        10.65         4.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        5.69         7.63         6.67         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51         6.74        38.60         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.75         3.45         4.67         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V 
        1.74         4.27         6.38         6.35        11.80        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HD 
       12.23        16.67         0.85         3.75         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       97.45        56.19         1.87        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN1 
       54.90        91.73         2.96         8.32         6.77        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.81               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             56.48             140.81 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             8.005             10.015 
[1] "1.8 - 56.5 (8.0)"   "0.1 - 140.8 (10.0)"
[1] "hr=" "1.6"
D33V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED          0       0       13        14       13
  18Q GAIN WILD-TYPE        1       2       73        79       79
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                13                 73
  STAGE III               14                 79
  STAGE IV                13                 79
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  18Q GAIN MUTATED          8  18   9
  18Q GAIN WILD-TYPE       74 118  30
D33V4, multiclass
          clus
vv         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1+T2                8                 74
  T3                     18                118
  T4                      9                 30
[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"
                    vv
clus                  N0  N1  N2  N3
  18Q GAIN MUTATED    24   3   9   1
  18Q GAIN WILD-TYPE 142  25  46   6
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               24                142
  N1                3                 25
  N2                9                 46
  N3                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED    15   1  24
  18Q GAIN WILD-TYPE 114   6 117
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0               15                114
  M1                1                  6
  MX               24                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    12  28
  18Q GAIN WILD-TYPE  65 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     12   28
  18Q GAIN WILD-TYPE   65  173
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               12                 65
  MALE                 28                173
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
D33V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         2    34
  18Q GAIN WILD-TYPE    31                        11   181
D33V11, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                 31
  BLACK OR AFRICAN AMERICAN                2                 11
  WHITE                                   34                181
[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"
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1  37
  18Q GAIN WILD-TYPE   4 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   37
  18Q GAIN WILD-TYPE    4  221
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               37                221
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    37  13
  19P GAIN WILD-TYPE 145  75
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                50                220 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                13                 75 
$`19P GAIN MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0F0 
        2.66         6.74        32.84         8.25        17.16         1.94 
TCGA-CF-A1HS TCGA-CF-A47V TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 
        0.43         0.10         0.10         5.46        16.31         2.53 
TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
       18.41         1.81       123.85        64.18        67.36        15.68 
TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3SR 
       30.67        26.17         0.56        12.99         1.22        19.79 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 
       14.93         3.62         2.07         2.66         2.20        15.19 
TCGA-FT-A3EE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A76B 
        3.25         0.85        52.67         1.12         7.73         7.36 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A40G TCGA-HQ-A2OE TCGA-S5-A6DX 
        4.73         4.41         6.41        19.07        38.60         0.85 
TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-AAN0 
        3.75         6.58        56.19        15.35        79.66        56.48 
TCGA-XF-AAN5 TCGA-YC-A8S6 
       75.39         4.83 

$`19P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33        12.39         6.58        11.93        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        5.06         8.35         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        2.07        15.42        28.70         9.99        28.41         8.98 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       23.01         0.46         0.69         0.13         0.07         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 
        0.10        12.92         4.90         7.20         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        9.34         2.14        66.41        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20         3.98         7.82         8.22        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
      140.81        48.00        17.98        41.56        76.60        41.06 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        24.66         0.10         0.49         0.53 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN 
        0.59         0.66         1.38         0.82        14.33         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       12.89        15.68         8.94         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       11.93        15.88        45.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
       12.82         5.52        13.18        46.78         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93        14.96        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
        6.87         5.36         5.69         6.84        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       49.68         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FD-A6TK 
       18.81         9.30         6.71         4.11         4.01        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13         3.48         4.08         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        5.69        26.93        35.24        17.26         7.04        20.12 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        19.46         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.91        14.07        17.75         2.66         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       20.98         2.20         6.41         7.59        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       27.09         5.62        10.65         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.79         4.14         6.67         6.41        11.54         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        6.74         3.06         9.01         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        4.67         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        4.27         6.38         6.35         3.45        11.80        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       12.23        16.67        14.24        45.04        88.93        97.45 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        1.87        17.88        64.80        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
        2.10        92.98        10.82        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 
        2.96         8.32         6.77        30.94        27.06         3.88 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       10.36         0.66         7.96         9.04 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.10               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            123.85             140.81 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              7.05               9.83 
[1] "0.1 - 123.8 (7.1)" "0.1 - 140.8 (9.8)"
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED          0       0       18        12       20
  19P GAIN WILD-TYPE        1       2       68        81       72
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                18                 68
  STAGE III               12                 81
  STAGE IV                20                 72
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  19P GAIN MUTATED         17  23  10
  19P GAIN WILD-TYPE       65 113  29
D34V4, multiclass
          clus
vv         19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1+T2               17                 65
  T3                     23                113
  T4                     10                 29
[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"
                    vv
clus                  N0  N1  N2  N3
  19P GAIN MUTATED    27   3  17   1
  19P GAIN WILD-TYPE 139  25  38   6
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               27                139
  N1                3                 25
  N2               17                 38
  N3                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  19P GAIN MUTATED    25   1  25
  19P GAIN WILD-TYPE 104   6 116
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               25                104
  M1                1                  6
  MX               25                116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    12  40
  19P GAIN WILD-TYPE  65 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     12   40
  19P GAIN WILD-TYPE   65  161
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               12                 65
  MALE                 40                161
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
D34V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED      11                         1    36
  19P GAIN WILD-TYPE    20                        12   179
D34V11, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                   11                 20
  BLACK OR AFRICAN AMERICAN                1                 12
  WHITE                                   36                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"
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  49
  19P GAIN WILD-TYPE   5 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   49
  19P GAIN WILD-TYPE    5  209
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               49                209
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    61  24
  19Q GAIN WILD-TYPE 121  64
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                85                185 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                24                 64 
$`19Q GAIN MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A20X 
        2.66         6.74        19.04        32.84         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 
       17.16         5.59        28.70         9.99         1.94        23.01 
TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 
        0.43         0.10         5.46        16.31         2.53        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL 
       18.41         8.91         1.81       123.85        87.32         3.98 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC 
       48.00        64.18        67.36        15.68        30.67        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV 
       15.35        26.17         0.59         0.56        12.99         1.22 
TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43X 
       24.30        19.79         1.97        22.98        14.93         3.62 
TCGA-FD-A5BZ TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK 
       27.45        18.81         2.07         2.66         2.20        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3VY 
       15.19         4.08         3.25        61.94        35.24         0.85 
TCGA-G2-AA3B TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A76B 
       52.67        15.91        14.07         1.12         7.73         7.36 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.31         4.73         4.41         6.41         5.69         7.63 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-R3-A69X 
        6.74        38.60         9.01         8.75         2.50        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG 
        0.85         3.75        45.04         6.58        56.19        15.35 
TCGA-XF-A9SI TCGA-XF-A9T3 TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YC-A8S6 
       79.66         2.24         6.77        56.48        75.39         4.83 
TCGA-YF-AA3M 
        9.04 

$`19Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
       40.08         7.33        12.39         6.58        11.93        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       17.88        19.50         5.06        14.89        14.96         8.35 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F 
        3.65         4.67        12.82         2.07        15.42        28.41 
TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        8.98         0.46         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
        0.07         0.10        12.92         4.90         7.20         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD 
        1.84         9.34         2.14        19.00       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK 
       16.14        17.62        15.62        10.59         7.79         2.20 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        10.49        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
        9.67         8.28        10.55       140.81        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       76.60        41.06        24.66         0.10         0.49         0.53 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 
        0.66         1.38         0.82        14.33         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.68         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        45.93        22.45         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR 
       13.18        46.78        14.93        14.96        12.13        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       37.15        11.01         6.87         5.36         5.69         6.84 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        6.87        49.68         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 
       50.66         9.30         6.71         4.11         4.01         7.13 
TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        3.48         6.48        30.61         5.69        26.93        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
        7.04        20.12         6.94        19.46         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.81         4.50        17.75         2.66         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 
       20.98         2.20         6.41         7.59         2.04        27.09 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        5.62        10.65         6.15         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE 
        6.41        19.07        11.54         1.51         3.06         8.22 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        3.45         4.67         6.48        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        4.27         6.38         6.35         3.45        11.80        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       12.23        16.67        88.93        97.45         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       64.80        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 
       54.90         7.63        91.73         2.96         8.32        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       27.06         3.88        10.36         0.66         7.96 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.10               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            123.85             140.81 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              9.04               9.30 
[1] "0.1 - 123.8 (9.0)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED          0       0       25        26       35
  19Q GAIN WILD-TYPE        1       2       61        67       57
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                25                 61
  STAGE III               26                 67
  STAGE IV                35                 57
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  19Q GAIN MUTATED         25 40 16
  19Q GAIN WILD-TYPE       57 96 23
D35V4, multiclass
          clus
vv         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1+T2               25                 57
  T3                     40                 96
  T4                     16                 23
[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"
                    vv
clus                  N0  N1  N2  N3
  19Q GAIN MUTATED    46   8  23   3
  19Q GAIN WILD-TYPE 120  20  32   4
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               46                120
  N1                8                 20
  N2               23                 32
  N3                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  19Q GAIN MUTATED   42  2 43
  19Q GAIN WILD-TYPE 87  5 98
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               42                 87
  M1                2                  5
  MX               43                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    25  63
  19Q GAIN WILD-TYPE  52 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     25   63
  19Q GAIN WILD-TYPE   52  138
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               25                 52
  MALE                 63                138
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
D35V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED      11                         4    64
  19Q GAIN WILD-TYPE    20                         9   151
D35V11, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                   11                 20
  BLACK OR AFRICAN AMERICAN                4                  9
  WHITE                                   64                151
[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"
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2  79
  19Q GAIN WILD-TYPE   3 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   79
  19Q GAIN WILD-TYPE    3  179
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               79                179
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   86 42
  20P GAIN WILD-TYPE 96 46
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               128                142 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                42                 46 
$`20P GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       22.29        11.97        98.33        40.08         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        6.58         5.06        14.89         5.06         8.35         8.25 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        3.65         2.07        28.70         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47T TCGA-CF-A47X 
        1.94        23.01         0.46         0.43         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 
       12.92         4.90         7.20         5.46         1.84         2.14 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
      130.88       112.44         1.81        10.59         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X2 
        2.20         3.98         8.22        20.02        10.55        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       67.36        15.68        30.67        43.59        15.35        26.17 
TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 
        0.59        12.99         1.22        12.89         6.87         4.01 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SQ 
       11.93        45.93        24.30        22.45        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       19.79         1.97        22.98        14.93         3.62        13.38 
TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD 
       11.01        27.45         4.83         6.38         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3ZE 
        4.11         2.07         2.20         4.01        10.85         3.48 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        3.25         6.48        61.94        30.61         5.69        35.24 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46         2.89         2.24        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A766 
        2.66         7.73         2.10         2.20         7.36         5.62 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WS 
        7.79         4.14        19.07         6.74         8.22         8.75 
TCGA-K4-A3WU TCGA-K4-A6FZ TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX 
        3.45         1.81        13.48        12.23        16.67         0.85 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SY 
       88.93        56.19        15.35         1.87        79.66        21.04 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMT 
        2.24        16.27        66.64        10.82        91.73         2.96 
TCGA-YC-A89H TCGA-YF-AA3M 
       10.36         9.04 

$`20P GAIN WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX 
       84.00       103.50         4.83         7.33        12.39        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U 
       19.04        32.84        12.16        17.88        19.50        14.96 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-CF-A27C 
       17.16         5.59         4.67        12.82        15.42         0.69 
TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A3QU TCGA-CU-A3YL 
        0.13         0.10         0.07         0.10         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.53        66.41        18.41        19.00         8.91 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IQ 
       16.14        17.62        15.62        87.32         7.82        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       50.27        21.30         9.67         8.28       140.81        48.00 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       64.18        41.56        76.60        41.06        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.49         0.53         0.56         0.66         1.38         0.82 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.33         0.46        15.68         8.94        12.43        15.88 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y 
        6.12        12.82         5.52        14.96        14.93        12.13 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       37.15         6.87         5.36         5.69         6.84         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG 
       49.68         2.66         6.28        50.66        18.81         2.66 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
       15.19         7.13         4.08        26.93        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3RB TCGA-GC-A3WC 
       20.12         0.85        52.67         6.94         4.50        17.75 
TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        1.12         3.12        20.98         6.41         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
        2.04        27.09         4.73         6.67         6.41        11.54 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AB 
        1.51        38.60         3.06         9.01         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
        6.48        10.52         1.74         4.27         6.38         6.35 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
        3.45        11.80        14.24         3.75        45.04         6.58 
TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
       97.45        17.88        64.80        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML 
       26.27        18.90         2.10        92.98        54.90         7.63 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        8.32         6.77        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88         4.83         0.66         7.96 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            130.88             140.81 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             8.550             10.505 
[1] "0.1 - 130.9 (8.6)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.1"
D36V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED          0       1       39        39       51
  20P GAIN WILD-TYPE        1       1       47        54       41
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                39                 47
  STAGE III               39                 54
  STAGE IV                51                 41
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  20P GAIN MUTATED         37 65 21
  20P GAIN WILD-TYPE       45 71 18
D36V4, multiclass
          clus
vv         20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1+T2               37                 45
  T3                     65                 71
  T4                     21                 18
[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"
                    vv
clus                 N0 N1 N2 N3
  20P GAIN MUTATED   73 14 31  6
  20P GAIN WILD-TYPE 93 14 24  1
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               73                 93
  N1               14                 14
  N2               31                 24
  N3                6                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED   57  5 70
  20P GAIN WILD-TYPE 72  2 71
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               57                 72
  M1                5                  2
  MX               70                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    35  97
  20P GAIN WILD-TYPE  42 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     35   97
  20P GAIN WILD-TYPE   42  104
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               35                 42
  MALE                 97                104
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
D36V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       9                         6   108
  20P GAIN WILD-TYPE    22                         7   107
D36V11, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    9                 22
  BLACK OR AFRICAN AMERICAN                6                  7
  WHITE                                  108                107
[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"
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1 123
  20P GAIN WILD-TYPE   4 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1  123
  20P GAIN WILD-TYPE    4  135
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO              123                135
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   102  48
  20Q GAIN WILD-TYPE  80  40
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               150                120 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                48                 40 
$`20Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13J 
       22.29        11.97       103.50        98.33        40.08         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20T 
        6.74         6.58        19.04        32.84        19.50        14.89 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E 
        8.35         8.25         3.65         2.07        28.70         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01         0.46         0.43 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.13         0.07         0.10        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
        5.46         1.84         2.14        66.41        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL 
      112.44         1.81        10.59         7.79       123.85         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X2 
        7.82         8.22        50.27        20.02        10.55        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       64.18        67.36        15.68        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B3 
       26.17         0.49         0.59        12.99         1.22        12.89 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP 
        6.87         4.01        11.93        45.93        24.30        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X 
       46.78        19.79         1.97        22.98        14.93         3.62 
TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
       13.38        11.01        27.45         6.87        49.68         4.83 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
        6.38         9.30         6.71         4.11         2.07         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P 
        4.01        10.85        15.19         3.48         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B 
       61.94        30.61         5.69        35.24         0.85        52.67 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46         2.89         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A76B 
       14.07         1.12         2.66         7.73         2.10         7.36 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
        7.59        11.31         5.62        10.65         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E 
        6.15         5.69         7.63         7.79         4.14         6.41 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC 
        6.74        38.60         3.06         8.75         3.45         6.48 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX 
        1.81         3.45        13.48        12.23        16.67         0.85 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SI 
       45.04        88.93        56.19        15.35         1.87        79.66 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       23.64        21.04         2.24        16.27        66.64         2.10 
TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-YF-AA3M 
       10.82        91.73         2.96         6.77        30.94         9.04 

$`20Q GAIN WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O 
       84.00         4.83         7.33        12.39        11.93        12.16 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB 
       17.88         5.06        14.96         5.06        17.16         5.59 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W 
        4.67        12.82        15.42         0.69         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA 
        0.10         5.19        16.31         9.34         2.53        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK 
        8.91        16.14        17.62        15.62        87.32         2.20 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       10.49        21.30         9.67         8.28       140.81        48.00 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       41.56        76.60        41.06        24.66         0.10         0.53 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN 
        0.56         0.66         1.38         0.82        14.33         0.46 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM 
       15.68         8.94        12.43        15.88        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS 
       12.82         5.52        14.96        14.93        12.13        37.15 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62P 
        6.87         5.36         5.69         6.84         2.66         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EL 
       50.66        18.81         2.66         7.13         4.08        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3WC TCGA-GD-A3OQ 
       17.26         7.04        20.12         6.94        17.75         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 
       20.98         2.20         6.41         2.04        27.09         4.73 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE 
        6.67        19.07        11.54         1.51         9.01         8.22 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        4.67         2.50        10.52         1.74         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HE 
        6.35        11.80        14.24         3.75         6.58        97.45 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       17.88        64.80        11.90        28.24        26.27        18.90 
TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 
       92.98        54.90         7.63         8.32        56.48        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            130.88             140.81 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             9.010              9.505 
[1] "0.1 - 130.9 (9.0)" "0.1 - 140.8 (9.5)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED          0       1       49        47       54
  20Q GAIN WILD-TYPE        1       1       37        46       38
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                49                 37
  STAGE III               47                 46
  STAGE IV                54                 38
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  20Q GAIN MUTATED         46 75 21
  20Q GAIN WILD-TYPE       36 61 18
D37V4, multiclass
          clus
vv         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1+T2               46                 36
  T3                     75                 61
  T4                     21                 18
[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"
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN MUTATED   87 15 34  6
  20Q GAIN WILD-TYPE 79 13 21  1
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               87                 79
  N1               15                 13
  N2               34                 21
  N3                6                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   67  4 82
  20Q GAIN WILD-TYPE 62  3 59
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               67                 62
  M1                4                  3
  MX               82                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    43 111
  20Q GAIN WILD-TYPE  34  90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     43  111
  20Q GAIN WILD-TYPE   34   90
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               43                 34
  MALE                111                 90
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
D37V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED      13                         6   121
  20Q GAIN WILD-TYPE    18                         7    94
D37V11, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                   13                 18
  BLACK OR AFRICAN AMERICAN                6                  7
  WHITE                                  121                 94
[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"
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     2 140
  20Q GAIN WILD-TYPE   3 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2  140
  20Q GAIN WILD-TYPE    3  118
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              140                118
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    55  21
  21Q GAIN WILD-TYPE 127  67
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                76                194 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                 67 
$`21Q GAIN MUTATED`
TCGA-2F-A9KQ TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W 
       84.00        40.08         2.66        12.39        32.84         8.35 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.16         3.65         2.07        28.70         8.98         1.94 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47V TCGA-CU-A3KJ TCGA-DK-A1A3 TCGA-DK-A1A7 
        0.43         0.69         0.10         5.46         2.53        18.41 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 
       50.27         9.67        48.00        17.98        67.36        15.68 
TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       15.35         0.49        12.99         6.87         4.01        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A5BZ 
       24.30        12.82        13.18        19.79        22.98        27.45 
TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.87         4.83         6.28         9.30         4.11         2.66 
TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3VY TCGA-G2-AA3B 
        2.20         4.08        61.94         5.69         0.85        52.67 
TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JX 
        2.89         7.73         2.10         6.41         6.41         6.15 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A6FZ 
        7.63         6.41        19.07         6.74         3.45         1.81 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HH 
        4.27         6.35        13.48        88.93        56.19         1.87 
TCGA-XF-A9SZ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-YF-AA3M 
       28.24        91.73         6.77         9.04 

$`21Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I 
       22.29        11.97       103.50        98.33         4.83         7.33 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        11.93        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        5.59         4.67        12.82        15.42         9.99        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X 
       23.01         0.46         0.13         0.07         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
        0.10        12.92         4.90         7.20         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
        1.84         9.34         2.14        66.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I2 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
        7.79         8.22        10.49        21.30        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
       10.55       140.81        64.18        41.56        76.60        41.06 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       30.67        43.59        26.17        24.66         0.10         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        0.59         0.56         0.66         1.38         0.82        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
        1.22         0.46        12.89        15.68         8.94        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ 
       11.93        15.88        22.45         6.12         5.52        46.78 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
        1.97        14.93        14.96        14.93         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       13.38        37.15        11.01         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        6.84        49.68         2.66         6.38        50.66        18.81 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.71         2.07         4.01        10.85        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
        3.48         3.25         6.48        30.61        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
       17.26         7.04        20.12         6.94        19.46         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
        2.66         3.12        20.98         2.20         7.36         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       11.31         2.04        27.09         5.62         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA 
        4.41         5.69         7.79         4.14         6.67        11.54 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51        38.60         3.06         9.01         8.22         8.75 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P 
        4.67         2.50         6.48        10.52         1.74         6.38 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        3.45        11.80        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HI 
        3.75        45.04         6.58        97.45        15.35        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
       64.80        79.66        11.90        23.64        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       10.82        54.90         7.63         2.96         8.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L 
        0.66         7.96 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.10               0.07 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            123.85             140.81 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             7.775             10.505 
[1] "0.1 - 123.8 (7.8)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.2"
D38V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED          0       1       24        22       28
  21Q GAIN WILD-TYPE        1       1       62        71       64
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                24                 62
  STAGE III               22                 71
  STAGE IV                28                 64
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  21Q GAIN MUTATED         21 40  8
  21Q GAIN WILD-TYPE       61 96 31
D38V4, multiclass
          clus
vv         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1+T2               21                 61
  T3                     40                 96
  T4                      8                 31
[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"
                    vv
clus                  N0  N1  N2  N3
  21Q GAIN MUTATED    41   7  20   0
  21Q GAIN WILD-TYPE 125  21  35   7
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               41                125
  N1                7                 21
  N2               20                 35
  N3                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  21Q GAIN MUTATED    38   2  36
  21Q GAIN WILD-TYPE  91   5 105
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0               38                 91
  M1                2                  5
  MX               36                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    17  60
  21Q GAIN WILD-TYPE  60 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     17   60
  21Q GAIN WILD-TYPE   60  141
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               17                 60
  MALE                 60                141
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
D38V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       7                         3    61
  21Q GAIN WILD-TYPE    24                        10   154
D38V11, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    7                 24
  BLACK OR AFRICAN AMERICAN                3                 10
  WHITE                                   61                154
[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"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2  71
  21Q GAIN WILD-TYPE   3 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2   71
  21Q GAIN WILD-TYPE    3  187
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               71                187
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    22  14
  22Q GAIN WILD-TYPE 160  74
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                36                234 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                14                 74 
$`22Q GAIN MUTATED`
TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20W TCGA-BT-A2LB TCGA-DK-A1A6 
      103.50        40.08         6.58         8.35         5.59        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX 
       18.41       112.44        87.32        50.27        20.02        10.55 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-FD-A3B7 TCGA-FD-A62O TCGA-G2-A2EO TCGA-G2-A2ES 
        0.49         0.59         4.01         4.83        35.24        17.26 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JZ 
        2.89         2.24        14.07         4.73         4.41         5.69 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A2OE TCGA-LT-A5Z6 
        7.79         4.14         6.67         6.41        38.60         3.45 
TCGA-S5-A6DX TCGA-XF-A9SI TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
        0.85        79.66         7.63        91.73         8.32         6.77 

$`22Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I 
       22.29        11.97        84.00        98.33         4.83         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66         6.74        12.39        11.93        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        5.06         8.25        17.16         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        2.07        15.42        28.70         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        1.94        23.01         0.46         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        9.34         2.53         2.14        19.00         8.91       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
      123.85         2.20         3.98         7.82         8.22        10.49 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       21.30         9.67         8.28       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       30.67        43.59        15.35        26.17        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.53         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.33         1.22         0.46        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        6.87        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79         1.97        22.98        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        12.13        13.38        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         6.84        27.45         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.66         6.28         6.38        50.66        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.71         4.11         2.07         2.66         2.20         4.01 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
       10.85        15.19         7.13         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        6.48        61.94        30.61         5.69        26.93         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
       20.12         0.85        52.67         6.94        19.46        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        17.75         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO 
        7.59        11.31         2.04        27.09         5.62        10.65 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        6.41         6.15         7.63        19.07        11.54         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        6.74         3.06         9.01         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        4.67         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        4.27         6.38         6.35        11.80        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       16.67        14.24         3.75        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       97.45        56.19        15.35         1.87        17.88        64.80 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       54.90         2.96        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         7.96         9.04 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.49               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            112.44             140.81 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              7.71               9.83 
[1] "0.5 - 112.4 (7.7)" "0.1 - 140.8 (9.8)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED          0       1       12        12       10
  22Q GAIN WILD-TYPE        1       1       74        81       82
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                12                 74
  STAGE III               12                 81
  STAGE IV                10                 82
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  22Q GAIN MUTATED         13  16   4
  22Q GAIN WILD-TYPE       69 120  35
D39V4, multiclass
          clus
vv         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1+T2               13                 69
  T3                     16                120
  T4                      4                 35
[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"
                    vv
clus                  N0  N1  N2  N3
  22Q GAIN MUTATED    20   3   7   1
  22Q GAIN WILD-TYPE 146  25  48   6
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               20                146
  N1                3                 25
  N2                7                 48
  N3                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  22Q GAIN MUTATED    18   0  18
  22Q GAIN WILD-TYPE 111   7 123
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               18                111
  M1                0                  7
  MX               18                123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     9  27
  22Q GAIN WILD-TYPE  68 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      9   27
  22Q GAIN WILD-TYPE   68  174
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                9                 68
  MALE                 27                174
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
D39V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       2                         2    30
  22Q GAIN WILD-TYPE    29                        11   185
D39V11, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    2                 29
  BLACK OR AFRICAN AMERICAN                2                 11
  WHITE                                   30                185
[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"
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  32
  22Q GAIN WILD-TYPE   5 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   32
  22Q GAIN WILD-TYPE    5  226
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               32                226
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    15  13
  XQ GAIN WILD-TYPE 167  75
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               242 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               13                75 
$`XQ GAIN MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q 
        2.66         6.74         6.58        32.84        17.88        19.50 
TCGA-BT-A42C TCGA-CF-A1HS TCGA-CU-A0YN TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-FD-A3B6 
       28.70         0.43        12.92        66.41        16.14         6.87 
TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A6TC TCGA-FD-A6TI TCGA-FT-A3EE TCGA-GC-A3I6 
       19.79        14.93         9.30         4.01         3.25         2.24 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-MV-A51V 
        2.66         7.73        20.98         5.69         7.79        13.48 
TCGA-XF-A8HI TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMX 
       17.88        66.64         7.63         6.77 

$`XQ GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
       40.08         7.33        12.39        11.93        19.04        12.16 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       15.42         9.99        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.10         0.10         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
       16.31         1.84         9.34         2.53         2.14        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00         8.91       130.88       112.44        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        3.98         7.82         8.22        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       20.02         9.67         8.28        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       41.06        30.67        43.59        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         0.53         0.59         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        1.38         0.82        12.99        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       12.89        15.68         8.94         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       15.88        45.93        24.30        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S 
        5.52        13.18        46.78         1.97        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93         3.62        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
        6.87         5.36         5.69         6.84        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       49.68         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.71         4.11         2.07         2.66         2.20 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P 
       10.85        15.19         7.13         3.48         4.08         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
        7.04        20.12         0.85        52.67         6.94        19.46 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.89        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        1.12         2.10         3.12         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.59        11.31         2.04        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QI 
       10.65         4.41         6.41         6.15         7.63         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.67         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        4.67         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
        4.27         6.38         6.35         3.45        11.80        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       16.67        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SH 
       88.93        97.45        56.19        15.35         1.87        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       79.66        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        16.27         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 
       54.90        91.73         2.96         8.32        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.43              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            66.64            140.81 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            8.545             9.190 
[1] "0.4 - 66.6 (8.5)"  "0.1 - 140.8 (9.2)"
[1] "hr=" "1.5"
D40V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED          0       0        8        11        9
  XQ GAIN WILD-TYPE        1       2       78        82       83
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                8                78
  STAGE III              11                82
  STAGE IV                9                83
[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"
                   vv
clus                T0+T1+T2  T3  T4
  XQ GAIN MUTATED          7  12   7
  XQ GAIN WILD-TYPE       75 124  32
D40V4, multiclass
          clus
vv         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1+T2               7                75
  T3                    12               124
  T4                     7                32
[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"
                   vv
clus                 N0  N1  N2  N3
  XQ GAIN MUTATED    18   3   5   1
  XQ GAIN WILD-TYPE 148  25  50   6
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              18               148
  N1               3                25
  N2               5                50
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  XQ GAIN MUTATED    12   0  17
  XQ GAIN WILD-TYPE 117   7 124
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              12               117
  M1               0                 7
  MX              17               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    10  19
  XQ GAIN WILD-TYPE  67 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     10   19
  XQ GAIN WILD-TYPE   67  182
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              10                67
  MALE                19               182
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
D40V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       2                         2    23
  XQ GAIN WILD-TYPE    29                        11   192
D40V11, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   2                29
  BLACK OR AFRICAN AMERICAN               2                11
  WHITE                                  23               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  27
  XQ GAIN WILD-TYPE   5 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   27
  XQ GAIN WILD-TYPE    5  231
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              27               231
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    13   6
  1P LOSS WILD-TYPE 169  82
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               19               251 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                82 
$`1P LOSS MUTATED`
TCGA-2F-A9KO TCGA-BT-A3PK TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A3IQ 
       22.29         2.07         0.10         4.90         7.20        10.49 
TCGA-DK-A3IT TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-FD-A62P TCGA-FD-A6TE TCGA-FJ-A3ZE 
       21.30        30.67        43.59         6.28         4.11         3.48 
TCGA-GU-A766 TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-XF-A8HF 
        5.62         3.06         8.75        12.23         0.85        56.19 
TCGA-XF-A8HG 
       15.35 

$`1P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C 
        5.59         3.65         4.67        12.82        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        9.99        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        0.10        12.92         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        9.34         2.53         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        8.91       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
        3.98         7.82         8.22        50.27        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        8.28        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ 
       41.56        76.60        67.36        15.68        41.06        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       26.17        24.66         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66         1.38         0.82        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22         0.46        12.89        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79         1.97        22.98        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        12.13        13.38        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         6.84        27.45         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.66         4.83         6.38        50.66        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        6.71         2.07         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       15.19         7.13         4.08         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12         0.85        52.67         6.94        19.46         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        1.12         2.66         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36         6.41         7.59        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       27.09         4.73        10.65         4.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        5.69         7.63         7.79         4.14         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND 
       19.07        11.54         1.51         6.74        38.60         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.22         3.45         4.67         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        1.74         1.81         4.27         6.38         6.35         3.45 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB 
       11.80        13.48        16.67        14.24         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
        6.58        88.93        97.45         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       79.66        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       10.82        54.90         7.63        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        6.77        56.48        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       10.36         4.83         0.66         7.96         9.04 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.10              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            56.19            140.81 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             7.20              9.34 
[1] "0.1 - 56.2 (7.2)"  "0.1 - 140.8 (9.3)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED          0       0        6         6        7
  1P LOSS WILD-TYPE        1       2       80        87       85
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                6                80
  STAGE III               6                87
  STAGE IV                7                85
[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"
                   vv
clus                T0+T1+T2  T3  T4
  1P LOSS MUTATED          7   9   1
  1P LOSS WILD-TYPE       75 127  38
D41V4, multiclass
          clus
vv         1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1+T2               7                75
  T3                     9               127
  T4                     1                38
[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"
                   vv
clus                 N0  N1  N2  N3
  1P LOSS MUTATED    11   2   4   1
  1P LOSS WILD-TYPE 155  26  51   6
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              11               155
  N1               2                26
  N2               4                51
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  1P LOSS MUTATED     7   1  11
  1P LOSS WILD-TYPE 122   6 130
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               7               122
  M1               1                 6
  MX              11               130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2  17
  1P LOSS WILD-TYPE  75 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   17
  1P LOSS WILD-TYPE   75  184
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               2                75
  MALE                17               184
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
D41V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         0    16
  1P LOSS WILD-TYPE    30                        13   199
D41V11, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                30
  BLACK OR AFRICAN AMERICAN               0                13
  WHITE                                  16               199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  17
  1P LOSS WILD-TYPE   5 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   17
  1P LOSS WILD-TYPE    5  241
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              17               241
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    12   8
  1Q LOSS WILD-TYPE 170  80
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               250 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8                80 
$`1Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-BT-A3PK TCGA-CU-A0YO TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT 
       22.29         2.07         4.90         1.81        10.49        21.30 
TCGA-DK-A3X1 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-FD-A62P TCGA-FD-A62S 
       48.00        30.67        43.59         0.49         6.28         6.38 
TCGA-FD-A6TE TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GU-A766 TCGA-GV-A3QH TCGA-S5-A6DX 
        4.11        20.12        15.91         5.62         7.79         0.85 
TCGA-XF-A8HC TCGA-XF-A8HF 
        6.58        56.19 

$`1Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C 
        5.59         3.65         4.67        12.82        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        9.99        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.10         0.10        12.92         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84         9.34         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU 
        2.20         3.98         7.82         8.22        50.27        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67         8.28        10.55       140.81        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ 
       41.56        76.60        67.36        15.68        41.06        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       26.17        24.66         0.10         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV 
        0.66         1.38         0.82        12.99        14.33         1.22 
TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        0.46        12.89        15.68         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.43        11.93        15.88        45.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
        6.12        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        1.97        22.98        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       12.13        13.38        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         6.84        27.45         6.87        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF 
        4.83        50.66        18.81         9.30         6.71         2.07 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.66         2.20         4.01        10.85        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        3.48         4.08         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
        5.69        26.93        35.24        17.26         7.04         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       52.67         6.94        19.46         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        14.07        17.75         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO 
        7.59        11.31         2.04        27.09         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
        4.41         6.41         6.15         5.69         7.63         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.67         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        4.67         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        4.27         6.38         6.35         3.45        11.80        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD 
       12.23        16.67        14.24         3.75        45.04        88.93 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       97.45        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        91.73         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.49              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            56.19            140.81 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            7.185             9.320 
[1] "0.5 - 56.2 (7.2)"  "0.1 - 140.8 (9.3)"
[1] "hr=" "1.3"
D42V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED          0       0        8         5        7
  1Q LOSS WILD-TYPE        1       2       78        88       85
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                8                78
  STAGE III               5                88
  STAGE IV                7                85
[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"
                   vv
clus                T0+T1+T2  T3  T4
  1Q LOSS MUTATED          6  10   1
  1Q LOSS WILD-TYPE       76 126  38
D42V4, multiclass
          clus
vv         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1+T2               6                76
  T3                    10               126
  T4                     1                38
[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"
                   vv
clus                 N0  N1  N2  N3
  1Q LOSS MUTATED     9   2   5   0
  1Q LOSS WILD-TYPE 157  26  50   7
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               9               157
  N1               2                26
  N2               5                50
  N3               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  1Q LOSS MUTATED     8   0  12
  1Q LOSS WILD-TYPE 121   7 129
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               8               121
  M1               0                 7
  MX              12               129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     4  16
  1Q LOSS WILD-TYPE  73 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4   16
  1Q LOSS WILD-TYPE   73  185
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               4                73
  MALE                16               185
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
D42V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       2                         1    17
  1Q LOSS WILD-TYPE    29                        12   198
D42V11, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   2                29
  BLACK OR AFRICAN AMERICAN               1                12
  WHITE                                  17               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"
D42V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  20
  1Q LOSS WILD-TYPE   5 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   20
  1Q LOSS WILD-TYPE    5  238
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              20               238
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    18  10
  2P LOSS WILD-TYPE 164  78
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               28               242 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10                78 
$`2P LOSS MUTATED`
TCGA-2F-A9KW TCGA-BT-A20N TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A2HX TCGA-DK-A3IS 
        4.83        32.84         5.46         5.19         1.81        50.27 
TCGA-DK-A3IV TCGA-E5-A4U1 TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A5BR TCGA-FJ-A3ZE 
        9.67        26.17         8.94        24.30        13.38         3.48 
TCGA-G2-A2EL TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GU-AATO TCGA-GV-A3JV 
       26.93        52.67        15.81         1.12        10.65         4.41 
TCGA-GV-A3JW TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A5RJ TCGA-MV-A51V TCGA-S5-AA26 
        6.41         8.22         3.45         1.74        13.48         3.75 
TCGA-XF-A8HH TCGA-XF-AAMF TCGA-XF-AAMT TCGA-YF-AA3M 
        1.87        10.82         2.96         9.04 

$`2P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 
       22.29        11.97        84.00       103.50        98.33        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       19.04        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        3.65         4.67        12.82         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        9.99        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL 
        0.10         0.10        12.92         4.90         7.20        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84         9.34         2.53         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        3.98         7.82         8.22        10.49        21.30        20.02 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        8.28        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        24.66         0.10         0.49         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.59         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
       14.33         1.22         0.46        12.89        15.68         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
        4.01        12.43        11.93        15.88        45.93        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
        6.12        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        1.97        22.98        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       12.13        37.15        11.01         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        6.84        27.45         6.87        49.68         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28         6.38        50.66        18.81         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        4.11         2.07         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       15.19         7.13         4.08         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61         5.69        35.24        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB 
        0.85         6.94        19.46         2.89         2.24         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07        17.75         2.66         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36         6.41         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JX 
       11.31         2.04        27.09         5.62         4.73         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        5.69         7.63         7.79         4.14         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        11.54         1.51         6.74        38.60         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01         8.75         4.67         2.50         6.48        10.52 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81         4.27         6.38         6.35         3.45        11.80 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HC 
       12.23        16.67        14.24         0.85        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH 
       88.93        97.45        56.19        15.35        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       79.66        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       54.90         7.63        91.73         8.32         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L 
        0.66         7.96 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1.12              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            52.67            140.81 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            8.580             9.665 
[1] "1.1 - 52.7 (8.6)"  "0.1 - 140.8 (9.7)"
[1] "hr=" "1.4"
D43V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED          0       0       11         8       11
  2P LOSS WILD-TYPE        1       2       75        85       81
D43V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               11                75
  STAGE III               8                85
  STAGE IV               11                81
[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"
                   vv
clus                T0+T1+T2  T3  T4
  2P LOSS MUTATED         12  12   3
  2P LOSS WILD-TYPE       70 124  36
D43V4, multiclass
          clus
vv         2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1+T2              12                70
  T3                    12               124
  T4                     3                36
[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"
                   vv
clus                 N0  N1  N2  N3
  2P LOSS MUTATED    16   4   6   1
  2P LOSS WILD-TYPE 150  24  49   6
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              16               150
  N1               4                24
  N2               6                49
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  2P LOSS MUTATED    14   1  15
  2P LOSS WILD-TYPE 115   6 126
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0              14               115
  M1               1                 6
  MX              15               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"
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     5  25
  2P LOSS WILD-TYPE  72 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5   25
  2P LOSS WILD-TYPE   72  176
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               5                72
  MALE                25               176
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
D43V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       2                         2    21
  2P LOSS WILD-TYPE    29                        11   194
D43V11, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   2                29
  BLACK OR AFRICAN AMERICAN               2                11
  WHITE                                  21               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"
D43V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  26
  2P LOSS WILD-TYPE   4 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   26
  2P LOSS WILD-TYPE    4  232
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              26               232
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    38  21
  2Q LOSS WILD-TYPE 144  67
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               59               211 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               21                67 
$`2Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V 
       22.29        84.00         4.83        32.84        14.89         5.06 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YN 
       17.16         4.67         8.98         0.43         0.10        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A2HX TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IV 
        5.46         5.19         1.81         2.20        50.27         9.67 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A541 
       17.98        64.18        67.36        30.67        26.17         0.59 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BV 
       15.68         8.94        24.30        19.79        13.38         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FT-A61P 
       27.45         2.66         4.11         2.07         2.20         6.48 
TCGA-G2-A2EL TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GU-AATO 
       26.93        52.67        15.81        14.07         2.10        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QK TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WU 
        4.41         6.41         6.67        38.60         8.22         3.45 
TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-S5-AA26 TCGA-XF-A8HG 
        6.48         1.74         3.45        13.48         3.75        15.35 
TCGA-XF-A8HH TCGA-XF-AAMF TCGA-XF-AAMT TCGA-YF-AA3L TCGA-YF-AA3M 
        1.87        10.82         2.96         7.96         9.04 

$`2Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       11.97       103.50        98.33        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        6.74        12.39         6.58        11.93        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        5.59         3.65        12.82         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
        9.99        28.41         1.94        23.01         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO 
        0.13         0.07         0.10         0.07         0.10         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20        16.31         1.84         9.34         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
       87.32         3.98         7.82         8.22        10.49        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW 
       20.02         8.28        10.55       140.81        48.00        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       76.60        15.68        41.06        43.59        15.35        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         0.49         0.53         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        0.82        12.99        14.33         1.22         0.46        12.89 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        6.87         4.01        12.43        11.93        15.88        45.93 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        1.97        22.98        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       12.13        37.15        11.01         6.87         5.69         6.84 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        6.87        49.68         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
       18.81         9.30         6.71         2.66         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
       15.19         7.13         3.48         4.08         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61         5.69        35.24        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB 
        0.85         6.94        19.46         2.89         2.24         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       15.91        17.75         1.12         2.66         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36         6.41         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3JZ 
        2.04        27.09         5.62         4.73         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        7.63         7.79         4.14         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV 
        1.51         6.74         3.06         9.01         8.75         4.67 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
        2.50        10.52         1.81         4.27         6.38         6.35 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB 
       11.80        12.23        16.67        14.24         0.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH 
        6.58        88.93        97.45        56.19        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       79.66        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       54.90         7.63        91.73         8.32         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC 
        0.66 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.10              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            84.00            140.81 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             8.94              9.99 
[1] "0.1 - 84.0 (8.9)"   "0.1 - 140.8 (10.0)"
[1] "hr=" "1.3"
D44V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED          0       0       19        16       24
  2Q LOSS WILD-TYPE        1       2       67        77       68
D44V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               19                67
  STAGE III              16                77
  STAGE IV               24                68
[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"
                   vv
clus                T0+T1+T2  T3  T4
  2Q LOSS MUTATED         19  30   8
  2Q LOSS WILD-TYPE       63 106  31
D44V4, multiclass
          clus
vv         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1+T2              19                63
  T3                    30               106
  T4                     8                31
[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"
                   vv
clus                 N0  N1  N2  N3
  2Q LOSS MUTATED    31   7  18   0
  2Q LOSS WILD-TYPE 135  21  37   7
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              31               135
  N1               7                21
  N2              18                37
  N3               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  2Q LOSS MUTATED    28   2  31
  2Q LOSS WILD-TYPE 101   5 110
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              28               101
  M1               2                 5
  MX              31               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    17  44
  2Q LOSS WILD-TYPE  60 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     17   44
  2Q LOSS WILD-TYPE   60  157
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              17                60
  MALE                44               157
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
D44V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       6                         4    43
  2Q LOSS WILD-TYPE    25                         9   172
D44V11, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   6                25
  BLACK OR AFRICAN AMERICAN               4                 9
  WHITE                                  43               172
[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"
D44V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  54
  2Q LOSS WILD-TYPE   3 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   54
  2Q LOSS WILD-TYPE    3  204
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              54               204
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    25  10
  3P LOSS WILD-TYPE 157  78
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               35               235 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10                78 
$`3P LOSS MUTATED`
TCGA-2F-A9KR TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 
      103.50         5.06         8.25        28.70         8.98         1.94 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A2I2 
        0.43        12.92         5.46        66.41         8.91         7.79 
TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A6B5 TCGA-E7-A4IJ TCGA-E7-A7DV TCGA-FD-A3B4 
        7.82        10.55        41.06         0.49         1.22        15.68 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A43Y TCGA-FD-A5C1 TCGA-G2-A3IB TCGA-G2-AA3B 
        6.87        11.93        12.13        49.68         7.04        52.67 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A767 TCGA-K4-A4AC TCGA-XF-A8HD 
        4.50        17.75         1.12         4.73         6.48        88.93 
TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-AAMT TCGA-XF-AAMW TCGA-YF-AA3M 
       26.27        66.64         2.96         8.32         9.04 

$`3P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       22.29        11.97        84.00        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       14.89        14.96         8.35        17.16         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82         2.07        15.42         9.99        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.46         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
        0.07         0.10         0.10         4.90         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
       16.31         1.84         9.34         2.53         2.14        18.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59       123.85        87.32         2.20         3.98 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
        8.28       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       76.60        67.36        15.68        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       26.17        24.66         0.10         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        0.66         1.38         0.82        12.99        14.33         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       12.89         8.94         4.01        12.43        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79         1.97        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.93         3.62        13.38        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
        5.36         5.69         6.84        27.45         6.87         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        4.83         6.28         6.38        50.66        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.71         4.11         2.07         2.66         2.20         4.01 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
       10.85        15.19         7.13         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       17.26        20.12         0.85         6.94        19.46         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 
        2.24        15.81        15.91        14.07         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO 
        7.59        11.31         2.04        27.09         5.62        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.14         6.67         6.41        19.07        11.54         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        6.74        38.60         3.06         9.01         8.22         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        3.45         4.67         2.50        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        4.27         6.38         6.35         3.45        11.80        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB 
       12.23        16.67        14.24         0.85         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
        6.58        97.45        56.19        15.35         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       64.80        79.66        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        16.27         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
       54.90         7.63        91.73         6.77        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L 
        7.96 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.43              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           103.50            140.81 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             8.91              9.67 
[1] "0.4 - 103.5 (8.9)" "0.1 - 140.8 (9.7)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED          0       0       10        12       13
  3P LOSS WILD-TYPE        1       2       76        81       79
D45V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               10                76
  STAGE III              12                81
  STAGE IV               13                79
[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"
                   vv
clus                T0+T1+T2  T3  T4
  3P LOSS MUTATED         10  17   7
  3P LOSS WILD-TYPE       72 119  32
D45V4, multiclass
          clus
vv         3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1+T2              10                72
  T3                    17               119
  T4                     7                32
[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"
                   vv
clus                 N0  N1  N2  N3
  3P LOSS MUTATED    21   4   5   2
  3P LOSS WILD-TYPE 145  24  50   5
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              21               145
  N1               4                24
  N2               5                50
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  3P LOSS MUTATED    18   1  17
  3P LOSS WILD-TYPE 111   6 124
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              18               111
  M1               1                 6
  MX              17               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    14  22
  3P LOSS WILD-TYPE  63 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     14   22
  3P LOSS WILD-TYPE   63  179
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              14                63
  MALE                22               179
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
D45V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       3                         4    25
  3P LOSS WILD-TYPE    28                         9   190
D45V11, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   3                28
  BLACK OR AFRICAN AMERICAN               4                 9
  WHITE                                  25               190
[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"
D45V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  31
  3P LOSS WILD-TYPE   4 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   31
  3P LOSS WILD-TYPE    4  227
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              31               227
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    10   4
  3Q LOSS WILD-TYPE 172  84
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               14               256 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                84 
$`3Q LOSS MUTATED`
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CU-A0YN TCGA-DK-A3WX TCGA-DK-A6B5 TCGA-E7-A7DV 
        8.98         1.94        12.92        10.55        41.06         1.22 
TCGA-FD-A43Y TCGA-FD-A5C1 TCGA-G2-A3IB TCGA-G2-AA3B TCGA-GU-A767 TCGA-K4-A4AC 
       12.13        49.68         7.04        52.67         4.73         6.48 
TCGA-XF-A8HD TCGA-XF-A9T0 
       88.93        26.27 

$`3Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
       15.42        28.70         9.99        28.41        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.10         0.10         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84         9.34         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20         3.98         7.82         8.22        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       50.27        21.30        20.02         9.67         8.28       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       15.68        30.67        43.59        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         0.53         0.59         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 
        1.38         0.82        12.99        14.33         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.68         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       15.88        45.93        24.30        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        13.18        46.78        19.79         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       14.93        14.96        14.93         3.62        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01         6.87         5.36         5.69         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        6.87         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         9.30         6.71         4.11         2.07         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.20         4.01        10.85        15.19         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.08         3.25         6.48        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       26.93        35.24        17.26        20.12         0.85         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46         2.89         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         1.12         2.66         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36         6.41         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV 
       11.31         2.04        27.09         5.62        10.65         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        6.41         6.15         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.67         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        4.67         2.50        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38         6.35         3.45        11.80        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       16.67        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       97.45        56.19        15.35         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 
       79.66        11.90        23.64        21.04        28.24        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        91.73         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.22              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            88.93            140.81 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           11.340             9.025 
[1] "1.2 - 88.9 (11.3)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.4"
D46V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED          0       0        5         6        4
  3Q LOSS WILD-TYPE        1       2       81        87       88
D46V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                5                81
  STAGE III               6                87
  STAGE IV                4                88
[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"
                   vv
clus                T0+T1+T2  T3  T4
  3Q LOSS MUTATED          4   7   3
  3Q LOSS WILD-TYPE       78 129  36
D46V4, multiclass
          clus
vv         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1+T2               4                78
  T3                     7               129
  T4                     3                36
[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"
                   vv
clus                 N0  N1  N2  N3
  3Q LOSS MUTATED    10   1   2   1
  3Q LOSS WILD-TYPE 156  27  53   6
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              10               156
  N1               1                27
  N2               2                53
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED     6   1   8
  3Q LOSS WILD-TYPE 123   6 133
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               6               123
  M1               1                 6
  MX               8               133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     4  11
  3Q LOSS WILD-TYPE  73 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4   11
  3Q LOSS WILD-TYPE   73  190
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               4                73
  MALE                11               190
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
D46V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         1    11
  3Q LOSS WILD-TYPE    30                        12   204
D46V11, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                30
  BLACK OR AFRICAN AMERICAN               1                12
  WHITE                                  11               204
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  13
  3Q LOSS WILD-TYPE   5 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   13
  3Q LOSS WILD-TYPE    5  245
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              13               245
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    59  30
  4P LOSS WILD-TYPE 123  58
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               89               181 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               30                58 
$`4P LOSS MUTATED`
TCGA-2F-A9KO TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W 
       22.29        19.04        32.84         5.06         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25         5.59         3.65         4.67        15.42         9.99 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-DK-A1A7 TCGA-DK-A1AD 
        0.46         0.43        12.92         4.90        18.41       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN 
        1.81        10.59        87.32         2.20         7.82         8.22 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       21.30         9.67        17.98        15.68        41.06        30.67 
TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.35        24.66         0.49        12.89         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BR 
        4.01        22.45         5.52         1.97        22.98        13.38 
TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        6.87         6.84        49.68         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3IB 
        6.38         2.66         2.20        15.19         4.08         7.04 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GD-A2C5 
       19.46         2.89        15.81         4.50         1.12         7.73 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A40G 
        2.20         7.59         2.04         4.41         6.41        19.07 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R 
        6.74         3.06         8.75         4.67         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        1.74         4.27        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SX TCGA-XF-A9SY 
        3.75         6.58        56.19        15.35        23.64        21.04 
TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-YF-AA3M 
       66.64        54.90         2.96        56.48         9.04 

$`4P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A2LA 
       12.16        17.88        19.50        14.89        14.96        17.16 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       12.82         2.07        28.70        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
        0.10         0.10         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
        1.84         9.34         2.53         2.14        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
        8.91       130.88        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WW 
      123.85         3.98        10.49        50.27        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 
       67.36        43.59        26.17         0.10         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66         1.38         0.82        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        1.22         0.46        15.68        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       45.93        24.30         6.12        12.82        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       19.79        14.93        14.96        14.93         3.62        12.13 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       37.15        11.01         5.36         5.69        27.45         6.87 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       50.66        18.81         9.30         6.71         4.11         2.07 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P 
        4.01        10.85         7.13         3.48         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC 
       20.12         0.85        52.67         6.94         2.24        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07        17.75         2.66         2.10         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.36         6.41        11.31        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       10.65         6.15         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND 
        6.67         6.41        11.54         1.51        38.60         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
        8.22         3.45         2.50         1.81         6.38         6.35 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
        3.45        11.80        13.48        45.04        88.93        97.45 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SZ 
        1.87        17.88        64.80        79.66        11.90        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       26.27        18.90         2.24        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN1 
       10.82         7.63        91.73         8.32         6.77        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L 
        7.96 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.43              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           112.44            140.81 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             7.82             10.82 
[1] "0.4 - 112.4 (7.8)"  "0.1 - 140.8 (10.8)"
[1] "hr=" "1.3"
D47V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED          0       0       24        27       38
  4P LOSS WILD-TYPE        1       2       62        66       54
D47V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               24                62
  STAGE III              27                66
  STAGE IV               38                54
[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"
                   vv
clus                T0+T1+T2 T3 T4
  4P LOSS MUTATED         23 52 11
  4P LOSS WILD-TYPE       59 84 28
D47V4, multiclass
          clus
vv         4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1+T2              23                59
  T3                    52                84
  T4                    11                28
[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"
                   vv
clus                 N0  N1  N2  N3
  4P LOSS MUTATED    45  13  24   1
  4P LOSS WILD-TYPE 121  15  31   6
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              45               121
  N1              13                15
  N2              24                31
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED   39  2 50
  4P LOSS WILD-TYPE 90  5 91
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              39                90
  M1               2                 5
  MX              50                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    22  69
  4P LOSS WILD-TYPE  55 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     22   69
  4P LOSS WILD-TYPE   55  132
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              22                55
  MALE                69               132
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       8                         8    70
  4P LOSS WILD-TYPE    23                         5   145
D47V11, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   8                23
  BLACK OR AFRICAN AMERICAN               8                 5
  WHITE                                  70               145
[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"
D47V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  85
  4P LOSS WILD-TYPE   4 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   85
  4P LOSS WILD-TYPE    4  173
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              85               173
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    60  27
  4Q LOSS WILD-TYPE 122  61
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               87               183 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               27                61 
$`4Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD 
       98.33        32.84         5.06         5.06         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR 
        4.67        15.42         9.99        28.41         1.94         0.46 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1AD TCGA-DK-A2HX 
        0.43        12.92         4.90         7.20       112.44         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN 
       10.59         7.79        87.32         2.20         7.82         8.22 
TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       21.30        64.18        15.68        41.06        30.67        15.35 
TCGA-E7-A541 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL 
        0.59        12.89         8.94         6.87         4.01        22.45 
TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5BZ 
        5.52        22.98        12.13        13.38         6.84        27.45 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TG 
       49.68         2.66         4.83         6.28         6.38         2.66 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A3BM 
        2.20        15.19         4.08        26.93         7.04         2.89 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
       15.81         4.50         7.73         2.20         7.59         2.04 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS 
        4.41         6.41        19.07         6.74         3.06         8.75 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        4.67         6.48        10.52         1.74         1.81         4.27 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-XF-A8HC TCGA-XF-A8HF 
       13.48        12.23        16.67        14.24         6.58        56.19 
TCGA-XF-A8HG TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAMT 
       15.35        23.64        21.04        66.64        54.90         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-YF-AA3M 
        8.32        56.48         9.04 

$`4Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A0C8 
       22.29        11.97        84.00       103.50         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       19.04        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
        8.35         8.25        17.16        12.82         2.07        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        8.98        23.01         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
        0.07         0.10         0.10         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84         9.34         2.53         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00         8.91       130.88        16.14        17.62        15.62 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
      123.85         3.98        10.49        50.27        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
        8.28        10.55       140.81        48.00        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       76.60        67.36        43.59        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.49         0.53         0.56         0.66         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B8 
       12.99        14.33         1.22         0.46        15.68        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        15.88        45.93        24.30         6.12        12.82 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S 
       13.18        46.78        19.79         1.97        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       14.93         3.62        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        5.69         6.87        50.66        18.81         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.11         2.07         4.01        10.85         7.13         3.48 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        3.25         6.48        61.94        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       17.26        20.12         0.85        52.67         6.94        19.46 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        2.24        15.91        14.07        17.75         1.12         2.66 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R 
        2.10         3.12        20.98         7.36         6.41        11.31 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ 
       27.09         5.62         4.73        10.65         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
        7.63         7.79         4.14         6.67         6.41        11.54 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB 
        1.51        38.60         9.01         8.22         3.45         2.50 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-S5-A6DX TCGA-S5-AA26 
        6.38         6.35         3.45        11.80         0.85         3.75 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       45.04        88.93        97.45         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       79.66        11.90        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMR 
       16.27         2.10        92.98        10.82         7.63        91.73 
TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
        6.77        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        4.83         0.66         7.96 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.43              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           112.44            140.81 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             7.82             10.55 
[1] "0.4 - 112.4 (7.8)"  "0.1 - 140.8 (10.6)"
[1] "hr=" "1"  
D48V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED          0       0       23        29       35
  4Q LOSS WILD-TYPE        1       2       63        64       57
D48V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               23                63
  STAGE III              29                64
  STAGE IV               35                57
[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"
                   vv
clus                T0+T1+T2 T3 T4
  4Q LOSS MUTATED         24 50 10
  4Q LOSS WILD-TYPE       58 86 29
D48V4, multiclass
          clus
vv         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1+T2              24                58
  T3                    50                86
  T4                    10                29
[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"
                   vv
clus                 N0  N1  N2  N3
  4Q LOSS MUTATED    50  12  21   1
  4Q LOSS WILD-TYPE 116  16  34   6
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              50               116
  N1              12                16
  N2              21                34
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED   37  2 50
  4Q LOSS WILD-TYPE 92  5 91
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              37                92
  M1               2                 5
  MX              50                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    25  64
  4Q LOSS WILD-TYPE  52 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     25   64
  4Q LOSS WILD-TYPE   52  137
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              25                52
  MALE                64               137
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
D48V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       8                         6    69
  4Q LOSS WILD-TYPE    23                         7   146
D48V11, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   8                23
  BLACK OR AFRICAN AMERICAN               6                 7
  WHITE                                  69               146
[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"
D48V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     1  82
  4Q LOSS WILD-TYPE   4 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   82
  4Q LOSS WILD-TYPE    4  176
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              82               176
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    28  12
  5P LOSS WILD-TYPE 154  76
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               40               230 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12                76 
$`5P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A2LB TCGA-BT-A2LD 
       22.29         4.83         6.58        19.04         5.59         3.65 
TCGA-BT-A3PH TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 
        4.67        23.01         0.46        18.41       112.44        10.59 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-E5-A2PC 
        3.98         7.82        50.27        21.30        48.00        43.59 
TCGA-E7-A6ME TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43U TCGA-FD-A5BZ 
       12.99         6.87        24.30        22.45        14.93        27.45 
TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A3VY TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GV-A3JW 
        3.48        61.94         0.85         2.66         2.20         6.41 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-R3-A69X 
       11.54         9.01         3.45         4.67         2.50        14.24 
TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-AAMX TCGA-XF-AAN0 
       15.35        79.66         6.77        56.48 

$`5P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I 
       11.97        84.00       103.50        98.33        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
        2.66         6.74        12.39        11.93        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        8.35         8.25        17.16        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS 
       28.70         9.99        28.41         8.98         1.94         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.10        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84         9.34         2.53         2.14        66.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00         8.91       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IN 
        1.81         7.79       123.85        87.32         2.20         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       10.49        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       41.06        30.67        15.35        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.82        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        8.94         4.01        12.43        11.93        15.88        45.93 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
        6.12        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
        1.97        22.98        14.93        14.96         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       13.38        37.15        11.01         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        6.84         6.87        49.68         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.38        50.66        18.81         9.30         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.07         2.66         2.20         4.01        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK 
        7.13         4.08         3.25         6.48        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       26.93        35.24        17.26         7.04        20.12        52.67 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        19.46         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07        17.75         1.12         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         7.36         6.41         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        2.04        27.09         5.62         4.73        10.65         4.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.15         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        6.41        19.07         1.51         6.74        38.60         3.06 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        8.22         8.75         6.48        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        4.27         6.38         6.35         3.45        11.80        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       12.23        16.67         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       88.93        97.45        56.19         1.87        17.88        64.80 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 
       54.90         7.63        91.73         2.96         8.32        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.46              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           112.44            140.81 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           11.065             9.010 
[1] "0.5 - 112.4 (11.1)" "0.1 - 140.8 (9.0)" 
[1] "hr=" "1.2"
D49V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED          1       0       12        13       15
  5P LOSS WILD-TYPE        0       2       74        80       77
D49V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               12                74
  STAGE III              13                80
  STAGE IV               15                77
[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"
                   vv
clus                T0+T1+T2  T3  T4
  5P LOSS MUTATED         13  20   6
  5P LOSS WILD-TYPE       69 116  33
D49V4, multiclass
          clus
vv         5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1+T2              13                69
  T3                    20               116
  T4                     6                33
[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"
                   vv
clus                 N0  N1  N2  N3
  5P LOSS MUTATED    24   5   8   2
  5P LOSS WILD-TYPE 142  23  47   5
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              24               142
  N1               5                23
  N2               8                47
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  5P LOSS MUTATED    19   2  20
  5P LOSS WILD-TYPE 110   5 121
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0              19               110
  M1               2                 5
  MX              20               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    14  28
  5P LOSS WILD-TYPE  63 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     14   28
  5P LOSS WILD-TYPE   63  173
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              14                63
  MALE                28               173
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
D49V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       5                         1    32
  5P LOSS WILD-TYPE    26                        12   183
D49V11, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   5                26
  BLACK OR AFRICAN AMERICAN               1                12
  WHITE                                  32               183
[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"
D49V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  37
  5P LOSS WILD-TYPE   5 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   37
  5P LOSS WILD-TYPE    5  221
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              37               221
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    68  35
  5Q LOSS WILD-TYPE 114  53
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              103               167 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               35                53 
$`5Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20R 
       22.29        11.97        98.33         6.58        19.04         5.06 
TCGA-BT-A20V TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E 
        5.06         3.65         4.67        12.82        15.42         9.99 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2I1 
       23.01         0.46         5.19         2.14       112.44        10.59 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        3.98         7.82         8.22        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
       20.02        10.55        48.00        64.18        15.68        41.06 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-FD-A3B5 
       43.59        15.35        24.66         0.49        12.99         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        6.87        11.93        24.30        22.45         6.12        12.82 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BV 
       13.18        19.79         1.97        14.93        13.38         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
        6.84        27.45         6.87         4.83         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK 
       18.81         9.30         6.71         2.07         2.66        10.85 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3IB TCGA-G2-A3IE 
        3.48         4.08         6.48        61.94         7.04        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
        0.85        52.67         2.66         7.73         2.10         2.20 
TCGA-GU-A42P TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        6.41        10.65         6.41         6.15         5.69         7.63 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07        11.54         6.74         3.06         9.01         8.22 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-PQ-A6FN TCGA-R3-A69X 
        3.45         2.50         6.48        10.52        16.67        14.24 
TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SZ TCGA-XF-A9T3 
        6.58        56.19        15.35        79.66        28.24         2.24 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
       54.90         7.63         2.96         6.77        56.48         7.96 
TCGA-YF-AA3M 
        9.04 

$`5Q LOSS WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       84.00       103.50         4.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.74        12.39        11.93        32.84        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       19.50        14.89        14.96         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        5.59         2.07        28.70        28.41         8.98         1.94 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.10         0.10        12.92         4.90         7.20         5.46 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         1.84         9.34         2.53        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00         8.91       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IV 
        1.81         7.79       123.85        87.32         2.20         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        8.28       140.81        17.98        41.56        76.60        67.36 
TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       30.67        26.17         0.10         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.66         1.38         0.82        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       12.89        15.68         4.01        12.43        15.88        45.93 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
        5.52        46.78        22.98        14.93        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 
       12.13        37.15        11.01         6.87         5.69        49.68 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
        2.66         6.28         4.11         2.20         4.01        15.19 
TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        7.13         3.25        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.26         6.94        19.46         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ 
        4.50        15.91        14.07        17.75         1.12         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98         7.36         7.59        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        5.62         4.73         4.41         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RJ 
        6.41         1.51        38.60         8.75         4.67         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81         4.27         6.38         6.35         3.45        11.80 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD 
       13.48        12.23         0.85         3.75        45.04        88.93 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX 
       97.45         1.87        17.88        64.80        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 
       92.98        10.82        91.73         8.32        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39         3.88        10.36         4.83         0.66 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.46              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           112.44            140.81 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             9.04              9.34 
[1] "0.5 - 112.4 (9.0)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED          1       0       28        32       43
  5Q LOSS WILD-TYPE        0       2       58        61       49
D50V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               28                58
  STAGE III              32                61
  STAGE IV               43                49
[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"
                   vv
clus                T0+T1+T2 T3 T4
  5Q LOSS MUTATED         29 53 16
  5Q LOSS WILD-TYPE       53 83 23
D50V4, multiclass
          clus
vv         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1+T2              29                53
  T3                    53                83
  T4                    16                23
[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"
                   vv
clus                 N0  N1  N2  N3
  5Q LOSS MUTATED    53  11  27   5
  5Q LOSS WILD-TYPE 113  17  28   2
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              53               113
  N1              11                17
  N2              27                28
  N3               5                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  5Q LOSS MUTATED   40  5 59
  5Q LOSS WILD-TYPE 89  2 82
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              40                89
  M1               5                 2
  MX              59                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    28  77
  5Q LOSS WILD-TYPE  49 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     28   77
  5Q LOSS WILD-TYPE   49  124
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              28                49
  MALE                77               124
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
D50V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       9                         7    80
  5Q LOSS WILD-TYPE    22                         6   135
D50V11, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   9                22
  BLACK OR AFRICAN AMERICAN               7                 6
  WHITE                                  80               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"
D50V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     3  96
  5Q LOSS WILD-TYPE   2 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   96
  5Q LOSS WILD-TYPE    2  162
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              96               162
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    44  20
  6P LOSS WILD-TYPE 138  68
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               64               206 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               20                68 
$`6P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A20X 
       22.29        98.33         4.83        32.84         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42C TCGA-CF-A1HR TCGA-CU-A3QU 
        5.59         3.65         4.67        28.70         0.46         5.19 
TCGA-CU-A5W6 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ 
        1.84         8.91         1.81       123.85         3.98        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       50.27        21.30        17.98        41.06        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43U 
       26.17         0.56        22.45        12.82        46.78        14.93 
TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.13         5.36         4.83         4.11        15.19         4.08 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A3OP 
       35.24        20.12        19.46         4.50        14.07         2.10 
TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        4.73         6.41         5.69         6.74        38.60         3.06 
TCGA-K4-A4AB TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
        2.50         1.81         3.45        13.48        16.67        14.24 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAMW 
       15.35         1.87        26.27         2.24        54.90         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-YF-AA3M 
       56.48        75.39         7.96         9.04 

$`6P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       11.97        84.00       103.50        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        6.74        12.39         6.58        11.93        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       17.88        19.50         5.06        14.89        14.96         8.35 
TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        12.82         2.07        15.42         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        8.98         1.94        23.01         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         7.20         5.46        16.31         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        66.41        18.41        19.00       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       16.14        17.62        15.62        10.59         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        2.20         7.82         8.22        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       67.36        15.68        43.59        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.53         0.59         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.33         1.22         0.46        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        6.87         4.01        12.43        11.93        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30         6.12         5.52        13.18        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       22.98        14.93        14.96         3.62        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01         6.87         5.69         6.84        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       49.68         2.66         6.28         6.38        50.66        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        9.30         6.71         2.07         2.66         2.20         4.01 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       10.85         7.13         3.48         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
       30.61         5.69        26.93        17.26         7.04         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       52.67         6.94         2.89         2.24        15.81        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       17.75         1.12         2.66         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36         6.41         7.59        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF 
       27.09         5.62        10.65         4.41         6.15         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        7.79         4.14         6.67         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         9.01         8.22         8.75         3.45         4.67 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
        6.48        10.52         1.74         4.27         6.38         6.35 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       11.80        12.23         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       88.93        97.45        56.19        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 
       11.90        23.64        21.04        28.24        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMR 
       66.64         2.10        92.98        10.82         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H 
        2.96         6.77        30.94        27.06         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC 
        4.83         0.66 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.46              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           123.85            140.81 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            9.765             9.155 
[1] "0.5 - 123.8 (9.8)" "0.1 - 140.8 (9.2)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED          0       0       12        24       27
  6P LOSS WILD-TYPE        1       2       74        69       65
D51V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               12                74
  STAGE III              24                69
  STAGE IV               27                65
[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"
                   vv
clus                T0+T1+T2  T3  T4
  6P LOSS MUTATED         11  34  14
  6P LOSS WILD-TYPE       71 102  25
D51V4, multiclass
          clus
vv         6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1+T2              11                71
  T3                    34               102
  T4                    14                25
[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"
                   vv
clus                 N0  N1  N2  N3
  6P LOSS MUTATED    33   4  20   1
  6P LOSS WILD-TYPE 133  24  35   6
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              33               133
  N1               4                24
  N2              20                35
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  6P LOSS MUTATED    33   2  30
  6P LOSS WILD-TYPE  96   5 111
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              33                96
  M1               2                 5
  MX              30               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    20  45
  6P LOSS WILD-TYPE  57 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     20   45
  6P LOSS WILD-TYPE   57  156
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              20                57
  MALE                45               156
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
D51V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       4                         2    53
  6P LOSS WILD-TYPE    27                        11   162
D51V11, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   4                27
  BLACK OR AFRICAN AMERICAN               2                11
  WHITE                                  53               162
[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"
D51V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     3  59
  6P LOSS WILD-TYPE   2 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3   59
  6P LOSS WILD-TYPE    2  199
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              59               199
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    69  30
  6Q LOSS WILD-TYPE 113  58
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               99               171 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               30                58 
$`6Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A2LB 
       22.29        98.33         4.83        32.84         5.06         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CU-A3QU 
        3.65         4.67        28.70         1.94         0.46         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
        1.84        66.41         8.91         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
      123.85         2.20         3.98        10.49        50.27        21.30 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       17.98        64.18        41.06        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3SL 
       26.17         0.49         0.56         1.22         8.94        22.45 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR 
       12.82        46.78        19.79        14.93        12.13        13.38 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62O 
        6.87         5.36         6.84        27.45         6.87         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
        6.28         6.38         9.30         4.11         2.66         2.20 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
       15.19         4.08         6.48        35.24        17.26        20.12 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I1 
       52.67        19.46         2.24         4.50        14.07         2.66 
TCGA-GD-A3OP TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JX 
        2.10        11.31         2.04         4.73         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
        5.69         7.63         7.79        11.54         6.74        38.60 
TCGA-HQ-A2OF TCGA-K4-A4AB TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
        3.06         2.50         1.81         3.45        13.48        16.67 
TCGA-R3-A69X TCGA-XF-A8HB TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SW TCGA-XF-A9T0 
       14.24        45.04        15.35         1.87        11.90        26.27 
TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 
        2.24        54.90         7.63        91.73         8.32        56.48 
TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-YF-AA3M 
       75.39         7.96         9.04 

$`6Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       11.97        84.00       103.50        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        6.74        12.39         6.58        11.93        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       17.88        19.50         5.06        14.89        14.96         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        12.82         2.07        15.42         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       28.41         8.98        23.01         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         7.20         5.46        16.31         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
        2.14        18.41        19.00       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU 
       17.62        15.62        87.32         7.82         8.22        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW 
        9.67         8.28        10.55       140.81        48.00        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       76.60        67.36        15.68        24.66         0.10         0.53 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.59         0.66         1.38         0.82        12.99        14.33 
TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.46        12.89        15.68         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO 
       11.93        15.88        45.93        24.30         6.12         5.52 
TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
       13.18         1.97        22.98        14.93        14.96         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A6TA 
       37.15        11.01         5.69        49.68         2.66        50.66 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
       18.81         6.71         2.07         4.01        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.48         3.25        61.94        30.61         5.69        26.93 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC 
        7.04         0.85         6.94         2.89        15.81        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       17.75         1.12         7.73         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO 
        7.36         6.41         7.59        27.09         5.62        10.65 
TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        4.41         4.14         6.67         6.41        19.07         1.51 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
        9.01         8.22         8.75         3.45         4.67         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT 
       10.52         1.74         4.27         6.38         6.35        11.80 
TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       12.23         0.85         3.75         6.58        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY 
       56.19        17.88        64.80        79.66        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       28.24        18.90        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 
       10.82         2.96         6.77        30.94        27.06         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       10.36         4.83         0.66 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.46              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           123.85            140.81 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             8.91              9.99 
[1] "0.5 - 123.8 (8.9)"  "0.1 - 140.8 (10.0)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED          1       0       27        30       41
  6Q LOSS WILD-TYPE        0       2       59        63       51
D52V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               27                59
  STAGE III              30                63
  STAGE IV               41                51
[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"
                   vv
clus                T0+T1+T2 T3 T4
  6Q LOSS MUTATED         27 49 17
  6Q LOSS WILD-TYPE       55 87 22
D52V4, multiclass
          clus
vv         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1+T2              27                55
  T3                    49                87
  T4                    17                22
[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"
                   vv
clus                 N0  N1  N2  N3
  6Q LOSS MUTATED    52   8  28   3
  6Q LOSS WILD-TYPE 114  20  27   4
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              52               114
  N1               8                20
  N2              28                27
  N3               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED   43  2 56
  6Q LOSS WILD-TYPE 86  5 85
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              43                86
  M1               2                 5
  MX              56                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    32  69
  6Q LOSS WILD-TYPE  45 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     32   69
  6Q LOSS WILD-TYPE   45  132
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              32                45
  MALE                69               132
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
D52V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       7                         5    80
  6Q LOSS WILD-TYPE    24                         8   135
D52V11, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   7                24
  BLACK OR AFRICAN AMERICAN               5                 8
  WHITE                                  80               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"
D52V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     4  92
  6Q LOSS WILD-TYPE   1 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4   92
  6Q LOSS WILD-TYPE    1  166
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 1
  NOT HISPANIC OR LATINO              92               166
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     5   4
  7P LOSS WILD-TYPE 177  84
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                9               261 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                84 
$`7P LOSS MUTATED`
TCGA-CF-A47X TCGA-DK-A1A5 TCGA-DK-A6B5 TCGA-FD-A5BY TCGA-FD-A6TA TCGA-GU-AATO 
        0.10         2.14        41.06         6.84        50.66        10.65 
TCGA-GV-A3QF TCGA-K4-A3WS TCGA-XF-AAML 
        7.63         8.75         7.63 

$`7P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       15.42        28.70         9.99        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       23.01         0.46         0.43         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.10         0.07         0.10        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84         9.34         2.53 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       10.49        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       76.60        67.36        15.68        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       26.17        24.66         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66         1.38         0.82        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22         0.46        12.89        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79         1.97        22.98        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        12.13        13.38        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         5.69        27.45         6.87        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        4.83         6.28         6.38        18.81         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        4.11         2.07         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
       15.19         7.13         3.48         4.08         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
        7.04        20.12         0.85        52.67         6.94        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        2.89         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75         1.12         2.66         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36         6.41         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
        2.04        27.09         5.62         4.73         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        6.15         5.69         7.79         4.14         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        11.54         1.51         6.74        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.22         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
       10.52         1.74         1.81         4.27         6.38         6.35 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        3.45        11.80        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        0.85         3.75        45.04         6.58        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       56.19        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       54.90        91.73         2.96         8.32         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        0.66         7.96         9.04 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.10              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            50.66            140.81 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             7.63              9.34 
[1] "0.1 - 50.7 (7.6)"  "0.1 - 140.8 (9.3)"
[1] "hr=" "1.6"
D53V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED          0       0        3         2        5
  7P LOSS WILD-TYPE        1       2       83        91       87
D53V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                3                83
  STAGE III               2                91
  STAGE IV                5                87
[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"
                   vv
clus                T0+T1+T2  T3  T4
  7P LOSS MUTATED          3   5   2
  7P LOSS WILD-TYPE       79 131  37
D53V4, multiclass
          clus
vv         7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1+T2               3                79
  T3                     5               131
  T4                     2                37
[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"
                   vv
clus                 N0  N1  N2  N3
  7P LOSS MUTATED     5   0   4   1
  7P LOSS WILD-TYPE 161  28  51   6
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               5               161
  N1               0                28
  N2               4                51
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  7P LOSS MUTATED     3   0   7
  7P LOSS WILD-TYPE 126   7 134
D53V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               3               126
  M1               0                 7
  MX               7               134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1   9
  7P LOSS WILD-TYPE  76 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    9
  7P LOSS WILD-TYPE   76  192
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               1                76
  MALE                 9               192
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
D53V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         0     7
  7P LOSS WILD-TYPE    30                        13   208
D53V11, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                30
  BLACK OR AFRICAN AMERICAN               0                13
  WHITE                                   7               208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   9
  7P LOSS WILD-TYPE   5 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    9
  7P LOSS WILD-TYPE    5  249
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               9               249
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    11   4
  7Q LOSS WILD-TYPE 171  84
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               15               255 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                84 
$`7Q LOSS MUTATED`
TCGA-CF-A47X TCGA-DK-A1A5 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-E7-A6ME 
        0.10         2.14       123.85         2.20         7.82        12.99 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-GU-A766 TCGA-GU-AATO TCGA-K4-A3WS 
        6.84         6.87         4.11         5.62        10.65         8.75 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-YF-AA3M 
        7.63         2.96         9.04 

$`7Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       15.42        28.70         9.99        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       23.01         0.46         0.43         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.10         0.07         0.10        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84         9.34         2.53 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32         3.98         8.22        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       20.02         9.67         8.28        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       41.06        30.67        43.59        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         0.53         0.59         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        1.38         0.82        14.33         1.22         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.68         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       15.88        45.93        24.30        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        13.18        46.78        19.79         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       14.93        14.96        14.93         3.62        12.13        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ 
       37.15        11.01         6.87         5.36         5.69        27.45 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       49.68         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         9.30         6.71         2.07         2.66         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.01        10.85        15.19         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61         5.69        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        17.26         7.04        20.12         0.85        52.67 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        19.46         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.91        14.07        17.75         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GV-A3JV 
        7.59        11.31         2.04        27.09         4.73         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        6.41         6.15         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.67         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         9.01         8.22         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.50         6.48        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38         6.35         3.45        11.80        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       16.67        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       88.93        97.45        56.19        15.35         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       64.80        79.66        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       92.98        10.82        54.90        91.73         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        4.83         0.66         7.96 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.10              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           123.85            140.81 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             6.87             10.36 
[1] "0.1 - 123.8 (6.9)"  "0.1 - 140.8 (10.4)"
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED          0       0        6         4        5
  7Q LOSS WILD-TYPE        1       2       80        89       87
D54V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                6                80
  STAGE III               4                89
  STAGE IV                5                87
[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"
                   vv
clus                T0+T1+T2  T3  T4
  7Q LOSS MUTATED          6   8   1
  7Q LOSS WILD-TYPE       76 128  38
D54V4, multiclass
          clus
vv         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1+T2               6                76
  T3                     8               128
  T4                     1                38
[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"
                   vv
clus                 N0  N1  N2  N3
  7Q LOSS MUTATED     8   0   5   0
  7Q LOSS WILD-TYPE 158  28  50   7
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               8               158
  N1               0                28
  N2               5                50
  N3               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  7Q LOSS MUTATED     6   0   9
  7Q LOSS WILD-TYPE 123   7 132
D54V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               6               123
  M1               0                 7
  MX               9               132
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2  13
  7Q LOSS WILD-TYPE  75 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2   13
  7Q LOSS WILD-TYPE   75  188
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               2                75
  MALE                13               188
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
D54V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       2                         0    11
  7Q LOSS WILD-TYPE    29                        13   204
D54V11, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   2                29
  BLACK OR AFRICAN AMERICAN               0                13
  WHITE                                  11               204
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  13
  7Q LOSS WILD-TYPE   4 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   13
  7Q LOSS WILD-TYPE    4  245
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              13               245
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   86 38
  8P LOSS WILD-TYPE 96 50
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              124               146 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               38                50 
$`8P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13J 
       22.29        11.97       103.50        98.33         4.83         2.66 
TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HS 
        5.59         2.07        28.70        28.41         8.98         0.43 
TCGA-CF-A47S TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 
        0.13        12.92         5.46         5.19         2.53        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 
      130.88       112.44         1.81        10.59       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV 
        2.20         3.98         7.82         8.22        21.30         9.67 
TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A677 
       64.18        41.06        15.35        26.17         0.59         1.38 
TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 
        1.22        15.68         8.94         6.87         4.01        11.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A43N 
       24.30        22.45         6.12         5.52        19.79        22.98 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       14.93        12.13        13.38         6.87         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TD 
       27.45         6.87         2.66         6.28        50.66         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        4.11         2.07         2.20        10.85        15.19         4.08 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F 
        6.48        61.94         5.69        20.12         6.94        19.46 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 
        4.50        15.91        14.07        17.75         1.12         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A766 
        2.10         3.12         7.36         6.41         2.04         5.62 
TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       10.65         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        6.41        19.07         6.74         9.01         8.22         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        3.45         4.67         2.50         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.81         4.27         3.45        11.80        12.23        16.67 
TCGA-R3-A69X TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SW 
       14.24        45.04         6.58         1.87        79.66        11.90 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT 
       26.27         2.24        66.64        54.90         7.63         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YC-A89H 
        8.32        56.48        75.39        10.36 

$`8P LOSS WILD-TYPE`
TCGA-2F-A9KQ TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       84.00        40.08         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E 
       17.16         3.65         4.67        12.82        15.42         9.99 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V 
        1.94        23.01         0.46         0.69         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL 
        0.07         0.10         0.10         4.90         7.20        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
        1.84         9.34         2.14        66.41        19.00         8.91 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IQ TCGA-DK-A3IS 
       16.14        17.62        15.62         7.79        10.49        50.27 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       20.02         8.28        10.55       140.81        48.00        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC 
       41.56        76.60        67.36        15.68        30.67        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         0.49         0.53         0.56         0.66 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B8 
        0.82        12.99        14.33         0.46        12.89        12.43 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
       15.88        45.93        12.82        13.18        46.78         1.97 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV 
       14.96        14.93         3.62        37.15        11.01         5.36 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG 
       49.68         4.83         6.38        18.81         9.30         2.66 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL 
        4.01         7.13         3.48         3.25        30.61        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM 
       35.24        17.26         7.04         0.85        52.67         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
        2.24        15.81         2.66        20.98         2.20         7.59 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A3QK 
       11.31        27.09         4.73         4.41         4.14         6.67 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A83P TCGA-LC-A66R 
       11.54         1.51        38.60         3.06         6.38         6.35 
TCGA-MV-A51V TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       13.48         0.85         3.75        88.93        97.45        56.19 
TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       15.35        17.88        64.80        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR 
       18.90        16.27         2.10        92.98        10.82        91.73 
TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
        6.77        30.94        27.06         3.88         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.13              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           130.88            140.81 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            7.805            11.425 
[1] "0.1 - 130.9 (7.8)"  "0.1 - 140.8 (11.4)"
[1] "hr=" "1"  
D55V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED          0       0       37        33       54
  8P LOSS WILD-TYPE        1       2       49        60       38
D55V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               37                49
  STAGE III              33                60
  STAGE IV               54                38
[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"
                   vv
clus                T0+T1+T2 T3 T4
  8P LOSS MUTATED         33 62 19
  8P LOSS WILD-TYPE       49 74 20
D55V4, multiclass
          clus
vv         8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1+T2              33                49
  T3                    62                74
  T4                    19                20
[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"
                   vv
clus                 N0  N1  N2  N3
  8P LOSS MUTATED    65  17  32   3
  8P LOSS WILD-TYPE 101  11  23   4
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              65               101
  N1              17                11
  N2              32                23
  N3               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED   45  5 75
  8P LOSS WILD-TYPE 84  2 66
D55V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              45                84
  M1               5                 2
  MX              75                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    34  91
  8P LOSS WILD-TYPE  43 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     34   91
  8P LOSS WILD-TYPE   43  110
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              34                43
  MALE                91               110
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
D55V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       8                         7   100
  8P LOSS WILD-TYPE    23                         6   115
D55V11, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   8                23
  BLACK OR AFRICAN AMERICAN               7                 6
  WHITE                                 100               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1 115
  8P LOSS WILD-TYPE   4 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1  115
  8P LOSS WILD-TYPE    4  143
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO             115               143
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    16   6
  8Q LOSS WILD-TYPE 166  82
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               248 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                6                82 
$`8Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-CF-A1HS TCGA-DK-A2HX TCGA-DK-A3IL TCGA-DK-A3IM 
       98.33         4.83         0.43         1.81         3.98         7.82 
TCGA-DK-A6B5 TCGA-E7-A677 TCGA-E7-A7DV TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A5BZ 
       41.06         1.38         1.22        22.45        19.79        27.45 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-GU-A762 TCGA-GU-AATO TCGA-H4-A2HQ TCGA-K4-A3WS 
       10.85        15.19         2.04        10.65         6.74         8.75 
TCGA-K4-A3WU TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-XF-AAN0 
        3.45         1.74         3.45        56.48 

$`8Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A13I 
       22.29        11.97        84.00       103.50        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        3.65         4.67        12.82         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        9.99        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.10        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84         9.34         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         8.22        10.49        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67         8.28        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       64.18        41.56        76.60        67.36        15.68        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        26.17        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME 
        0.53         0.59         0.56         0.66         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.33         0.46        12.89        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
        6.12        12.82         5.52        13.18        46.78         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        14.93        14.96        14.93         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       13.38        37.15        11.01         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        6.84         6.87        49.68         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.38        50.66        18.81         9.30         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.07         2.66         2.20         4.01         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.08         3.25         6.48        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        17.26         7.04        20.12         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       52.67         6.94        19.46         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        6.41         7.59        11.31        27.09         5.62         4.73 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.14         6.67         6.41        19.07        11.54         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB 
       38.60         3.06         9.01         8.22         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
        6.48        10.52         1.81         4.27         6.38         6.35 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       11.80        13.48        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.75        45.04         6.58        88.93        97.45        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW 
       15.35         1.87        17.88        64.80        79.66        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN1 
        7.63        91.73         2.96         8.32         6.77        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.43              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            98.33            140.81 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            7.280             9.505 
[1] "0.4 - 98.3 (7.3)"  "0.1 - 140.8 (9.5)"
[1] "hr=" "1"  
D56V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED          0       0        4         5       12
  8Q LOSS WILD-TYPE        1       2       82        88       80
D56V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                4                82
  STAGE III               5                88
  STAGE IV               12                80
[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"
                   vv
clus                T0+T1+T2  T3  T4
  8Q LOSS MUTATED          3   8   9
  8Q LOSS WILD-TYPE       79 128  30
D56V4, multiclass
          clus
vv         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1+T2               3                79
  T3                     8               128
  T4                     9                30
[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"
                   vv
clus                 N0  N1  N2  N3
  8Q LOSS MUTATED     9   1   9   1
  8Q LOSS WILD-TYPE 157  27  46   6
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               9               157
  N1               1                27
  N2               9                46
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED     8   2  12
  8Q LOSS WILD-TYPE 121   5 129
D56V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               8               121
  M1               2                 5
  MX              12               129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6  16
  8Q LOSS WILD-TYPE  71 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   16
  8Q LOSS WILD-TYPE   71  185
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               6                71
  MALE                16               185
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       2                         1    17
  8Q LOSS WILD-TYPE    29                        12   198
D56V11, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   2                29
  BLACK OR AFRICAN AMERICAN               1                12
  WHITE                                  17               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"
D56V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  20
  8Q LOSS WILD-TYPE   5 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   20
  8Q LOSS WILD-TYPE    5  238
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              20               238
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    76  34
  9P LOSS WILD-TYPE 106  54
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              110               160 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               34                54 
$`9P LOSS MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BT-A0S7 
       11.97        84.00       103.50        98.33         4.83         6.58 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20W 
       19.04        32.84        17.88        19.50        14.89         8.35 
TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47V 
        5.59         9.99        23.01         0.46         0.69         0.10 
TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        0.10         4.90         5.46         1.84         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK 
        2.14        19.00         8.91        17.62        15.62         2.20 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X1 
        8.22        10.49        50.27        21.30        10.55        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 
       17.98        64.18        15.68        41.06        43.59        26.17 
TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A7DV TCGA-FD-A3B5 
       24.66         0.59         0.56         0.66         1.22         8.94 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        6.12        12.82        46.78        19.79         1.97        22.98 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 
        3.62        12.13        13.38         5.36        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
       49.68         4.83         6.28        50.66        18.81         6.71 
TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3VY 
        2.66        10.85         6.48        35.24         7.04         0.85 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
       52.67        19.46         2.89        14.07         1.12         2.66 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO 
        2.20         7.36         7.59         2.04         4.73        10.65 
TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.41         7.79         6.67        11.54         6.74        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB 
        3.06         8.75         3.45         4.67         2.50         4.27 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       11.80        12.23        16.67        14.24         0.85         3.75 
TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9T0 TCGA-XF-A9T4 TCGA-XF-AAMR TCGA-XF-AAMX 
       56.19        17.88        26.27        16.27        91.73         6.77 
TCGA-XF-AAN1 TCGA-YF-AA3L 
       30.94         7.96 

$`9P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       22.29        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       11.93        12.16         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       17.16         3.65         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47S 
       28.70        28.41         8.98         1.94         0.43         0.13 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU 
        0.07         0.07         0.10        12.92         7.20         5.19 
TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       16.31        66.41        18.41       130.88       112.44        16.14 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL 
        1.81        10.59         7.79       123.85        87.32         3.98 
TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW 
        7.82        20.02         9.67         8.28       140.81        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       76.60        67.36        30.67        15.35         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        0.53         1.38         0.82        12.99        14.33         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       12.89        15.68         6.87         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SP 
       15.88        45.93        24.30        22.45         5.52        13.18 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.93        14.96        14.93        37.15        11.01         6.87 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE 
        5.69         6.84         2.66         6.38         9.30         4.11 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.07         2.20         4.01        15.19         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        4.08         3.25        61.94        30.61         5.69        26.93 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       17.26        20.12         6.94         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        17.75         7.73         2.10         3.12        20.98 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX 
        6.41        11.31        27.09         5.62         4.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        5.69         7.63         4.14         6.41        19.07         1.51 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.01         8.22         6.48        10.52         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HB TCGA-XF-A8HC 
        6.38         6.35         3.45        13.48        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI 
       88.93        97.45        15.35         1.87        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        28.24        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        92.98        10.82        54.90         7.63 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        2.96         8.32        56.48        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
       10.36         4.83         0.66         9.04 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.10              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           103.50            140.81 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             9.14              9.17 
[1] "0.1 - 103.5 (9.1)" "0.1 - 140.8 (9.2)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED          1       0       33        43       36
  9P LOSS WILD-TYPE        0       2       53        50       56
D57V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               33                53
  STAGE III              43                50
  STAGE IV               36                56
[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"
                   vv
clus                T0+T1+T2 T3 T4
  9P LOSS MUTATED         36 60 16
  9P LOSS WILD-TYPE       46 76 23
D57V4, multiclass
          clus
vv         9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1+T2              36                46
  T3                    60                76
  T4                    16                23
[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"
                   vv
clus                N0 N1 N2 N3
  9P LOSS MUTATED   74  9 24  2
  9P LOSS WILD-TYPE 92 19 31  5
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              74                92
  N1               9                19
  N2              24                31
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED   56  2 57
  9P LOSS WILD-TYPE 73  5 84
D57V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              56                73
  M1               2                 5
  MX              57                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    29  87
  9P LOSS WILD-TYPE  48 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     29   87
  9P LOSS WILD-TYPE   48  114
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              29                48
  MALE                87               114
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
D57V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED      14                         5    85
  9P LOSS WILD-TYPE    17                         8   130
D57V11, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                  14                17
  BLACK OR AFRICAN AMERICAN               5                 8
  WHITE                                  85               130
[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"
D57V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2 106
  9P LOSS WILD-TYPE   3 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  106
  9P LOSS WILD-TYPE    3  152
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             106               152
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    73  32
  9Q LOSS WILD-TYPE 109  56
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              105               165 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               32                56 
$`9Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A2LB 
        6.58        32.84        17.88        19.50        14.89         5.59 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
       28.70         9.99        23.01         0.46         0.69         0.13 
TCGA-CF-A47V TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
        0.10         0.10         4.90         5.46         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG 
        9.34         2.14        19.00       112.44        17.62        15.62 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6AV 
       10.49        50.27        21.30        10.55        17.98        64.18 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE 
       41.06        43.59        26.17        24.66         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3SM TCGA-FD-A3SQ 
        0.66         1.22         8.94         6.87         6.12        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       19.79         1.97        22.98         3.62        12.13        13.38 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA 
       27.45         6.87        49.68         4.83         6.28        50.66 
TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL 
       18.81         2.07         2.66         6.48         5.69        26.93 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD 
       35.24         0.85        52.67        19.46         2.89        14.07 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A763 TCGA-GU-A767 
        2.66         7.73         2.10         2.20        27.09         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A40G TCGA-GV-A6ZA 
       10.65         4.41         6.41         7.79        19.07        11.54 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       38.60         3.06         8.75         3.45         4.67         2.50 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HF 
       11.80        16.67        14.24         0.85         3.75        56.19 
TCGA-XF-A8HI TCGA-XF-A9T0 TCGA-XF-A9T4 TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       17.88        26.27        16.27        91.73         8.32         6.77 
TCGA-XF-AAN1 TCGA-YF-AA3L TCGA-YF-AA3M 
       30.94         7.96         9.04 

$`9Q LOSS WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.04        12.16         5.06        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        17.16         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47T 
       15.42        28.41         8.98         1.94         0.43         0.07 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A3 
        0.07         0.10        12.92         7.20        16.31         2.53 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A2HX 
       66.41        18.41         8.91       130.88        16.14         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        7.82         8.22        20.02         9.67         8.28       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       48.00        41.56        76.60        67.36        15.68        30.67 
TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 
       15.35         0.10         0.49         0.53         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 
       12.99        14.33         0.46        12.89        15.68         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.43        11.93        15.88        45.93        24.30        22.45 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       12.82         5.52        13.18        14.93        14.96        14.93 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       37.15        11.01         6.87         5.36         5.69         6.84 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
        2.66         6.38         9.30         6.71         4.11         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.01        10.85        15.19         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        3.25        61.94        30.61        17.26         7.04        20.12 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
        6.94         2.24        15.81         4.50        15.91        17.75 
TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        1.12         3.12        20.98         7.36         6.41         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.31         2.04         5.62         6.15         5.69         7.63 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND 
        4.14         6.67         6.41         1.51         6.74         9.01 
TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        8.22         6.48        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HB 
        6.38         6.35         3.45        13.48        12.23        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SH 
        6.58        88.93        97.45        15.35         1.87        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 
       79.66        11.90        23.64        21.04        28.24        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
        2.24        66.64         2.10        92.98        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        7.63         2.96        56.48        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       10.36         4.83         0.66 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.10              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           112.44            140.81 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            10.49              8.91 
[1] "0.1 - 112.4 (10.5)" "0.1 - 140.8 (8.9)" 
[1] "hr=" "1.2"
D58V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED          1       0       34        38       34
  9Q LOSS WILD-TYPE        0       2       52        55       58
D58V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               34                52
  STAGE III              38                55
  STAGE IV               34                58
[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"
                   vv
clus                T0+T1+T2 T3 T4
  9Q LOSS MUTATED         37 54 14
  9Q LOSS WILD-TYPE       45 82 25
D58V4, multiclass
          clus
vv         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1+T2              37                45
  T3                    54                82
  T4                    14                25
[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"
                   vv
clus                N0 N1 N2 N3
  9Q LOSS MUTATED   69  9 24  2
  9Q LOSS WILD-TYPE 97 19 31  5
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              69                97
  N1               9                19
  N2              24                31
  N3               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED   54  2 53
  9Q LOSS WILD-TYPE 75  5 88
D58V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              54                75
  M1               2                 5
  MX              53                88
[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"
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    27  83
  9Q LOSS WILD-TYPE  50 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     27   83
  9Q LOSS WILD-TYPE   50  118
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              27                50
  MALE                83               118
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
D58V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED      13                         3    81
  9Q LOSS WILD-TYPE    18                        10   134
D58V11, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                  13                18
  BLACK OR AFRICAN AMERICAN               3                10
  WHITE                                  81               134
[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"
D58V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2  99
  9Q LOSS WILD-TYPE   3 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   99
  9Q LOSS WILD-TYPE    3  159
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              99               159
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    34  15
  10P LOSS WILD-TYPE 148  73
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                49                221 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                15                 73 
$`10P LOSS MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A42C 
       11.97       103.50        14.96        17.16         3.65        28.70 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        1.94        23.01         0.69         4.90         7.20         5.46 
TCGA-DK-A2I2 TCGA-DK-A3IS TCGA-DK-A6B1 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 
        7.79        50.27        67.36        43.59        15.35         0.59 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SR TCGA-FD-A43N 
       15.68         8.94         4.01        11.93        19.79        22.98 
TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A6TD TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       12.13         6.84         6.71        15.19         3.48         4.08 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GV-A3JX TCGA-GV-A3QI 
       26.93         7.04         2.89        15.91         6.15         4.14 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       19.07         6.74         3.45         3.45        13.48        12.23 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMX 
       97.45         1.87        79.66        10.82        54.90         6.77 
TCGA-YF-AA3L 
        7.96 

$`10P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I 
       22.29        84.00        98.33         4.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ 
        5.06         8.35         8.25         5.59         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR 
        2.07        15.42         9.99        28.41         8.98         0.46 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.43         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        0.10        12.92         5.19        16.31         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        2.53         2.14        66.41        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        10.49        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 
       76.60        15.68        41.06        30.67        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         0.49         0.53         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        0.82        12.99        14.33         1.22         0.46        12.89 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        6.87        12.43        15.88        45.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
        6.12        12.82         5.52        13.18        46.78         1.97 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       14.93        14.96        14.93         3.62        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01         6.87         5.36         5.69        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       49.68         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         9.30         4.11         2.07         2.66         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        4.01        10.85         7.13         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY 
       30.61         5.69        35.24        17.26        20.12         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       52.67         6.94        19.46         2.24        15.81         4.50 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         1.12         2.66         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36         6.41         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       11.31         2.04        27.09         5.62         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        4.41         6.41         5.69         7.63         7.79         6.67 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        6.41        11.54         1.51        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.22         8.75         4.67         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT 
        1.74         1.81         4.27         6.38         6.35        11.80 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       16.67        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW 
       88.93        56.19        15.35        17.88        64.80        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAML TCGA-XF-AAMR 
       16.27        66.64         2.10        92.98         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         9.04 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.59               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            103.50             140.81 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             10.82               9.04 
[1] "0.6 - 103.5 (10.8)" "0.1 - 140.8 (9.0)" 
[1] "hr=" "1.1"
D59V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED          0       0       15        19       14
  10P LOSS WILD-TYPE        1       2       71        74       78
D59V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                15                 71
  STAGE III               19                 74
  STAGE IV                14                 78
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  10P LOSS MUTATED         14  21   7
  10P LOSS WILD-TYPE       68 115  32
D59V4, multiclass
          clus
vv         10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1+T2               14                 68
  T3                     21                115
  T4                      7                 32
[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"
                    vv
clus                  N0  N1  N2  N3
  10P LOSS MUTATED    33   3   8   2
  10P LOSS WILD-TYPE 133  25  47   5
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               33                133
  N1                3                 25
  N2                8                 47
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  10P LOSS MUTATED    20   2  27
  10P LOSS WILD-TYPE 109   5 114
D59V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               20                109
  M1                2                  5
  MX               27                114
[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"
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    13  36
  10P LOSS WILD-TYPE  64 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     13   36
  10P LOSS WILD-TYPE   64  165
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               13                 64
  MALE                 36                165
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
D59V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       3                         7    34
  10P LOSS WILD-TYPE    28                         6   181
D59V11, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    3                 28
  BLACK OR AFRICAN AMERICAN                7                  6
  WHITE                                   34                181
[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"
D59V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  44
  10P LOSS WILD-TYPE   4 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   44
  10P LOSS WILD-TYPE    4  214
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               44                214
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    62  25
  10Q LOSS WILD-TYPE 120  63
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                87                183 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                25                 63 
$`10Q LOSS MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-BT-A20N TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LD 
       11.97       103.50        32.84        14.96        17.16         3.65 
TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CU-A0YO 
       15.42        28.70         1.94        23.01         0.69         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A2I2 
        7.20         5.46         5.19         2.14         1.81         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3X1 
       87.32         2.20         3.98         7.82        50.27        48.00 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A4IJ 
       67.36        30.67        43.59        15.35        24.66         0.49 
TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SR 
        0.59        12.99         1.22         4.01        11.93        19.79 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A5C1 
       22.98        14.93        14.93        12.13         6.84        49.68 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        6.71         4.11         2.07        15.19         3.48         4.08 
TCGA-FT-A61P TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RC 
        6.48         7.04        20.12         0.85         2.89        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P TCGA-GV-A3JW 
       14.07        17.75         2.10         7.36         6.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-GV-A6ZA 
        6.15         7.63         7.79         4.14        19.07        11.54 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC 
        6.74         3.06         9.01         8.75         3.45         6.48 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HC TCGA-XF-A8HF 
        1.81         3.45        13.48        12.23         6.58        56.19 
TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMW 
        1.87        79.66        10.82        54.90         7.63         8.32 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-YF-AA3M 
        6.77         7.96         9.04 

$`10Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I 
       22.29        84.00        98.33         4.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        11.93        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         8.25         5.59         4.67        12.82         2.07 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
        9.99        28.41         8.98         0.46         0.43         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         1.84         9.34         2.53        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
       15.62        10.59       123.85         8.22        10.49        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       20.02         9.67         8.28        10.55       140.81        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4U1 
       64.18        41.56        76.60        15.68        41.06        26.17 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         0.53         0.56         0.66         1.38         0.82 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.33         0.46        12.89        15.68         8.94         6.87 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        15.88        45.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S 
       12.82         5.52        13.18        46.78         1.97        14.96 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        13.38        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        5.69        27.45         6.87         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH 
        6.38        50.66        18.81         9.30         2.66         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
        4.01        10.85         7.13         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3C 
        5.69        26.93        35.24        17.26        52.67         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I1 
       19.46         2.24        15.81         4.50         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        7.73         3.12        20.98         2.20         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        2.04        27.09         5.62         4.73        10.65         4.41 
TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE 
        5.69         6.67         6.41         1.51        38.60         8.22 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        4.67         2.50        10.52         1.74         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
        6.35        11.80        16.67        14.24         0.85         3.75 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH 
       45.04        88.93        97.45        15.35        17.88        64.80 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMR 
        2.24        16.27        66.64         2.10        92.98        91.73 
TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        2.96        56.48        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       10.36         4.83         0.66 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.49               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            103.50             140.81 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              7.79              10.52 
[1] "0.5 - 103.5 (7.8)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1"  
D60V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED          1       0       28        27       30
  10Q LOSS WILD-TYPE        0       2       58        66       62
D60V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                28                 58
  STAGE III               27                 66
  STAGE IV                30                 62
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  10Q LOSS MUTATED         27 41  9
  10Q LOSS WILD-TYPE       55 95 30
D60V4, multiclass
          clus
vv         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1+T2               27                 55
  T3                     41                 95
  T4                      9                 30
[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"
                    vv
clus                  N0  N1  N2  N3
  10Q LOSS MUTATED    47   7  18   3
  10Q LOSS WILD-TYPE 119  21  37   4
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               47                119
  N1                7                 21
  N2               18                 37
  N3                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED   35  3 48
  10Q LOSS WILD-TYPE 94  4 93
D60V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               35                 94
  M1                3                  4
  MX               48                 93
[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"
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    24  63
  10Q LOSS WILD-TYPE  53 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     24   63
  10Q LOSS WILD-TYPE   53  138
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               24                 53
  MALE                 63                138
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
D60V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       7                         6    64
  10Q LOSS WILD-TYPE    24                         7   151
D60V11, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    7                 24
  BLACK OR AFRICAN AMERICAN                6                  7
  WHITE                                   64                151
[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"
D60V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     2  77
  10Q LOSS WILD-TYPE   3 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   77
  10Q LOSS WILD-TYPE    3  181
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               77                181
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    74  33
  11P LOSS WILD-TYPE 108  55
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               107                163 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                33                 55 
$`11P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BT-A20N TCGA-BT-A20T 
       22.29       103.50        98.33        40.08        32.84        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
        5.06         8.35        17.16         4.67        15.42        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X 
        8.98        23.01         0.46         0.43         0.69         0.10 
TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB 
        5.46         1.84         9.34         2.14        66.41         8.91 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
      112.44         1.81        10.59        87.32         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV 
        7.82        10.49        50.27        21.30        17.98        64.18 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 
       43.59        15.35        26.17        24.66         0.49         0.59 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
        0.56        12.99         8.94        24.30        22.45        12.82 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FD-A5C0 
        1.97        22.98        12.13        13.38        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
       49.68         2.66         4.83         6.38        50.66         9.30 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A61P 
        2.07         2.66         2.20        15.19         3.48         6.48 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD 
       35.24        17.26        52.67        19.46         2.89        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
        1.12         7.73         2.10         2.20         7.36         7.59 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A40G 
       11.31         4.73         4.41         6.41         7.63        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A6MB 
       11.54         6.74        38.60         3.06         9.01         4.27 
TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HG TCGA-XF-A9SH 
       11.80        14.24         0.85         3.75        15.35        64.80 
TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       11.90        66.64         2.10        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
        2.96         8.32         6.77        56.48         7.96 

$`11P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       11.97        84.00         4.83         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        11.93        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       19.50         5.06        14.96         8.25         5.59         3.65 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A47S 
       12.82         2.07         9.99        28.41         1.94         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.07         0.10         0.07         0.10        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA 
        7.20         5.19        16.31         2.53        18.41        19.00 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
      130.88        16.14        17.62        15.62         7.79       123.85 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        8.22        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       48.00        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       30.67         0.10         0.53         0.66         1.38         0.82 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
       14.33         1.22         0.46        12.89        15.68         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM 
        4.01        12.43        11.93        15.88        45.93         6.12 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S 
        5.52        13.18        46.78        19.79        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       14.93         3.62        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
        5.69         6.84         6.28        18.81         6.71         4.11 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
        4.01        10.85         7.13         4.08         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       30.61         5.69        26.93         7.04        20.12         0.85 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
        6.94         2.24        15.81         4.50        15.91        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 
        2.66         3.12        20.98         6.41         2.04        27.09 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI 
        5.62        10.65         6.15         5.69         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        6.67         6.41         1.51         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        4.67         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38         6.35         3.45        13.48        12.23        16.67 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
       45.04         6.58        88.93        97.45        56.19         1.87 
TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       17.88        79.66        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAN1 
       18.90         2.24        16.27        92.98        10.82        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3M 
        9.04 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.10               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            112.44             140.81 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              9.30               9.04 
[1] "0.1 - 112.4 (9.3)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED          1       1       31        29       47
  11P LOSS WILD-TYPE        0       1       55        64       45
D61V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  1                  1
  STAGE II                31                 55
  STAGE III               29                 64
  STAGE IV                47                 45
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  11P LOSS MUTATED         37 60 12
  11P LOSS WILD-TYPE       45 76 27
D61V4, multiclass
          clus
vv         11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1+T2               37                 45
  T3                     60                 76
  T4                     12                 27
[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"
                    vv
clus                  N0  N1  N2  N3
  11P LOSS MUTATED    60  15  28   2
  11P LOSS WILD-TYPE 106  13  27   5
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               60                106
  N1               15                 13
  N2               28                 27
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED   57  5 51
  11P LOSS WILD-TYPE 72  2 90
D61V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               57                 72
  M1                5                  2
  MX               51                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    32  81
  11P LOSS WILD-TYPE  45 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     32   81
  11P LOSS WILD-TYPE   45  120
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               32                 45
  MALE                 81                120
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
D61V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED      17                         6    79
  11P LOSS WILD-TYPE    14                         7   136
D61V11, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                   17                 14
  BLACK OR AFRICAN AMERICAN                6                  7
  WHITE                                   79                136
[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"
D61V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2 102
  11P LOSS WILD-TYPE   3 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2  102
  11P LOSS WILD-TYPE    3  156
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              102                156
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    51  26
  11Q LOSS WILD-TYPE 131  62
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                77                193 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                26                 62 
$`11Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BT-A20N TCGA-BT-A20T 
       22.29       103.50        98.33        40.08        32.84        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
        5.06         8.35        17.16         4.67        15.42        28.70 
TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A5W6 
        8.98         0.43         0.69         0.10         5.46         1.84 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 
        2.14        66.41         8.91       112.44        10.59        87.32 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6B6 
        3.98         8.22        10.49        50.27        64.18        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME 
       43.59        15.35         0.49         0.59         0.56        12.99 
TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY 
        8.94        24.30        22.98        12.13         5.36         6.84 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TC 
        6.87        49.68         2.66         4.83         6.38         9.30 
TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3YS 
        2.20         6.48        35.24        17.26         2.89         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
        2.66         7.73         2.10         2.20         7.36         7.59 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE 
        4.41         6.41         6.67        19.07         6.74        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-XF-A8HG TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 
        3.06         9.01        15.35        11.90        66.64         2.10 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       54.90         7.63         2.96         8.32        56.48 

$`11Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       11.97        84.00         4.83         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        11.93        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       19.50         5.06        14.96         8.25         5.59         3.65 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
       12.82         2.07         9.99        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.46         0.13         0.07         0.10         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
       12.92         4.90         7.20         5.19        16.31         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
        2.53        18.41        19.00       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
       15.62         1.81         7.79       123.85         2.20         7.82 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        17.98        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF 
       41.06        26.17        24.66         0.10         0.53         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        1.38         0.82        14.33         1.22         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       15.68         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       45.93        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79         1.97        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        13.38        37.15        11.01         6.87         5.69 
TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
       27.45         6.28        50.66        18.81         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.07         2.66         4.01        10.85        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         4.08         3.25        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93         7.04        20.12         0.85        52.67         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 
       17.75         3.12        20.98         6.41        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ 
       27.09         5.62         4.73        10.65         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.63         7.79         4.14         6.41        11.54         1.51 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22         8.75         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
       10.52         1.74         1.81         4.27         6.38         6.35 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        3.45        11.80        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        0.85         3.75        45.04         6.58        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX 
       56.19         1.87        17.88        64.80        79.66        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 
       92.98        10.82        91.73         6.77        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 
TCGA-YF-AA3M 
        9.04 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.10               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            112.44             140.81 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              8.35              10.52 
[1] "0.1 - 112.4 (8.3)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED          0       1       23        24       30
  11Q LOSS WILD-TYPE        1       1       63        69       62
D62V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                23                 63
  STAGE III               24                 69
  STAGE IV                30                 62
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  11Q LOSS MUTATED         28 40 10
  11Q LOSS WILD-TYPE       54 96 29
D62V4, multiclass
          clus
vv         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1+T2               28                 54
  T3                     40                 96
  T4                     10                 29
[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"
                    vv
clus                  N0  N1  N2  N3
  11Q LOSS MUTATED    45  12  17   0
  11Q LOSS WILD-TYPE 121  16  38   7
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               45                121
  N1               12                 16
  N2               17                 38
  N3                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  11Q LOSS MUTATED    41   2  38
  11Q LOSS WILD-TYPE  88   5 103
D62V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               41                 88
  M1                2                  5
  MX               38                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"
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    26  55
  11Q LOSS WILD-TYPE  51 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     26   55
  11Q LOSS WILD-TYPE   51  146
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               26                 51
  MALE                 55                146
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED      13                         4    57
  11Q LOSS WILD-TYPE    18                         9   158
D62V11, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                   13                 18
  BLACK OR AFRICAN AMERICAN                4                  9
  WHITE                                   57                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"
D62V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0  73
  11Q LOSS WILD-TYPE   5 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   73
  11Q LOSS WILD-TYPE    5  185
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               73                185
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    22  10
  12P LOSS WILD-TYPE 160  78
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                32                238 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                10                 78 
$`12P LOSS MUTATED`
TCGA-2F-A9KW TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 
        4.83        17.16         1.94         0.10         5.19         1.84 
TCGA-DK-A1AC TCGA-DK-A3IV TCGA-E5-A2PC TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR 
      130.88         9.67        43.59        22.45        46.78        19.79 
TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-FD-A6TH 
       22.98         3.62         5.69         6.87         4.11         2.20 
TCGA-G2-AA3F TCGA-GC-A3YS TCGA-GD-A76B TCGA-GV-A3JW TCGA-LC-A66R TCGA-PQ-A6FN 
       19.46         1.12         7.36         6.41         6.35        16.67 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMW 
       56.19        15.35         1.87         2.24        10.82         8.32 
TCGA-XF-AAN0 TCGA-YF-AA3L 
       56.48         7.96 

$`12P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 
       22.29        11.97        84.00       103.50        98.33        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB 
       14.89        14.96         5.06         8.35         8.25         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        3.65         4.67        12.82         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
        9.99        28.41         8.98        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E 
       12.92         4.90         7.20         5.46        16.31         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        2.53         2.14        66.41        18.41        19.00         8.91 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
        8.22        10.49        50.27        21.30        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       76.60        67.36        15.68        41.06        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       26.17        24.66         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66         1.38         0.82        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22         0.46        12.89        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FD-A43P 
        6.12        12.82         5.52        13.18         1.97        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        14.93        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N 
        6.87         5.36         6.84        27.45        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        4.83         6.28         6.38        50.66        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        6.71         2.07         2.66         4.01        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        7.13         3.48         4.08         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 
       20.12         0.85        52.67         6.94         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 
       15.81         4.50        15.91        14.07        17.75         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         2.20         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.59        11.31         2.04        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       10.65         4.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.14         6.67         6.41        19.07        11.54         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        6.74        38.60         3.06         9.01         8.22         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        3.45         4.67         2.50         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        1.81         4.27         6.38         3.45        11.80        13.48 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       12.23        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW 
       88.93        97.45        17.88        64.80        79.66        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 
       23.64        21.04        28.24        26.27        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       66.64         2.10        92.98        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        2.96         6.77        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
       10.36         4.83         0.66         9.04 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.10               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            130.88             140.81 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             7.660              9.665 
[1] "0.1 - 130.9 (7.7)" "0.1 - 140.8 (9.7)"
[1] "hr=" "1"  
D63V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED          0       0        8         8       17
  12P LOSS WILD-TYPE        1       2       78        85       75
D63V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 8                 78
  STAGE III                8                 85
  STAGE IV                17                 75
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  12P LOSS MUTATED         10  16   6
  12P LOSS WILD-TYPE       72 120  33
D63V4, multiclass
          clus
vv         12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1+T2               10                 72
  T3                     16                120
  T4                      6                 33
[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"
                    vv
clus                  N0  N1  N2  N3
  12P LOSS MUTATED    15   5  11   0
  12P LOSS WILD-TYPE 151  23  44   7
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               15                151
  N1                5                 23
  N2               11                 44
  N3                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  12P LOSS MUTATED    12   1  20
  12P LOSS WILD-TYPE 117   6 121
D63V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               12                117
  M1                1                  6
  MX               20                121
[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"
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     8  25
  12P LOSS WILD-TYPE  69 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      8   25
  12P LOSS WILD-TYPE   69  176
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                8                 69
  MALE                 25                176
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
D63V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       2                         0    29
  12P LOSS WILD-TYPE    29                        13   186
D63V11, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    2                 29
  BLACK OR AFRICAN AMERICAN                0                 13
  WHITE                                   29                186
[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"
D63V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  30
  12P LOSS WILD-TYPE   4 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   30
  12P LOSS WILD-TYPE    4  228
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               30                228
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    23  10
  12Q LOSS WILD-TYPE 159  78
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                33                237 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                10                 78 
$`12Q LOSS MUTATED`
TCGA-BT-A2LD TCGA-C4-A0F0 TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A2I6 TCGA-DK-A3IV 
        3.65         1.94         0.10         5.19        87.32         9.67 
TCGA-E5-A2PC TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
       43.59        22.45         5.52        46.78         1.97        22.98 
TCGA-FD-A43X TCGA-FD-A5BX TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-AA3F 
        3.62         5.69         4.11         2.20         6.48        19.46 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A76B TCGA-GV-A3JW TCGA-HQ-A5NE TCGA-K4-A4AC 
       14.07         1.12         7.36         6.41         8.22         6.48 
TCGA-K4-A5RJ TCGA-LC-A66R TCGA-PQ-A6FN TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9T3 
        1.74         6.35        16.67        56.19        15.35         2.24 
TCGA-XF-AAMF TCGA-XF-AAMW TCGA-XF-AAN0 
       10.82         8.32        56.48 

$`12Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       17.16         5.59         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR 
       28.70         9.99        28.41         8.98        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
        0.10        12.92         4.90         7.20         5.46        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84         9.34         2.53         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        3.98         7.82         8.22        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       20.02         8.28        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       30.67        15.35        26.17        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.53         0.59         0.56         0.66         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.99        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR 
       45.93        24.30         6.12        12.82        13.18        19.79 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.93        14.96        14.93        12.13        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01         6.87         5.36         6.84        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       49.68         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       18.81         9.30         6.71         2.07         2.66         4.01 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
       10.85        15.19         7.13         3.48         4.08         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM 
        7.04        20.12         0.85        52.67         6.94         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 
        2.24        15.81         4.50        15.91        17.75         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         2.20         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.59        11.31         2.04        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       10.65         4.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.14         6.67         6.41        19.07        11.54         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        6.74        38.60         3.06         9.01         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        4.67         2.50        10.52         1.81         4.27         6.38 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
        3.45        11.80        13.48        12.23        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH 
        3.75        45.04         6.58        88.93        97.45         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       17.88        64.80        79.66        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX 
       92.98        54.90         7.63        91.73         2.96         6.77 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        0.66         7.96         9.04 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.10               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             87.32             140.81 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              6.48              10.36 
[1] "0.1 - 87.3 (6.5)"   "0.1 - 140.8 (10.4)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED          0       0        9         6       19
  12Q LOSS WILD-TYPE        1       2       77        87       73
D64V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 9                 77
  STAGE III                6                 87
  STAGE IV                19                 73
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  12Q LOSS MUTATED         12  16   5
  12Q LOSS WILD-TYPE       70 120  34
D64V4, multiclass
          clus
vv         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1+T2               12                 70
  T3                     16                120
  T4                      5                 34
[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"
                    vv
clus                  N0  N1  N2  N3
  12Q LOSS MUTATED    14   8   9   1
  12Q LOSS WILD-TYPE 152  20  46   6
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               14                152
  N1                8                 20
  N2                9                 46
  N3                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  12Q LOSS MUTATED    12   1  21
  12Q LOSS WILD-TYPE 117   6 120
D64V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0               12                117
  M1                1                  6
  MX               21                120
[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"
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     7  27
  12Q LOSS WILD-TYPE  70 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      7   27
  12Q LOSS WILD-TYPE   70  174
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                7                 70
  MALE                 27                174
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
D64V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       2                         0    30
  12Q LOSS WILD-TYPE    29                        13   185
D64V11, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    2                 29
  BLACK OR AFRICAN AMERICAN                0                 13
  WHITE                                   30                185
[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"
D64V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  32
  12Q LOSS WILD-TYPE   5 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   32
  12Q LOSS WILD-TYPE    5  226
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               32                226
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    33  19
  13Q LOSS WILD-TYPE 149  69
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                52                218 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                19                 69 
$`13Q LOSS MUTATED`
TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        2.66        32.84        14.89         5.06         8.25        17.16 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CU-A5W6 
        4.67        15.42        28.70         9.99         1.94         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM 
        2.53         2.14       130.88         7.79        87.32         7.82 
TCGA-DK-A3IN TCGA-DK-A6B6 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A7DV 
        8.22        30.67        24.66         0.49         0.56         1.22 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A43P TCGA-FD-A5BV 
        8.94         4.01        24.30        12.82        14.93         5.36 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3F 
       49.68         2.66         4.08        35.24        17.26        19.46 
TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JW 
        2.89         1.12         2.66         2.20         7.59         6.41 
TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A6FZ 
        4.14        38.60         9.01         4.67         6.48         1.81 
TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAMX 
       21.04        66.64        54.90         6.77 

$`13Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F 
        8.35         5.59         3.65        12.82         2.07        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        8.98        23.01         0.46         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
        4.90         7.20         5.46         5.19        16.31         9.34 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41        19.00         8.91       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62         1.81        10.59       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        3.98        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        8.28        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC 
       41.56        76.60        67.36        15.68        41.06        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF 
       15.35        26.17         0.10         0.53         0.59         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 
        1.38         0.82        12.99        14.33         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.68         6.87        12.43        11.93        15.88        45.93 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       22.45         6.12         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
        1.97        22.98        14.96        14.93         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       13.38        37.15        11.01         6.87         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       27.45         6.87         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         9.30         6.71         4.11         2.07         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.20         4.01        10.85        15.19         7.13         3.48 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61         5.69        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 
        7.04        20.12         0.85        52.67         6.94         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A2C5 
       15.81         4.50        15.91        14.07        17.75         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R 
        2.10         3.12        20.98         7.36         6.41        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        2.04        27.09         5.62         4.73        10.65         4.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
        6.15         5.69         7.63         7.79         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE 
       19.07        11.54         1.51         6.74         3.06         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB 
        8.75         3.45         2.50        10.52         1.74         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38         6.35         3.45        11.80        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       16.67        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       88.93        97.45        56.19        15.35         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 
       64.80        79.66        11.90        23.64        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        16.27         2.10        92.98        10.82 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 
        7.63        91.73         2.96         8.32        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.49               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            130.88             140.81 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             7.805             10.505 
[1] "0.5 - 130.9 (7.8)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.3"
D65V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED          0       0       14        19       18
  13Q LOSS WILD-TYPE        1       2       72        74       74
D65V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                14                 72
  STAGE III               19                 74
  STAGE IV                18                 74
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  13Q LOSS MUTATED         15  28   6
  13Q LOSS WILD-TYPE       67 108  33
D65V4, multiclass
          clus
vv         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1+T2               15                 67
  T3                     28                108
  T4                      6                 33
[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"
                    vv
clus                  N0  N1  N2  N3
  13Q LOSS MUTATED    30   8   8   2
  13Q LOSS WILD-TYPE 136  20  47   5
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               30                136
  N1                8                 20
  N2                8                 47
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  13Q LOSS MUTATED    27   0  25
  13Q LOSS WILD-TYPE 102   7 116
D65V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               27                102
  M1                0                  7
  MX               25                116
[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"
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    11  41
  13Q LOSS WILD-TYPE  66 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11   41
  13Q LOSS WILD-TYPE   66  160
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               11                 66
  MALE                 41                160
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
D65V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       4                         5    38
  13Q LOSS WILD-TYPE    27                         8   177
D65V11, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    4                 27
  BLACK OR AFRICAN AMERICAN                5                  8
  WHITE                                   38                177
[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"
D65V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  45
  13Q LOSS WILD-TYPE   4 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   45
  13Q LOSS WILD-TYPE    4  213
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               45                213
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    50  25
  14Q LOSS WILD-TYPE 132  63
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                75                195 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                 63 
$`14Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BT-A20J 
       22.29        11.97       103.50        98.33         4.83        19.04 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A3PK TCGA-CF-A1HR TCGA-CF-A1HS 
       14.89         5.06         5.59         2.07         0.46         0.43 
TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        0.10         4.90         7.20         1.84         2.53         2.14 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88       112.44        10.59        87.32        10.49        50.27 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ 
       48.00        64.18        41.06        15.35        26.17         0.49 
TCGA-E7-A6ME TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43U 
       12.99        12.82        13.18        46.78        22.98        14.93 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG 
        6.87        49.68         6.28        50.66         9.30         2.66 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3IE 
        2.20        15.19         4.08         6.48        61.94        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3RD TCGA-GD-A76B TCGA-GU-A42Q TCGA-GV-A3JZ 
        0.85        52.67        14.07         7.36         7.59         5.69 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
        7.63         6.41        19.07        11.54         6.74        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
        3.06         3.45         4.27        12.23        14.24         0.85 
TCGA-XF-A8HH TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-AAMJ TCGA-XF-AAML 
        1.87        23.64        28.24        26.27        54.90         7.63 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3M 
        6.77        56.48         9.04 

$`14Q LOSS WILD-TYPE`
TCGA-2F-A9KQ TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       84.00        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        11.93        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
        5.06        14.96         8.35         8.25        17.16         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82        15.42        28.70         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        8.98         1.94        23.01         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.10         0.07         0.10        12.92         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       16.31         9.34        66.41        18.41        19.00         8.91 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         3.98         7.82         8.22        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
        9.67         8.28        10.55       140.81        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3X6 
       76.60        67.36        15.68        30.67        43.59        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.82        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SR 
       45.93        24.30        22.45         6.12         5.52        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
        1.97        14.93        14.96         3.62        12.13        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       37.15        11.01         6.87         5.36         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD 
       27.45         2.66         4.83         6.38        18.81         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.11         2.07         4.01        10.85         7.13         3.48 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        3.25        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.04         6.94        19.46         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        17.75         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42R 
        2.10         3.12        20.98         2.20         6.41        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        2.04        27.09         5.62         4.73        10.65         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO 
        6.41         6.15         7.79         4.14         6.67         1.51 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.22         8.75         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
       10.52         1.74         1.81         6.38         6.35         3.45 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       11.80        13.48        16.67         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH 
       88.93        97.45        56.19        15.35        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       79.66        11.90        21.04        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMT 
       66.64         2.10        92.98        10.82        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
        8.32        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        4.83         0.66         7.96 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.10               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            130.88             140.81 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             11.54               8.91 
[1] "0.1 - 130.9 (11.5)" "0.1 - 140.8 (8.9)" 
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED          1       0       24        20       29
  14Q LOSS WILD-TYPE        0       2       62        73       63
D66V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                24                 62
  STAGE III               20                 73
  STAGE IV                29                 63
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  14Q LOSS MUTATED         24  36  11
  14Q LOSS WILD-TYPE       58 100  28
D66V4, multiclass
          clus
vv         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1+T2               24                 58
  T3                     36                100
  T4                     11                 28
[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"
                    vv
clus                  N0  N1  N2  N3
  14Q LOSS MUTATED    42   4  23   1
  14Q LOSS WILD-TYPE 124  24  32   6
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               42                124
  N1                4                 24
  N2               23                 32
  N3                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  14Q LOSS MUTATED    37   1  38
  14Q LOSS WILD-TYPE  92   6 103
D66V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               37                 92
  M1                1                  6
  MX               38                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"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    18  59
  14Q LOSS WILD-TYPE  59 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     18   59
  14Q LOSS WILD-TYPE   59  142
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               18                 59
  MALE                 59                142
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
D66V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED      10                         3    56
  14Q LOSS WILD-TYPE    21                        10   159
D66V11, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                   10                 21
  BLACK OR AFRICAN AMERICAN                3                 10
  WHITE                                   56                159
[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"
D66V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     2  69
  14Q LOSS WILD-TYPE   3 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   69
  14Q LOSS WILD-TYPE    3  189
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               69                189
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    66  27
  15Q LOSS WILD-TYPE 116  61
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                93                177 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                27                 61 
$`15Q LOSS MUTATED`
TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20W 
        4.83        40.08         6.58        19.04        32.84         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        8.25         5.59         3.65        15.42        28.70         9.99 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A3KJ TCGA-DK-A1A7 
        8.98         1.94         0.43         0.10         5.46        18.41 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A6B2 
        7.79       123.85        87.32         7.82         8.22        15.68 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B3 
       41.06        43.59         0.49         0.59         1.22        12.89 
TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BY 
       45.93        12.82        13.18        22.98         5.36         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TD 
       27.45         6.87        49.68         2.66         6.38         6.71 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        2.20        10.85        15.19         4.08         6.48        61.94 
TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS 
       26.93        20.12        52.67        15.81         4.50         1.12 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 
        2.66         2.10         2.20         7.36         6.41         2.04 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E 
        5.62        10.65         6.15         7.63         7.79         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.07        11.54         6.74        38.60         8.22         8.75 
TCGA-K4-A4AB TCGA-K4-A5RJ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
        2.50         1.74         6.35         3.45        13.48        16.67 
TCGA-R3-A69X TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SW 
       14.24        88.93        56.19        15.35         1.87        11.90 
TCGA-XF-A9SX TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMT 
       23.64        26.27         2.24        66.64         7.63         2.96 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-YF-AA3M 
        6.77         7.96         9.04 

$`15Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A13I 
       22.29        11.97        84.00       103.50        98.33         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.74        12.39        11.93        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA 
       19.50         5.06        14.89        14.96         5.06        17.16 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
        4.67        12.82         2.07        28.41        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90         7.20         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.53         2.14        66.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       10.59         2.20         3.98        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       20.02         9.67         8.28        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
       17.98        64.18        41.56        76.60        67.36        30.67 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE 
       15.35        26.17        24.66         0.10         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        0.66         1.38         0.82        12.99        14.33         0.46 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.68         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ 
       15.88        24.30        22.45         6.12         5.52        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79         1.97        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       12.13        13.38        37.15        11.01         6.87         5.69 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        4.83         6.28        50.66        18.81         9.30         4.11 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        2.07         2.66         4.01         7.13         3.48         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
       30.61         5.69        35.24        17.26         7.04         0.85 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        19.46         2.89         2.24        15.91        14.07 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R 
       17.75         7.73         3.12        20.98         7.59        11.31 
TCGA-GU-A763 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QI 
       27.09         4.73         4.41         6.41         5.69         4.14 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A3WV 
        6.67         1.51         3.06         9.01         3.45         4.67 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A8JT 
        6.48        10.52         1.81         4.27         6.38        11.80 
TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE 
       12.23         0.85         3.75        45.04         6.58        97.45 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 
       17.88        64.80        79.66        21.04        28.24        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR 
       16.27         2.10        92.98        10.82        54.90        91.73 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        8.32        56.48        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       10.36         4.83         0.66 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.10               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            123.85             140.81 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              8.22              10.55 
[1] "0.1 - 123.8 (8.2)"  "0.1 - 140.8 (10.6)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED          1       1       24        34       31
  15Q LOSS WILD-TYPE        0       1       62        59       61
D67V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  1                  1
  STAGE II                24                 62
  STAGE III               34                 59
  STAGE IV                31                 61
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  15Q LOSS MUTATED         22 51 11
  15Q LOSS WILD-TYPE       60 85 28
D67V4, multiclass
          clus
vv         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1+T2               22                 60
  T3                     51                 85
  T4                     11                 28
[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"
                    vv
clus                  N0  N1  N2  N3
  15Q LOSS MUTATED    55  10  18   2
  15Q LOSS WILD-TYPE 111  18  37   5
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               55                111
  N1               10                 18
  N2               18                 37
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED   32  2 59
  15Q LOSS WILD-TYPE 97  5 82
D67V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               32                 97
  M1                2                  5
  MX               59                 82
[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"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    27  66
  15Q LOSS WILD-TYPE  50 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     27   66
  15Q LOSS WILD-TYPE   50  135
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               27                 50
  MALE                 66                135
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
D67V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       4                         3    78
  15Q LOSS WILD-TYPE    27                        10   137
D67V11, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    4                 27
  BLACK OR AFRICAN AMERICAN                3                 10
  WHITE                                   78                137
[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"
D67V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3  84
  15Q LOSS WILD-TYPE   2 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3   84
  15Q LOSS WILD-TYPE    2  174
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               84                174
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    51  17
  16P LOSS WILD-TYPE 131  71
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                68                202 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                17                 71 
$`16P LOSS MUTATED`
TCGA-2F-A9KO TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A3PJ TCGA-BT-A42E TCGA-CF-A1HS 
       22.29        32.84         5.06        12.82         9.99         0.43 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A2HX 
       12.92         5.46         5.19         1.84         2.53         1.81 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 
      123.85        87.32        10.55        17.98        67.36        30.67 
TCGA-E7-A541 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
        0.59        12.89         6.87         5.52        13.18        22.98 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       12.13        13.38         5.36        27.45         2.66         4.83 
TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2EF 
        6.38         6.71         4.11         2.20        15.19        61.94 
TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
       20.12        15.91        14.07         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH 
        2.10         2.20         6.41         6.15         5.69         7.79 
TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
       11.54        38.60         6.48        10.52         1.74         1.81 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG 
        3.45        13.48        12.23         6.58        56.19        15.35 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAN0 
       79.66        11.90        23.64        21.04         2.24        56.48 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

$`16P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       19.04        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ 
        4.67         2.07        15.42        28.70        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94        23.01         0.46         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR 
        0.10         0.07         0.10         0.10         4.90         7.20 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       16.31         9.34         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        8.91       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
       10.59         7.79         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       10.49        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
      140.81        48.00        64.18        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       41.06        43.59        15.35        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.49         0.53         0.56         0.66         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.99        14.33         1.22         0.46        15.68         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       22.45         6.12        12.82        46.78        19.79         1.97 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93        14.96        14.93         3.62        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
        6.87         5.69         6.84         6.87        49.68         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       50.66        18.81         9.30         2.07         2.66         4.01 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
       10.85         7.13         3.48         4.08         3.25         6.48 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
        0.85        52.67         6.94        19.46         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B 
       15.81         4.50        17.75         3.12        20.98         7.36 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.59        11.31         2.04        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
       10.65         4.41         6.41         7.63         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
        6.41        19.07         1.51         6.74         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB 
        8.22         8.75         3.45         4.67         2.50         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        6.38         6.35        11.80        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
        3.75        45.04        88.93        97.45         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       64.80        28.24        26.27        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
        2.10        92.98        10.82        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
        3.88        10.36         4.83         0.66 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.43               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            123.85             140.81 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             9.515              9.155 
[1] "0.4 - 123.8 (9.5)" "0.1 - 140.8 (9.2)"
[1] "hr=" "1.3"
D68V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED          1       0       18        24       23
  16P LOSS WILD-TYPE        0       2       68        69       69
D68V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                18                 68
  STAGE III               24                 69
  STAGE IV                23                 69
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  16P LOSS MUTATED         17 40  6
  16P LOSS WILD-TYPE       65 96 33
D68V4, multiclass
          clus
vv         16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1+T2               17                 65
  T3                     40                 96
  T4                      6                 33
[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"
                    vv
clus                  N0  N1  N2  N3
  16P LOSS MUTATED    37   8  16   2
  16P LOSS WILD-TYPE 129  20  39   5
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               37                129
  N1                8                 20
  N2               16                 39
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16P LOSS MUTATED    23   0  45
  16P LOSS WILD-TYPE 106   7  96
D68V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               23                106
  M1                0                  7
  MX               45                 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"
D68V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    18  50
  16P LOSS WILD-TYPE  59 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     18   50
  16P LOSS WILD-TYPE   59  151
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               18                 59
  MALE                 50                151
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
D68V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       4                         1    59
  16P LOSS WILD-TYPE    27                        12   156
D68V11, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    4                 27
  BLACK OR AFRICAN AMERICAN                1                 12
  WHITE                                   59                156
[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"
D68V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     2  64
  16P LOSS WILD-TYPE   3 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2   64
  16P LOSS WILD-TYPE    3  194
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               64                194
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    43  20
  16Q LOSS WILD-TYPE 139  68
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                63                207 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                20                 68 
$`16Q LOSS MUTATED`
TCGA-BT-A42E TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
        9.99         0.43        12.92         5.46         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IV TCGA-DK-A3X2 
        2.53         1.81       123.85        87.32         9.67        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-FD-A3SO 
       67.36        30.67        15.35         0.49         0.59         5.52 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ 
        1.97        22.98        14.93        13.38         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 
        2.66         4.83         6.38         6.71         4.11        15.19 
TCGA-FT-A61P TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A6C6 
        6.48        20.12        15.91        14.07         2.10         2.20 
TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-HQ-A2OE 
        6.41         4.41         6.15         5.69         7.79        38.60 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V 
        4.67         6.48         1.74         1.81         3.45        13.48 
TCGA-PQ-A6FI TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI 
       12.23         6.58        97.45        56.19        15.35        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAML TCGA-XF-AAMX 
       11.90        23.64        21.04         2.24         7.63         6.77 
TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-YF-AA3M 
       56.48         7.96         9.04 

$`16Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       15.42        28.70        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E 
        0.10         0.10         4.90         7.20        16.31         9.34 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20         3.98         7.82         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        20.02         8.28        10.55       140.81        48.00 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC 
       64.18        41.56        76.60        15.68        41.06        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF 
       26.17        24.66         0.10         0.53         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        1.38         0.82        12.99        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       12.89        15.68         8.94         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       11.93        15.88        45.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S 
       12.82        13.18        46.78        19.79        14.93        14.96 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        12.13        37.15        11.01         6.87         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        6.84         6.87        49.68         6.28        50.66        18.81 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        9.30         2.07         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13         3.48         4.08         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
        5.69        26.93        35.24        17.26         7.04         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       52.67         6.94        19.46         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ 
        4.50        17.75         1.12         2.66         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98         7.36         7.59        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QI 
        5.62         4.73        10.65         6.41         7.63         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.67         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        3.06         9.01         8.22         8.75         3.45         2.50 
TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN 
       10.52         4.27         6.38         6.35        11.80        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HH 
       14.24         0.85         3.75        45.04        88.93         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 
       17.88        64.80        28.24        26.27        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR 
       66.64         2.10        92.98        10.82        54.90        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        2.96         8.32        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       10.36         4.83         0.66 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.43               0.07 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            123.85             140.81 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              7.63              10.49 
[1] "0.4 - 123.8 (7.6)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED          0       0       18        20       23
  16Q LOSS WILD-TYPE        1       2       68        73       69
D69V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                18                 68
  STAGE III               20                 73
  STAGE IV                23                 69
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  16Q LOSS MUTATED         16  34   8
  16Q LOSS WILD-TYPE       66 102  31
D69V4, multiclass
          clus
vv         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1+T2               16                 66
  T3                     34                102
  T4                      8                 31
[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"
                    vv
clus                  N0  N1  N2  N3
  16Q LOSS MUTATED    31   6  17   2
  16Q LOSS WILD-TYPE 135  22  38   5
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               31                135
  N1                6                 22
  N2               17                 38
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16Q LOSS MUTATED    20   0  43
  16Q LOSS WILD-TYPE 109   7  98
D69V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               20                109
  M1                0                  7
  MX               43                 98
[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"
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    15  48
  16Q LOSS WILD-TYPE  62 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     15   48
  16Q LOSS WILD-TYPE   62  153
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               15                 62
  MALE                 48                153
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
D69V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       5                         2    52
  16Q LOSS WILD-TYPE    26                        11   163
D69V11, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    5                 26
  BLACK OR AFRICAN AMERICAN                2                 11
  WHITE                                   52                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     2  59
  16Q LOSS WILD-TYPE   3 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2   59
  16Q LOSS WILD-TYPE    3  199
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               59                199
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    73  42
  17P LOSS WILD-TYPE 109  46
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               115                155 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                42                 46 
$`17P LOSS MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P 
      103.50        98.33        12.39        19.04        32.84        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       19.50        14.89         8.25        17.16         5.59         4.67 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        2.07         9.99         1.94         0.46         0.43         0.69 
TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2HX 
        0.10         5.46         1.84         8.91       112.44         1.81 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32         3.98         8.22        10.49        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-E5-A2PC 
        9.67        48.00        17.98        64.18        41.06        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A677 TCGA-E7-A6ME 
       15.35        26.17         0.49         0.59         1.38        12.99 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO 
       15.68         8.94        45.93        24.30        12.82         5.52 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X 
       46.78         1.97        22.98        14.93        14.93         3.62 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       13.38         5.36         6.84         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3ZE 
       50.66        18.81         6.71         2.66        10.85         3.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        30.61        26.93        35.24         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A6C6 
        0.85         2.89        14.07         1.12         2.10         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3QF 
        7.36         7.59        11.31         4.73         6.41         7.63 
TCGA-GV-A40E TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC 
        6.41         6.74         3.06         9.01         8.22         6.48 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        1.74         4.27        12.23        16.67        14.24         0.85 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SI 
       88.93        97.45        56.19        15.35         1.87        79.66 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR 
       23.64        28.24         2.24        10.82        54.90        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-YF-AA3L 
        2.96         8.32         6.77        56.48        30.94         7.96 
TCGA-YF-AA3M 
        9.04 

$`17P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I 
       22.29        11.97        84.00         4.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20R 
        2.66         6.74         6.58        11.93        12.16         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42B 
       14.96         5.06         8.35         3.65        12.82        15.42 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A47S TCGA-CF-A47T 
       28.70        28.41         8.98        23.01         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.10         0.07         0.10        12.92         4.90         7.20 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.19        16.31         9.34         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       18.41        19.00       130.88        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IU 
       10.59         7.79       123.85         2.20         7.82        20.02 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        8.28        10.55       140.81        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE 
       15.68        30.67        24.66         0.10         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        0.66         0.82        14.33         1.22         0.46        12.89 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL 
        6.87         4.01        12.43        11.93        15.88        22.45 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS 
        6.12        13.18        19.79        14.96        12.13        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       11.01         6.87         5.69        27.45         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI 
        2.66         9.30         4.11         2.07         2.20         4.01 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK 
       15.19         7.13         4.08         3.25         6.48         5.69 
TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.26        52.67         6.94        19.46         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ 
        4.50        15.91        17.75         2.66         7.73         3.12 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO 
       20.98         6.41         2.04        27.09         5.62        10.65 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        4.41         6.15         5.69         7.79         4.14         6.67 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07        11.54         1.51        38.60         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
        4.67         2.50        10.52         1.81         6.38         6.35 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
        3.45        11.80        13.48         3.75        45.04         6.58 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       17.88        64.80        11.90        21.04        26.27        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAML TCGA-XF-AAN4 
       16.27        66.64         2.10        92.98         7.63        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39         3.88        10.36         4.83         0.66 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            112.44             140.81 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              9.67               8.98 
[1] "0.1 - 112.4 (9.7)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED          0       0       37        38       39
  17P LOSS WILD-TYPE        1       2       49        55       53
D70V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                37                 49
  STAGE III               38                 55
  STAGE IV                39                 53
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  17P LOSS MUTATED         33 58 15
  17P LOSS WILD-TYPE       49 78 24
D70V4, multiclass
          clus
vv         17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1+T2               33                 49
  T3                     58                 78
  T4                     15                 24
[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"
                    vv
clus                 N0 N1 N2 N3
  17P LOSS MUTATED   69  8 26  2
  17P LOSS WILD-TYPE 97 20 29  5
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               69                 97
  N1                8                 20
  N2               26                 29
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED   52  2 62
  17P LOSS WILD-TYPE 77  5 79
D70V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               52                 77
  M1                2                  5
  MX               62                 79
[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"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    31  86
  17P LOSS WILD-TYPE  46 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     31   86
  17P LOSS WILD-TYPE   46  115
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               31                 46
  MALE                 86                115
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, continuous
D70V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED      13                         7    86
  17P LOSS WILD-TYPE    18                         6   129
D70V11, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                   13                 18
  BLACK OR AFRICAN AMERICAN                7                  6
  WHITE                                   86                129
[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"
D70V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     3 107
  17P LOSS WILD-TYPE   2 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3  107
  17P LOSS WILD-TYPE    2  151
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO              107                151
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    19   6
  17Q LOSS WILD-TYPE 163  82
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                245 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                 82 
$`17Q LOSS MUTATED`
TCGA-BT-A20P TCGA-CF-A1HR TCGA-CF-A1HS TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A6AV 
       17.88         0.46         0.43         8.91         8.22        64.18 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43U 
       15.35        26.17        45.93         1.97        14.93        14.93 
TCGA-FD-A43X TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A3IB TCGA-G2-A3IE 
        3.62         6.38        10.85         3.48         7.04        20.12 
TCGA-GC-A3YS TCGA-GV-A3JW TCGA-HQ-A2OF TCGA-K4-A4AC TCGA-PQ-A6FN TCGA-XF-A9SI 
        1.12         6.41         3.06         6.48        16.67        79.66 
TCGA-XF-AAMX 
        6.77 

$`17Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        32.84        12.16        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        5.59         3.65         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70         9.99        28.41         8.98         1.94        23.01 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.10        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84         9.34         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        2.20         3.98         7.82        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       20.02         9.67         8.28        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       17.98        41.56        76.60        67.36        15.68        41.06 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       30.67        43.59        24.66         0.10         0.49         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.59         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.33         1.22         0.46        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ 
        6.87         4.01        12.43        11.93        15.88        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        22.98        14.96        12.13        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01         6.87         5.36         5.69         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA 
        6.87        49.68         2.66         4.83         6.28        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         9.30         6.71         4.11         2.07         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.20         4.01        15.19         7.13         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       17.26         0.85        52.67         6.94        19.46         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        2.66         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36         6.41         7.59        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
        5.62         4.73        10.65         4.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        7.63         7.79         4.14         6.67         6.41        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE 
       11.54         1.51         6.74        38.60         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ 
        8.75         3.45         4.67         2.50        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81         4.27         6.38         6.35         3.45        11.80 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB 
       13.48        12.23        14.24         0.85         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        88.93        97.45        56.19        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       17.88        64.80        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT 
       92.98        10.82        54.90         7.63        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        8.32        56.48        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       10.36         4.83         0.66         7.96         9.04 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.43               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             79.66             140.81 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              8.22               9.34 
[1] "0.4 - 79.7 (8.2)"  "0.1 - 140.8 (9.3)"
[1] "hr=" "1.2"
D71V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED          0       0       11         7        6
  17Q LOSS WILD-TYPE        1       2       75        86       86
D71V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                11                 75
  STAGE III                7                 86
  STAGE IV                 6                 86
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  17Q LOSS MUTATED          9   9   5
  17Q LOSS WILD-TYPE       73 127  34
D71V4, multiclass
          clus
vv         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1+T2                9                 73
  T3                      9                127
  T4                      5                 34
[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"
                    vv
clus                  N0  N1  N2  N3
  17Q LOSS MUTATED    17   1   2   2
  17Q LOSS WILD-TYPE 149  27  53   5
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               17                149
  N1                1                 27
  N2                2                 53
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  17Q LOSS MUTATED     9   1  16
  17Q LOSS WILD-TYPE 120   6 125
D71V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                9                120
  M1                1                  6
  MX               16                125
[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"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     9  17
  17Q LOSS WILD-TYPE  68 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9   17
  17Q LOSS WILD-TYPE   68  184
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                9                 68
  MALE                 17                184
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, continuous
D71V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       5                         4    15
  17Q LOSS WILD-TYPE    26                         9   200
D71V11, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    5                 26
  BLACK OR AFRICAN AMERICAN                4                  9
  WHITE                                   15                200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  25
  17Q LOSS WILD-TYPE   5 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   25
  17Q LOSS WILD-TYPE    5  233
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               25                233
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    45  19
  18P LOSS WILD-TYPE 137  69
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                64                206 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                19                 69 
$`18P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BT-A20J TCGA-BT-A20N 
       22.29        84.00       103.50         4.83        19.04        32.84 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42B TCGA-CF-A1HR 
        5.06        14.89         8.25        17.16        15.42         0.46 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        0.13         0.07         1.84         9.34         2.53         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
       18.41         8.91       112.44        17.62         1.81        10.59 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV 
        3.98        10.49        50.27        21.30        17.98        64.18 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A5KE TCGA-E7-A7DV 
       15.68        41.06        43.59        24.66         0.56         1.22 
TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A62O TCGA-FD-A62S 
        4.01        24.30        12.82        46.78         4.83         6.38 
TCGA-FD-A6TA TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS 
       50.66        20.12        52.67         2.89        14.07         1.12 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A40E TCGA-HQ-A2OE TCGA-HQ-A2OF 
        4.73        10.65         6.41         6.41        38.60         3.06 
TCGA-K4-A5RJ TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-AAMR 
        1.74        12.23        16.67        11.90        66.64        91.73 
TCGA-XF-AAMW TCGA-YC-A89H TCGA-YF-AA3L TCGA-YF-AA3M 
        8.32        10.36         7.96         9.04 

$`18P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       11.97        98.33        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        11.93        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         5.06         8.35         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         2.07        28.70         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W 
        1.94        23.01         0.43         0.69         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.10         0.10        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE 
        5.19        16.31        66.41        19.00       130.88        16.14 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM 
       15.62         7.79       123.85        87.32         2.20         7.82 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        8.22        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       48.00        41.56        76.60        67.36        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF 
       26.17         0.10         0.49         0.53         0.59         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 
        1.38         0.82        12.99        14.33         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       15.68         8.94         6.87        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR 
       45.93        22.45         6.12         5.52        13.18        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        1.97        22.98        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       12.13        13.38        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         6.84        27.45         6.87        49.68         2.66 
TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
        6.28        18.81         9.30         6.71         4.11         2.07 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.66         2.20         4.01        10.85        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        3.48         4.08         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
        5.69        26.93        35.24        17.26         7.04         0.85 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        6.94        19.46         2.24        15.81         4.50        15.91 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       17.75         2.66         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36         6.41         7.59        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       27.09         5.62         4.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.79         4.14         6.67        19.07        11.54         1.51 
TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        6.74         9.01         8.22         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        2.50         6.48        10.52         1.81         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX 
        6.35         3.45        11.80        13.48        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.75        45.04         6.58        88.93        97.45        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX 
       15.35         1.87        17.88        64.80        79.66        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT 
        2.10        92.98        10.82        54.90         7.63         2.96 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        6.77        56.48        30.94        27.06        75.39         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC 
        4.83         0.66 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            112.44             140.81 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            11.275              8.315 
[1] "0.1 - 112.4 (11.3)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED          0       0       22        15       28
  18P LOSS WILD-TYPE        1       2       64        78       64
D72V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                22                 64
  STAGE III               15                 78
  STAGE IV                28                 64
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  18P LOSS MUTATED         23  35   6
  18P LOSS WILD-TYPE       59 101  33
D72V4, multiclass
          clus
vv         18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1+T2               23                 59
  T3                     35                101
  T4                      6                 33
[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"
                    vv
clus                  N0  N1  N2  N3
  18P LOSS MUTATED    33   8  18   1
  18P LOSS WILD-TYPE 133  20  37   6
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               33                133
  N1                8                 20
  N2               18                 37
  N3                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  18P LOSS MUTATED    37   0  30
  18P LOSS WILD-TYPE  92   7 111
D72V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               37                 92
  M1                0                  7
  MX               30                111
[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"
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    22  45
  18P LOSS WILD-TYPE  55 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     22   45
  18P LOSS WILD-TYPE   55  156
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               22                 55
  MALE                 45                156
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, continuous
D72V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       8                         2    50
  18P LOSS WILD-TYPE    23                        11   165
D72V11, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    8                 23
  BLACK OR AFRICAN AMERICAN                2                 11
  WHITE                                   50                165
[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"
D72V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  59
  18P LOSS WILD-TYPE   2 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   59
  18P LOSS WILD-TYPE    2  199
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               59                199
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    69  25
  18Q LOSS WILD-TYPE 113  63
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                94                176 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                25                 63 
$`18Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BT-A20J TCGA-BT-A20N 
       22.29        84.00       103.50         4.83        19.04        32.84 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42B 
        5.06        14.89         8.35         8.25        17.16        15.42 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CU-A0YN TCGA-CU-A0YR 
        0.46         0.43         0.13         0.07        12.92         7.20 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD 
        1.84         9.34         2.14        18.41         8.91       112.44 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62         1.81        10.59        87.32         2.20         3.98 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 
       10.49        50.27        21.30        48.00        64.18        15.68 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3B4 
       41.06        43.59        24.66         0.56         1.22        15.68 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
        4.01        45.93        12.82         5.52        13.18        46.78 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
        1.97        22.98         2.66         4.83         6.38        50.66 
TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM 
        4.08        61.94        20.12        52.67        19.46         2.89 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A762 
       15.91        14.07         1.12        20.98         2.20         2.04 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A40E 
        5.62         4.73        10.65         6.41         6.15         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS 
       19.07        11.54         6.74        38.60         3.06         8.75 
TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        4.67         1.74         6.35        13.48        12.23        16.67 
TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9T5 TCGA-XF-AAMJ 
        6.58        56.19        11.90        23.64        66.64        54.90 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-YF-AA3L TCGA-YF-AA3M 
       91.73         2.96         7.96         9.04 

$`18Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       11.97        98.33        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        11.93        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         5.06         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        2.07        28.70         9.99        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       23.01         0.69         0.10         0.07         0.10         0.10 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 
        4.90         5.46         5.19        16.31         2.53        66.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
       19.00       130.88        16.14        15.62         7.79       123.85 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        7.82         8.22        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
      140.81        17.98        41.56        76.60        67.36        30.67 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       15.35        26.17         0.10         0.49         0.53         0.59 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        0.66         1.38         0.82        12.99        14.33         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       12.89         8.94         6.87        12.43        11.93        15.88 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S 
       24.30        22.45         6.12        19.79        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93         3.62        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
        6.87         5.36         5.69         6.84        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       49.68         6.28        18.81         9.30         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.07         2.66         2.20         4.01        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK 
        7.13         3.48         3.25         6.48        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3C 
       26.93        35.24        17.26         7.04         0.85         6.94 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 
        2.24        15.81         4.50        17.75         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12         7.36         6.41         7.59        11.31 
TCGA-GU-A763 TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       27.09         4.41         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB 
        6.67         1.51         9.01         8.22         3.45         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 
        6.48        10.52         1.81         4.27         6.38         3.45 
TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD 
       11.80        14.24         0.85         3.75        45.04        88.93 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       97.45        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX 
        2.10        92.98        10.82         7.63         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC 
        4.83         0.66 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            112.44             140.81 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            11.095              8.300 
[1] "0.1 - 112.4 (11.1)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1.5"
D73V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED          1       0       28        28       36
  18Q LOSS WILD-TYPE        0       2       58        65       56
D73V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                28                 58
  STAGE III               28                 65
  STAGE IV                36                 56
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  18Q LOSS MUTATED         29 51 10
  18Q LOSS WILD-TYPE       53 85 29
D73V4, multiclass
          clus
vv         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1+T2               29                 53
  T3                     51                 85
  T4                     10                 29
[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"
                    vv
clus                  N0  N1  N2  N3
  18Q LOSS MUTATED    53  11  22   2
  18Q LOSS WILD-TYPE 113  17  33   5
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               53                113
  N1               11                 17
  N2               22                 33
  N3                2                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED   48  1 47
  18Q LOSS WILD-TYPE 81  6 94
D73V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               48                 81
  M1                1                  6
  MX               47                 94
[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"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    28  68
  18Q LOSS WILD-TYPE  49 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     28   68
  18Q LOSS WILD-TYPE   49  133
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               28                 49
  MALE                 68                133
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, continuous
D73V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED      11                         4    72
  18Q LOSS WILD-TYPE    20                         9   143
D73V11, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                   11                 20
  BLACK OR AFRICAN AMERICAN                4                  9
  WHITE                                   72                143
[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"
D73V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3  86
  18Q LOSS WILD-TYPE   2 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   86
  18Q LOSS WILD-TYPE    2  172
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               86                172
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    38  30
  19P LOSS WILD-TYPE 144  58
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                68                202 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                30                 58 
$`19P LOSS MUTATED`
TCGA-2F-A9KW TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD 
        4.83        19.04         5.06         5.06         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F6 
        4.67         2.07        15.42         9.99         8.98        23.01 
TCGA-CU-A0YN TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN 
       12.92         2.14       112.44        87.32         3.98         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-FD-A3SJ 
       10.49        21.30        17.98        43.59         0.49        24.30 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BY 
        6.12         5.52         1.97        22.98         5.36         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TB TCGA-FD-A6TE TCGA-FJ-A3ZE 
       27.45         6.87        49.68        18.81         4.11         3.48 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
        4.08         6.48        17.26         7.04        20.12         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GU-A42P 
       19.46         2.24         4.50         2.66         2.20         6.41 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-AATO TCGA-GV-A3JZ TCGA-H4-A2HQ TCGA-HQ-A5ND 
        7.59         2.04        10.65         5.69         6.74         9.01 
TCGA-K4-A3WS TCGA-K4-A54R TCGA-K4-A5RJ TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
        8.75        10.52         1.74         6.35        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-XF-A8HB TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 
       16.67        14.24        45.04        11.90        66.64         2.10 
TCGA-XF-AAMX TCGA-YF-AA3M 
        6.77         9.04 

$`19P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 
       22.29        11.97        84.00       103.50        98.33        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       32.84        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F 
        8.35         8.25        17.16        12.82        28.70        28.41 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94         0.46         0.43         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR 
        0.10         0.07         0.10         0.10         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84         9.34         2.53 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       66.41        18.41        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        2.20         7.82        50.27        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 
       67.36        15.68        41.06        30.67        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         0.53         0.59         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        1.38         0.82        12.99        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       12.89        15.68         8.94         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SP 
       11.93        15.88        45.93        22.45        12.82        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       46.78        19.79        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       12.13        13.38        37.15        11.01         6.87         5.69 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
        2.66         4.83         6.28         6.38        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        6.71         2.07         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       15.19         7.13         3.25        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3OO 
       26.93        35.24         0.85        52.67         2.89        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07        17.75         1.12         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 
        3.12        20.98         7.36        11.31        27.09         5.62 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
        4.73         4.41         6.41         6.15         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.14         6.67         6.41        19.07        11.54         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       38.60         3.06         8.22         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT 
        6.48         1.81         4.27         6.38         3.45        11.80 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        0.85         3.75         6.58        88.93        97.45        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX 
       15.35         1.87        17.88        64.80        79.66        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT 
       92.98        10.82        54.90         7.63        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        8.32        56.48        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       10.36         4.83         0.66         7.96 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.49               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            112.44             140.81 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             7.315             10.705 
[1] "0.5 - 112.4 (7.3)"  "0.1 - 140.8 (10.7)"
[1] "hr=" "1.9"
D74V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED          0       0       13        24       31
  19P LOSS WILD-TYPE        1       2       73        69       61
D74V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                13                 73
  STAGE III               24                 69
  STAGE IV                31                 61
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  19P LOSS MUTATED         13 43  7
  19P LOSS WILD-TYPE       69 93 32
D74V4, multiclass
          clus
vv         19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1+T2               13                 69
  T3                     43                 93
  T4                      7                 32
[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"
                    vv
clus                  N0  N1  N2  N3
  19P LOSS MUTATED    33  13  14   3
  19P LOSS WILD-TYPE 133  15  41   4
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               33                133
  N1               13                 15
  N2               14                 41
  N3                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  19P LOSS MUTATED    27   4  37
  19P LOSS WILD-TYPE 102   3 104
D74V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               27                102
  M1                4                  3
  MX               37                104
[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"
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    20  48
  19P LOSS WILD-TYPE  57 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     20   48
  19P LOSS WILD-TYPE   57  153
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               20                 57
  MALE                 48                153
[1] 2 2
[1] FALSE
D74V8, continuous
D74V9, continuous
D74V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         4    57
  19P LOSS WILD-TYPE    30                         9   158
D74V11, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                 30
  BLACK OR AFRICAN AMERICAN                4                  9
  WHITE                                   57                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"
D74V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2  61
  19P LOSS WILD-TYPE   3 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   61
  19P LOSS WILD-TYPE    3  197
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               61                197
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    23  17
  19Q LOSS WILD-TYPE 159  71
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                40                230 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                 71 
$`19Q LOSS MUTATED`
TCGA-2F-A9KW TCGA-BT-A20R TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        4.83         5.06         3.65         4.67         2.07        15.42 
TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A1AD TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
        8.98        12.92       112.44         8.22        10.49        21.30 
TCGA-DK-A3X2 TCGA-E7-A4IJ TCGA-FD-A3SO TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 
       17.98         0.49         5.52         5.36         6.84        49.68 
TCGA-FD-A6TE TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        4.11         3.48         6.48        17.26         7.04        20.12 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-AATO TCGA-K4-A54R 
        2.24         4.50         2.20         2.04        10.65        10.52 
TCGA-K4-A5RJ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.74         6.35         3.45        13.48        12.23        16.67 
TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAML 
       11.90        66.64         2.10         7.63 

$`19Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 
       22.29        11.97        84.00       103.50        98.33        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       19.04        32.84        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.96         5.06         8.35         8.25        17.16         5.59 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
       12.82        28.70         9.99        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.07         0.10         0.10         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84         9.34         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       66.41        18.41        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IU 
       87.32         2.20         3.98         7.82        50.27        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV 
        9.67         8.28        10.55       140.81        48.00        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       41.56        76.60        67.36        15.68        41.06        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       43.59        15.35        26.17        24.66         0.10         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.59         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.33         1.22         0.46        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        6.87         4.01        12.43        11.93        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        22.45         6.12        12.82        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79         1.97        22.98        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        12.13        13.38        37.15        11.01         6.87 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        5.69        27.45         6.87         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF 
        6.38        50.66        18.81         9.30         6.71         2.07 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.66         2.20         4.01        10.85        15.19         7.13 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        4.08         3.25        61.94        30.61         5.69        26.93 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       35.24         0.85        52.67         6.94        19.46         2.89 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81        15.91        14.07        17.75         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV 
        7.59        11.31        27.09         5.62         4.73         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        6.41         6.15         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.67         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60         3.06         9.01         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        4.67         2.50         6.48         1.81         4.27         6.38 
TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       11.80        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       88.93        97.45        56.19        15.35         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       64.80        79.66        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       18.90         2.24        16.27        92.98        10.82        54.90 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
       91.73         2.96         8.32         6.77        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.49               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            112.44             140.81 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             6.940             10.175 
[1] "0.5 - 112.4 (6.9)"  "0.1 - 140.8 (10.2)"
[1] "hr=" "1.9"
D75V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED          0       0       10        14       16
  19Q LOSS WILD-TYPE        1       2       76        79       76
D75V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                10                 76
  STAGE III               14                 79
  STAGE IV                16                 76
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  19Q LOSS MUTATED          6  26   4
  19Q LOSS WILD-TYPE       76 110  35
D75V4, multiclass
          clus
vv         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1+T2                6                 76
  T3                     26                110
  T4                      4                 35
[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"
                    vv
clus                  N0  N1  N2  N3
  19Q LOSS MUTATED    20   6   9   1
  19Q LOSS WILD-TYPE 146  22  46   6
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               20                146
  N1                6                 22
  N2                9                 46
  N3                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  19Q LOSS MUTATED    13   2  25
  19Q LOSS WILD-TYPE 116   5 116
D75V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               13                116
  M1                2                  5
  MX               25                116
[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"
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    10  30
  19Q LOSS WILD-TYPE  67 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     10   30
  19Q LOSS WILD-TYPE   67  171
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               10                 67
  MALE                 30                171
[1] 2 2
[1] FALSE
D75V8, continuous
D75V9, continuous
D75V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         1    37
  19Q LOSS WILD-TYPE    30                        12   178
D75V11, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                 30
  BLACK OR AFRICAN AMERICAN                1                 12
  WHITE                                   37                178
[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"
D75V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0  38
  19Q LOSS WILD-TYPE   5 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   38
  19Q LOSS WILD-TYPE    5  220
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               38                220
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    12   8
  20P LOSS WILD-TYPE 170  80
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                20                250 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                 80 
$`20P LOSS MUTATED`
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-CF-A47S TCGA-DK-A1A3 TCGA-DK-A3IM 
       19.04        32.84        17.88         0.13         2.53         7.82 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-FD-A5C0 TCGA-FD-A6TB TCGA-G2-A3VY 
        9.67        48.00        64.18         6.87        18.81         0.85 
TCGA-GU-A42R TCGA-GV-A40E TCGA-HQ-A2OE TCGA-K4-A4AC TCGA-XF-A8HE TCGA-XF-A9SW 
       11.31         6.41        38.60         6.48        97.45        11.90 
TCGA-XF-AAML TCGA-XF-AAMX 
        7.63         6.77 

$`20P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       11.93        12.16        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         2.07        15.42        28.70         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.69         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84         9.34         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        8.91       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        3.98         8.22        10.49        50.27        21.30        20.02 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        17.98        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       67.36        15.68        41.06        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       26.17        24.66         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66         1.38         0.82        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22         0.46        12.89        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79         1.97        22.98        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        12.13        13.38        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         5.69         6.84        27.45        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
        4.83         6.28         6.38        50.66         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        4.11         2.07         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
       15.19         7.13         3.48         4.08         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
        7.04        20.12        52.67         6.94        19.46         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        1.12         2.66         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 
        2.20         7.36         6.41         7.59         2.04        27.09 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        5.62         4.73        10.65         4.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
        5.69         7.63         7.79         4.14         6.67        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       11.54         1.51         6.74         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ 
        8.75         3.45         4.67         2.50        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81         4.27         6.38         6.35         3.45        11.80 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         0.85         3.75 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58        88.93        56.19        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       17.88        64.80        79.66        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       92.98        10.82        54.90        91.73         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.13               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             97.45             140.81 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            10.490              9.025 
[1] "0.1 - 97.5 (10.5)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED          0       0       10         7        3
  20P LOSS WILD-TYPE        1       2       76        86       89
D76V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                10                 76
  STAGE III                7                 86
  STAGE IV                 3                 89
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  20P LOSS MUTATED          7  10   0
  20P LOSS WILD-TYPE       75 126  39
D76V4, multiclass
          clus
vv         20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1+T2                7                 75
  T3                     10                126
  T4                      0                 39
[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"
                    vv
clus                  N0  N1  N2  N3
  20P LOSS MUTATED    13   0   4   0
  20P LOSS WILD-TYPE 153  28  51   7
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               13                153
  N1                0                 28
  N2                4                 51
  N3                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  20P LOSS MUTATED     8   0  12
  20P LOSS WILD-TYPE 121   7 129
D76V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                8                121
  M1                0                  7
  MX               12                129
[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"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     4  17
  20P LOSS WILD-TYPE  73 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4   17
  20P LOSS WILD-TYPE   73  184
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                4                 73
  MALE                 17                184
[1] 2 2
[1] FALSE
D76V8, continuous
D76V9, continuous
D76V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       4                         1    14
  20P LOSS WILD-TYPE    27                        12   201
D76V11, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    4                 27
  BLACK OR AFRICAN AMERICAN                1                 12
  WHITE                                   14                201
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  19
  20P LOSS WILD-TYPE   5 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   19
  20P LOSS WILD-TYPE    5  239
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               19                239
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     3   6
  20Q LOSS WILD-TYPE 179  82
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                261 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                 82 
$`20Q LOSS MUTATED`
TCGA-BT-A20P TCGA-BT-A20V TCGA-DK-A1A3 TCGA-DK-A2I6 TCGA-DK-A3IV TCGA-HQ-A5NE 
       17.88         5.06         2.53        87.32         9.67         8.22 
TCGA-XF-A9SW TCGA-XF-AAML TCGA-XF-AAMW 
       11.90         7.63         8.32 

$`20Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        32.84        12.16        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.89        14.96         8.35         8.25        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        3.65         4.67        12.82         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        9.99        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.10         0.10        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.19        16.31         1.84         9.34         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20         3.98         7.82         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        20.02         8.28        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       41.06        30.67        43.59        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         0.53         0.59         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        1.38         0.82        12.99        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       12.89        15.68         8.94         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       11.93        15.88        45.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       12.82         5.52        13.18        46.78        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        14.93        14.96        14.93         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       13.38        37.15        11.01         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        6.84        27.45         6.87        49.68         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28         6.38        50.66        18.81         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        4.11         2.07         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
       15.19         7.13         3.48         4.08         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
        7.04        20.12         0.85        52.67         6.94        19.46 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        2.89         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75         1.12         2.66         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36         6.41         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        2.04        27.09         5.62         4.73        10.65         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        6.41         6.15         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.67         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         9.01         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.50         6.48        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38         6.35         3.45        11.80        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       16.67        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       88.93        97.45        56.19        15.35         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       64.80        79.66        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 
       10.82        54.90        91.73         2.96         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        0.66         7.96         9.04 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.53               0.07 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             87.32             140.81 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              8.32               9.30 
[1] "2.5 - 87.3 (8.3)"  "0.1 - 140.8 (9.3)"
[1] "hr=" "2.3"
D77V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED          0       0        2         2        5
  20Q LOSS WILD-TYPE        1       2       84        91       87
D77V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 2                 84
  STAGE III                2                 91
  STAGE IV                 5                 87
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  20Q LOSS MUTATED          3   4   1
  20Q LOSS WILD-TYPE       79 132  38
D77V4, multiclass
          clus
vv         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1+T2                3                 79
  T3                      4                132
  T4                      1                 38
[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"
                    vv
clus                  N0  N1  N2  N3
  20Q LOSS MUTATED     4   1   3   0
  20Q LOSS WILD-TYPE 162  27  52   7
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                4                162
  N1                1                 27
  N2                3                 52
  N3                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  20Q LOSS MUTATED     6   0   3
  20Q LOSS WILD-TYPE 123   7 138
D77V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                6                123
  M1                0                  7
  MX                3                138
[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"
D77V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   6
  20Q LOSS WILD-TYPE  74 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    6
  20Q LOSS WILD-TYPE   74  195
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                3                 74
  MALE                  6                195
[1] 2 2
[1] FALSE
D77V8, continuous
D77V9, continuous
D77V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         1     7
  20Q LOSS WILD-TYPE    31                        12   208
D77V11, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                 31
  BLACK OR AFRICAN AMERICAN                1                 12
  WHITE                                    7                208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   8
  20Q LOSS WILD-TYPE   5 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    8
  20Q LOSS WILD-TYPE    5  250
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                8                250
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    27  17
  21Q LOSS WILD-TYPE 155  71
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                44                226 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                17                 71 
$`21Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42E TCGA-CF-A1HR 
       22.29        14.89         5.06         8.25         9.99         0.46 
TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A3IN TCGA-DK-A3IQ 
        0.10        12.92         5.19         1.84         8.22        10.49 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43X 
       30.67        43.59         8.94        22.45         5.52         3.62 
TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TF 
       12.13         5.36         6.84        50.66         6.71         2.07 
TCGA-FD-A6TK TCGA-G2-A2EJ TCGA-G2-AA3F TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GU-A767 
       10.85        30.61        19.46         1.12         2.66         4.73 
TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A4AB 
        4.41         4.14        11.54         3.06         9.01         2.50 
TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SX 
        6.48         1.74         3.45        15.35        79.66        23.64 
TCGA-XF-A9T5 TCGA-XF-AAML 
       66.64         7.63 

$`21Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         8.35        17.16         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         2.07        15.42        28.70        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94        23.01         0.43         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.10         0.07         0.10         4.90         7.20         5.46 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         9.34         2.53         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         3.98         7.82        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67         8.28        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        41.56        76.60        67.36        15.68        41.06 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        26.17        24.66         0.10         0.49         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.59         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
       14.33         1.22         0.46        12.89        15.68         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
        6.12        12.82        13.18        46.78        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS 
       22.98        14.93        14.96        14.93        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       11.01         6.87         5.69        27.45         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC 
        2.66         4.83         6.28         6.38        18.81         9.30 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        4.11         2.66         2.20         4.01        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK 
        3.48         4.08         3.25         6.48        61.94         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        17.26         7.04        20.12         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       52.67         6.94         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.91        14.07        17.75         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36         6.41         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX 
        2.04        27.09         5.62        10.65         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        5.69         7.63         7.79         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        1.51         6.74        38.60         8.22         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
        4.67        10.52         1.81         4.27         6.38         6.35 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       11.80        13.48        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.75        45.04         6.58        88.93        97.45        56.19 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ 
        1.87        17.88        64.80        11.90        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       26.27        18.90         2.24        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       10.82        54.90        91.73         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             79.66             140.81 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             7.925             10.440 
[1] "0.1 - 79.7 (7.9)"   "0.1 - 140.8 (10.4)"
[1] "hr=" "1.5"
D78V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED          1       0       10        14       18
  21Q LOSS WILD-TYPE        0       2       76        79       74
D78V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                10                 76
  STAGE III               14                 79
  STAGE IV                18                 74
[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"
                    vv
clus                 T0+T1+T2  T3  T4
  21Q LOSS MUTATED         11  23   7
  21Q LOSS WILD-TYPE       71 113  32
D78V4, multiclass
          clus
vv         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1+T2               11                 71
  T3                     23                113
  T4                      7                 32
[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"
                    vv
clus                  N0  N1  N2  N3
  21Q LOSS MUTATED    24  11   7   0
  21Q LOSS WILD-TYPE 142  17  48   7
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               24                142
  N1               11                 17
  N2                7                 48
  N3                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  21Q LOSS MUTATED    16   2  26
  21Q LOSS WILD-TYPE 113   5 115
D78V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               16                113
  M1                2                  5
  MX               26                115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    11  33
  21Q LOSS WILD-TYPE  66 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     11   33
  21Q LOSS WILD-TYPE   66  168
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               11                 66
  MALE                 33                168
[1] 2 2
[1] FALSE
D78V8, continuous
D78V9, continuous
D78V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       3                         2    36
  21Q LOSS WILD-TYPE    28                        11   179
D78V11, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    3                 28
  BLACK OR AFRICAN AMERICAN                2                 11
  WHITE                                   36                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"
D78V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     0  42
  21Q LOSS WILD-TYPE   5 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0   42
  21Q LOSS WILD-TYPE    5  216
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               42                216
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    70  35
  22Q LOSS WILD-TYPE 112  53
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               105                165 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                35                 53 
$`22Q LOSS MUTATED`
TCGA-2F-A9KP TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A42B TCGA-BT-A42C 
       11.97         2.66        19.04         5.06        15.42        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CU-A0YN 
        9.99         8.98         1.94        23.01         0.10        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
        5.46         5.19         1.81        10.59         7.79       123.85 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV 
        3.98         7.82         8.22        10.49        21.30         9.67 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ 
       17.98        67.36        15.68        41.06        43.59        15.35 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.56        12.99         1.22        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR 
        6.87        11.93        24.30        12.82         5.52        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY 
        1.97        22.98        14.93        12.13         5.36         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC 
       27.45         6.87         2.66         6.28        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.71         4.11         2.07        10.85        15.19         4.08 
TCGA-FT-A61P TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3RC TCGA-GC-A3YS 
        6.48         7.04        20.12         0.85        15.91         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
        2.66         7.73         2.10         2.20         7.36         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A40G 
       11.31         2.04         5.62        10.65         6.15        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A5RJ 
       11.54         6.74         8.22         8.75         3.45         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.81         4.27         6.35        13.48        12.23        16.67 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SW TCGA-XF-A9SX 
       45.04         6.58        56.19        15.35        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMT 
       21.04        28.24        26.27         2.24        10.82         2.96 
TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-YF-AA3M 
       56.48         7.96         9.04 

$`22Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       22.29        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        7.33         6.74        12.39         6.58        11.93        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       12.82         2.07        28.41         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO 
        0.13         0.07         0.10         0.07         0.10         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20        16.31         1.84         9.34         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IS 
       16.14        17.62        15.62        87.32         2.20        50.27 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV 
       20.02         8.28        10.55       140.81        48.00        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       41.56        76.60        30.67        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.49         0.53         0.59         0.66         1.38         0.82 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       14.33         0.46         4.01        12.43        15.88        45.93 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S 
       22.45         6.12        13.18        46.78        14.93        14.96 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        13.38        37.15        11.01         6.87         5.69 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FD-A6TH 
       49.68         4.83         6.38        50.66         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
        4.01         7.13         3.48         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3C 
        5.69        26.93        35.24        17.26        52.67         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
       19.46         2.89         2.24        15.81         4.50        14.07 
TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-A767 
       17.75         3.12        20.98         6.41        27.09         4.73 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        4.41         6.41         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        6.67         6.41         1.51        38.60         3.06         9.01 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A83P TCGA-LT-A5Z6 
        4.67         2.50         6.48        10.52         6.38         3.45 
TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HD TCGA-XF-A8HE 
       11.80        14.24         0.85         3.75        88.93        97.45 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9T2 TCGA-XF-A9T4 
        1.87        17.88        64.80        79.66        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       66.64         2.10        92.98        54.90         7.63        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        8.32         6.77        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       10.36         4.83         0.66 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.10               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            123.85             140.81 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              9.04               9.34 
[1] "0.1 - 123.8 (9.0)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED          1       0       27        33       45
  22Q LOSS WILD-TYPE        0       2       59        60       47
D79V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                27                 59
  STAGE III               33                 60
  STAGE IV                45                 47
[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"
                    vv
clus                 T0+T1+T2 T3 T4
  22Q LOSS MUTATED         26 53 19
  22Q LOSS WILD-TYPE       56 83 20
D79V4, multiclass
          clus
vv         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1+T2               26                 56
  T3                     53                 83
  T4                     19                 20
[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"
                    vv
clus                  N0  N1  N2  N3
  22Q LOSS MUTATED    55  11  29   3
  22Q LOSS WILD-TYPE 111  17  26   4
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               55                111
  N1               11                 17
  N2               29                 26
  N3                3                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   34  3 68
  22Q LOSS WILD-TYPE 95  4 73
D79V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               34                 95
  M1                3                  4
  MX               68                 73
[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"
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    29  77
  22Q LOSS WILD-TYPE  48 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     29   77
  22Q LOSS WILD-TYPE   48  124
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               29                 48
  MALE                 77                124
[1] 2 2
[1] FALSE
D79V8, continuous
D79V9, continuous
D79V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       7                         5    84
  22Q LOSS WILD-TYPE    24                         8   131
D79V11, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    7                 24
  BLACK OR AFRICAN AMERICAN                5                  8
  WHITE                                   84                131
[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"
D79V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     4  96
  22Q LOSS WILD-TYPE   1 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4   96
  22Q LOSS WILD-TYPE    1  162
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO               96                162
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    38  14
  XQ LOSS WILD-TYPE 144  74
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               52               218 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               14                74 
$`XQ LOSS MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A3PH 
      103.50        98.33         4.83        14.89         5.59         4.67 
TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AB 
       15.42         0.69         0.10         5.19         2.14         8.91 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6B5 
      130.88        87.32        50.27        21.30         9.67        41.06 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-FD-A3B4 TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A5BY 
       43.59        24.66        15.68        12.82         1.97         6.84 
TCGA-FD-A62N TCGA-FD-A6TF TCGA-FJ-A3Z7 TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3F 
        2.66         2.07        15.19        26.93         7.04        19.46 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A40G 
        2.20         6.41        11.31         6.15         4.14        19.07 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ 
       38.60         3.06         9.01         4.67        10.52         1.74 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HC 
        1.81         3.45        12.23         0.85         3.75         6.58 
TCGA-XF-A8HF TCGA-XF-A9SZ TCGA-XF-AAMT TCGA-YF-AA3L 
       56.19        28.24         2.96         7.96 

$`XQ LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       22.29        11.97        84.00        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        11.93        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         8.25        17.16         3.65        12.82         2.07 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70         9.99        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.43         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
        0.10        12.92         4.90         7.20         5.46        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84         9.34         2.53        66.41        18.41        19.00 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        7.79       123.85         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       10.49        20.02         8.28        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       30.67        15.35        26.17         0.10         0.49         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.59         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.33         1.22         0.46        12.89         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       22.45         6.12         5.52        13.18        46.78        19.79 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        14.93        14.96        14.93         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       13.38        37.15        11.01         6.87         5.36         5.69 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45         6.87        49.68         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       50.66        18.81         9.30         6.71         4.11         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.20         4.01        10.85         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        3.25         6.48        61.94        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM 
       17.26        20.12         0.85        52.67         6.94         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        1.12         2.66         7.73         2.10         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.36         7.59         2.04        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       10.65         4.41         6.41         5.69         7.63         7.79 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5NE 
        6.67         6.41        11.54         1.51         6.74         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A6MB TCGA-K4-A83P 
        8.75         3.45         2.50         6.48         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-XF-A8HB 
        6.35        11.80        13.48        16.67        14.24        45.04 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       88.93        97.45        15.35         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       79.66        11.90        23.64        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       54.90         7.63        91.73         8.32         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3M 
        0.66         9.04 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.10              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           130.88            140.81 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            8.435             9.665 
[1] "0.1 - 130.9 (8.4)" "0.1 - 140.8 (9.7)"
[1] "hr=" "1.2"
D80V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED          0       0       18        15       19
  XQ LOSS WILD-TYPE        1       2       68        78       73
D80V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               18                68
  STAGE III              15                78
  STAGE IV               19                73
[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"
                   vv
clus                T0+T1+T2  T3  T4
  XQ LOSS MUTATED         17  26   6
  XQ LOSS WILD-TYPE       65 110  33
D80V4, multiclass
          clus
vv         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1+T2              17                65
  T3                    26               110
  T4                     6                33
[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"
                   vv
clus                 N0  N1  N2  N3
  XQ LOSS MUTATED    30   8   9   1
  XQ LOSS WILD-TYPE 136  20  46   6
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              30               136
  N1               8                20
  N2               9                46
  N3               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  XQ LOSS MUTATED    24   1  29
  XQ LOSS WILD-TYPE 105   6 112
D80V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              24               105
  M1               1                 6
  MX              29               112
[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"
D80V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    13  41
  XQ LOSS WILD-TYPE  64 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13   41
  XQ LOSS WILD-TYPE   64  160
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              13                64
  MALE                41               160
[1] 2 2
[1] FALSE
D80V8, continuous
D80V9, continuous
D80V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       6                         3    39
  XQ LOSS WILD-TYPE    25                        10   176
D80V11, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   6                25
  BLACK OR AFRICAN AMERICAN               3                10
  WHITE                                  39               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  46
  XQ LOSS WILD-TYPE   3 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   46
  XQ LOSS WILD-TYPE    3  212
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              46               212
[1] 2 2
[1] FALSE
