[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/10005789/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/10013675/transformed.cor.cli.txt"

nPatients in clinical file=218, in cluster file=264, common to both=214
[1]  80 214
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               164 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               164 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               71               143 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               71               143 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               63               151 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               63               151 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               30               184 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               30               184 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               72               142 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               72               142 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               95               119 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               95               119 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               24               190 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               24               190 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               200 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               200 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               83               131 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               83               131 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               29               185 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               29               185 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               31               183 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               31               183 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               18               196 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               18               196 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               93               121 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               93               121 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               84               130 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               84               130 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               44               170 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               44               170 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               97               117 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               97               117 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               34               180 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               34               180 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               30               184 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               30               184 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                59                155 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                59                155 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                18                196 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                18                196 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                192 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                192 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                30                184 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                30                184 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                61                153 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                61                153 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                168 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                168 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                53                161 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                53                161 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                39                175 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                39                175 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                21                193 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                21                193 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                33                181 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                33                181 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                42                172 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                42                172 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                182 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                182 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                72                142 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                72                142 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                63                151 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                63                151 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                35                179 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                35                179 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                42                172 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                42                172 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                68                146 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                68                146 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               109                105 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               109                105 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               124                 90 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               124                 90 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                68                146 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                68                146 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                28                186 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                28                186 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               24               190 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               24               190 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16               198 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16               198 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               197 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               197 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               22               192 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               22               192 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               48               166 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               48               166 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               27               187 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               27               187 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               204 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               204 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               72               142 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               72               142 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               76               138 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               76               138 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               180 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               180 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               81               133 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               81               133 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               51               163 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               51               163 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               80               134 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               80               134 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               10               204 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               10               204 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               203 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               203 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               94               120 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               94               120 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               192 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               192 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               91               123 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               91               123 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               82               132 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               82               132 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                41                173 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                41                173 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                71                143 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                71                143 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                82                132 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                82                132 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                63                151 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                63                151 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                23                191 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                23                191 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                27                187 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                27                187 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                46                168 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                46                168 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                58                156 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                58                156 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                73                141 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                73                141 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                60                154 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                60                154 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                53                161 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                53                161 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                90                124 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                90                124 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                189 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                189 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                50                164 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                50                164 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                76                138 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                76                138 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                55                159 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                55                159 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                34                180 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                34                180 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                16                198 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                16                198 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                209 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                209 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                34                180 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                34                180 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                84                130 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                84                130 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               41               173 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               41               173 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [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 214 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
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-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
           3            3           NA           NA          219          166 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
         158          496           NA          284           77           NA 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
         955          560          578          271         3981         3420 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
         491          536          475           55          322           NA 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        3767         2656           67          121          238           NA 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
         319         1529          648          609           NA          252 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
          NA         4283         1460           NA         1952         1476 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
        2330         2049          477          982          933         1326 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
          NA          796          750            3           15           16 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
          NA           18           17           20           42           25 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
          37          392          477           NA          209           NA 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
         378          363          483         1397           NA          683 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
         501          390           NA          401           NA           NA 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
          60          699          454          455          454          110 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
         369          407         1130           NA          209           NA 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
          NA          208           NA          209         1511           81 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
         147           NA          194         1541          283          204 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
         125           81           67          122          462          217 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
         106          124           NA          197         1884          931 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
         173           NA         1072          525          214           NA 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
          26           88           68          481          137          484 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
         428          540           34           81          235           64 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
          95          638           67          195          233          344 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QG 
         134          195          187          173          232           NA 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
         237          126          203          195          580          351 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
          46          205         1174          266          105          142 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
          76          197          320           53           55          130 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
         194          193          105          410          372          507 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        2705         2964         1709           NA 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=146,	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=1,	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=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=15,	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=TRUE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=24,	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"                       
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 214 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=47, 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  60 101  32 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
      62      101       32 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   1  60 101  32 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
      62      101       32 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
130  22  38   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
130  22  38   7 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
130  22  38   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
130  22  38   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=48, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=15, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    30  19
  1P GAIN WILD-TYPE 121  38
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               159 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               19                38 
$`1P GAIN MUTATED`
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-CU-A0YN 
        5.06        14.89        17.16        12.82         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-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A5C0 TCGA-FD-A6TG 
       19.79         1.97        22.98         6.87         6.87         2.66 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A3IE TCGA-GC-A3BM 
        4.01        15.19         4.08         3.25        20.12         2.89 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JV 
       15.81         4.50         1.12        20.98         6.41         4.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-LT-A5Z6 TCGA-MV-A51V 
        5.69         7.63         4.14        11.54         3.45        13.48 
TCGA-XF-A8HD 
       88.93 

$`1P GAIN WILD-TYPE`
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-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-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67         2.07        15.42        28.70         9.99        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-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        31.40        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        48.53        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       15.68        32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
        1.22        12.89        15.68         6.87        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       15.88        22.45        16.47        12.82        13.18        46.78 
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-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       37.15        11.01         5.36         5.69         6.84        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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        9.30         6.71         4.11         2.20         7.13         3.48 
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-A3VY TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
       17.26         7.04         0.85         2.24        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 
       17.75         2.66         7.73         2.10         3.12         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QK 
        7.66        11.31         6.41         6.15         7.79         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
        6.41        19.07         1.51         6.74        38.60         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-PQ-A6FI TCGA-PQ-A6FN 
        1.81         4.27         6.38         6.35        12.23        16.67 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       97.45        56.19        15.35 

  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 
             7.79              8.98 
[1] "0.6 - 123.8 (7.8)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.8"
D1V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED          1       0       15        15       19
  1P GAIN WILD-TYPE        0       2       53        57       48
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               15                53
  STAGE III              15                57
  STAGE IV               19                48
[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         15 23  8
  1P GAIN WILD-TYPE       47 78 24
D1V4, multiclass
          clus
vv         1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1+T2              15                47
  T3                    23                78
  T4                     8                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
  1P GAIN MUTATED    27   8   8   4
  1P GAIN WILD-TYPE 103  14  30   3
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              27               103
  N1               8                14
  N2               8                30
  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
  1P GAIN MUTATED   25  0 25
  1P GAIN WILD-TYPE 81  5 77
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              25                81
  M1               0                 5
  MX              25                77
[1] 3 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     9  41
  1P GAIN WILD-TYPE  41 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      9   41
  1P GAIN WILD-TYPE   41  123
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               9                41
  MALE                41               123
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       3                         3    42
  1P GAIN WILD-TYPE    19                         8   128
D1V11, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   3                19
  BLACK OR AFRICAN AMERICAN               3                 8
  WHITE                                  42               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    48  22
  1Q GAIN WILD-TYPE 103  35
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               70               138 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               22                35 
$`1Q GAIN MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LD 
        2.66         6.74        14.89         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        16.47         5.52 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BU TCGA-FD-A5C0 
       19.79         1.97        22.98         3.62         6.87         6.87 
TCGA-FD-A5C1 TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-GC-A3BM 
       49.68         2.66         4.01         3.48         3.25         2.89 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.81         4.50        17.75         1.12         7.73         2.10 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI 
       20.98         6.41         4.41         6.15         5.69         4.14 
TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A5RJ TCGA-LC-A66R TCGA-LT-A5Z6 
       11.54        38.60         8.75         1.74         6.35         3.45 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HG 
       13.48        12.23        88.93        15.35 

$`1Q GAIN WILD-TYPE`
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-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       32.84        12.16        17.88        19.50         5.06        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        31.40 
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        48.53        76.60        15.68        32.28 
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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
        1.38         0.82         1.22        12.89        15.68         6.87 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       12.43        11.93        15.88        12.82        13.18        46.78 
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-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
       11.01         5.36         5.69         6.84        27.45         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-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A61P 
        4.11         2.20        15.19         7.13         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-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
        7.04        20.12         0.85         2.24        15.91        14.07 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW 
        2.66         3.12         2.20         7.66        11.31         6.41 
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-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        6.74         3.45         4.67         2.50         6.48        10.52 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A8HF 
        1.81         4.27         6.38        16.67        97.45        56.19 

  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 
             7.30              9.83 
[1] "0.1 - 112.4 (7.3)" "0.1 - 140.8 (9.8)"
[1] "hr=" "1.4"
D2V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED          1       0       21        19       29
  1Q GAIN WILD-TYPE        0       2       47        53       38
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               21                47
  STAGE III              19                53
  STAGE IV               29                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
  1Q GAIN MUTATED         21 32 13
  1Q GAIN WILD-TYPE       41 69 19
D2V4, multiclass
          clus
vv         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1+T2              21                41
  T3                    32                69
  T4                    13                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
  1Q GAIN MUTATED   38 10 16  4
  1Q GAIN WILD-TYPE 92 12 22  3
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              38                92
  N1              10                12
  N2              16                22
  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
  1Q GAIN MUTATED   32  4 35
  1Q GAIN WILD-TYPE 74  1 67
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              32                74
  M1               4                 1
  MX              35                67
[1] 3 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    14  57
  1Q GAIN WILD-TYPE  36 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     14   57
  1Q GAIN WILD-TYPE   36  107
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              14                36
  MALE                57               107
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       4                         4    58
  1Q GAIN WILD-TYPE    18                         7   112
D2V11, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   4                18
  BLACK OR AFRICAN AMERICAN               4                 7
  WHITE                                  58               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"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    46  16
  2P GAIN WILD-TYPE 105  41
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               62               146 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               16                41 
$`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        31.40        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-FD-A3NA TCGA-FD-A3SQ 
       15.68        30.67        43.59         0.59        45.93        46.78 
TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TE 
       19.79        14.93        14.93        27.45         4.83         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A3VY 
        2.66         2.20         4.08         3.25         6.48         0.85 
TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GV-A3QF TCGA-GV-A3QH 
       14.07         7.73         2.10        20.98         7.63         7.79 
TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A6FZ 
        6.67         6.74        38.60         8.75         4.67         1.81 
TCGA-K4-A6MB TCGA-XF-A8HD 
        4.27        88.93 

$`2P GAIN WILD-TYPE`
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        48.53        76.60        32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        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        16.47        12.82         5.52        13.18 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
        1.97        22.98        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-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        6.87        49.68         2.66         6.28         6.38        50.66 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        9.30         6.71         4.01        15.19         7.13         3.48 
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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        7.04        20.12         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 
       15.91        17.75         1.12         2.66         3.12         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        6.41         7.66        11.31         4.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        5.69         4.14         6.41        19.07        11.54         1.51 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P 
        3.45         2.50         6.48        10.52         1.74         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        6.35         3.45        13.48        12.23        16.67        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

  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 
            8.865             8.265 
[1] "0.1 - 130.9 (8.9)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.3"
D3V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED          0       0       16        16       29
  2P GAIN WILD-TYPE        1       2       52        56       38
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               16                52
  STAGE III              16                56
  STAGE IV               29                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
  2P GAIN MUTATED         16 31  9
  2P GAIN WILD-TYPE       46 70 23
D3V4, multiclass
          clus
vv         2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1+T2              16                46
  T3                    31                70
  T4                     9                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
  2P GAIN MUTATED    27   9  20   2
  2P GAIN WILD-TYPE 103  13  18   5
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              27               103
  N1               9                13
  N2              20                18
  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   31  2 29
  2P GAIN WILD-TYPE 75  3 73
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              31                75
  M1               2                 3
  MX              29                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"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    24  39
  2P GAIN WILD-TYPE  26 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     24   39
  2P GAIN WILD-TYPE   26  125
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              24                26
  MALE                39               125
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       5                         3    50
  2P GAIN WILD-TYPE    17                         8   120
D3V11, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   5                17
  BLACK OR AFRICAN AMERICAN               3                 8
  WHITE                                  50               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"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    22   7
  2Q GAIN WILD-TYPE 129  50
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               29               179 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                50 
$`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-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 
        7.20        31.40       130.88       112.44        10.59         7.79 
TCGA-DK-A3IN TCGA-E5-A2PC TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A62O TCGA-FD-A6TG 
        8.22        43.59        45.93        46.78         4.83         2.66 
TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GD-A3OS TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40G 
        4.08         0.85        20.98         7.63         7.79        19.07 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-XF-A8HD 
        6.74         8.75         4.67         1.81        88.93 

$`2Q GAIN WILD-TYPE`
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-A1AE TCGA-DK-A1AF 
        2.14        18.41        19.00         8.91        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62         1.81       123.85        87.32         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82        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-DK-A6B6 
       48.53        76.60        67.36        15.68        32.28        30.67 
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-A7DV 
        0.59         0.56         0.66         1.38         0.82         1.22 
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        16.47        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        13.18        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-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-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        6.87        49.68         2.66         6.28         6.38        50.66 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
        9.30         6.71         4.11         2.20         4.01        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13         3.48         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-A3IE 
        5.69        26.93        35.24        17.26         7.04        20.12 
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-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        2.20         6.41         7.66        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
        6.15         5.69         4.14         6.67         6.41        11.54 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        1.51        38.60         3.45         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.74         4.27         6.38         6.35         3.45        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        16.67        97.45        56.19        15.35 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.85              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           130.88            140.81 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            10.59              8.28 
[1] "0.8 - 130.9 (10.6)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1.6"
D4V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED          0       0       10         9       11
  2Q GAIN WILD-TYPE        1       2       58        63       56
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               10                58
  STAGE III               9                63
  STAGE IV               11                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
  2Q GAIN MUTATED          9 12  3
  2Q GAIN WILD-TYPE       53 89 29
D4V4, multiclass
          clus
vv         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1+T2               9                53
  T3                    12                89
  T4                     3                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
  2Q GAIN MUTATED    15   4   6   1
  2Q GAIN WILD-TYPE 115  18  32   6
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              15               115
  N1               4                18
  N2               6                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
  2Q GAIN MUTATED   11  1 17
  2Q GAIN WILD-TYPE 95  4 85
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              11                95
  M1               1                 4
  MX              17                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"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     9  21
  2Q GAIN WILD-TYPE  41 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9   21
  2Q GAIN WILD-TYPE   41  143
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               9                41
  MALE                21               143
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       2                         1    25
  2Q GAIN WILD-TYPE    20                        10   145
D4V11, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   2                20
  BLACK OR AFRICAN AMERICAN               1                10
  WHITE                                  25               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"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    48  21
  3P GAIN WILD-TYPE 103  36
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               69               139 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               21                36 
$`3P GAIN MUTATED`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20W TCGA-BT-A2LD 
        7.33         2.66        12.39        19.04         8.35         3.65 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL 
        4.67         2.07         0.46         4.90         7.20        16.31 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX 
        1.84         2.53         2.14       130.88       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-FD-A43U TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TE 
        0.56        14.93         6.87         4.83         6.28         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.66         2.20         4.01         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY 
        6.48        61.94        30.61        35.24        17.26         0.85 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JV 
        2.24        15.81         2.10        20.98         6.41         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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6MB 
        6.74        38.60         8.75         3.45         4.67         4.27 
TCGA-PQ-A6FI TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        56.19        15.35 

$`3P GAIN WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
       40.08         6.74         6.58        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-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C 
        8.25        17.16         5.59        12.82        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS 
        9.99        28.41         8.98         1.94        23.01         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-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A6 
        0.10        12.92         5.46         5.19         9.34        31.40 
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-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 
       48.53        76.60        67.36        15.68        32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.22        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 
       16.47        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-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-A6TC TCGA-FD-A6TD TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-G2-A2EK TCGA-G2-A2EL 
        9.30         6.71        15.19         7.13         5.69        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        7.04        20.12         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-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E 
        7.66        11.31         6.15         5.69         4.14         6.41 
TCGA-H4-A2HO TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        1.51         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD 
        6.38         6.35         3.45        13.48        16.67        88.93 
TCGA-XF-A8HE 
       97.45 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           130.88            140.81 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             7.20              9.67 
[1] "0.1 - 130.9 (7.2)" "0.1 - 140.8 (9.7)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED          1       0       25        16       28
  3P GAIN WILD-TYPE        0       2       43        56       39
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               25                43
  STAGE III              16                56
  STAGE IV               28                39
[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         22 28 12
  3P GAIN WILD-TYPE       40 73 20
D5V4, multiclass
          clus
vv         3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1+T2              22                40
  T3                    28                73
  T4                    12                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
  3P GAIN MUTATED   37  7 20  2
  3P GAIN WILD-TYPE 93 15 18  5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              37                93
  N1               7                15
  N2              20                18
  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   35  2 34
  3P GAIN WILD-TYPE 71  3 68
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              35                71
  M1               2                 3
  MX              34                68
[1] 3 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    15  57
  3P GAIN WILD-TYPE  35 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     15   57
  3P GAIN WILD-TYPE   35  107
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              15                35
  MALE                57               107
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       6                         1    60
  3P GAIN WILD-TYPE    16                        10   110
D5V11, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   6                16
  BLACK OR AFRICAN AMERICAN               1                10
  WHITE                                  60               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"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   68 24
  3Q GAIN WILD-TYPE 83 33
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               92               116 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               24                33 
$`3Q GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66        12.39        11.93        19.04 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25        17.16         3.65         4.67 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YO 
        2.07        28.70         9.99         0.46         0.43         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
        7.20         5.46        16.31         1.84         2.53        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 
       18.41       130.88       112.44         1.81        10.59        87.32 
TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV 
        2.20         8.22        50.27        20.02        17.98        64.18 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       15.68        30.67        43.59        15.35         0.10         0.49 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ 
        0.59         0.56        12.89         6.87        11.93        24.30 
TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P 
       22.45        14.93        14.93         6.87         4.83         6.28 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE 
        9.30         4.11         2.66         2.20         4.01         3.48 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES 
        4.08         6.48        61.94        30.61        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A3WC 
        7.04         0.85         2.24        15.81        14.07        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JW 
        2.66         2.10        20.98         6.41         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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6MB TCGA-PQ-A6FI 
       38.60         8.75         3.45         4.67         4.27        12.23 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`3Q GAIN WILD-TYPE`
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42B 
        5.06        14.89        14.96         5.59        12.82        15.42 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S 
       28.41         8.98         1.94        23.01         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-A3QU TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
        5.19         9.34         2.14        19.00         8.91        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM 
       17.62        15.62         7.79       123.85         3.98         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       10.49        21.30         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A4U1 
       48.00        48.53        76.60        67.36        32.28        26.17 
TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV 
       24.66         0.53         0.66         1.38         0.82         1.22 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.68         8.94         4.01        12.43        15.88        45.93 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       16.47        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
        1.97        22.98        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-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD 
       27.45        49.68         2.66         6.38        50.66         6.71 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IE 
       15.19         7.13         3.25         5.69        26.93        20.12 
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-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI 
        2.20         7.66        11.31         6.15         5.69         4.14 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        6.41         1.51         2.50         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
        1.81         6.38         6.35         3.45        13.48        16.67 
TCGA-XF-A8HD TCGA-XF-A8HE 
       88.93        97.45 

  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 
            8.235             8.960 
[1] "0.1 - 130.9 (8.2)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED          1       1       31        23       36
  3Q GAIN WILD-TYPE        0       1       37        49       31
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 1                 1
  STAGE II               31                37
  STAGE III              23                49
  STAGE IV               36                31
[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         29 39 15
  3Q GAIN WILD-TYPE       33 62 17
D6V4, multiclass
          clus
vv         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1+T2              29                33
  T3                    39                62
  T4                    15                17
[1] 3 2
[1] 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   49  9 26  2
  3Q GAIN WILD-TYPE 81 13 12  5
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              49                81
  N1               9                13
  N2              26                12
  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   48  3 43
  3Q GAIN WILD-TYPE 58  2 59
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              48                58
  M1               3                 2
  MX              43                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"
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   23 72
  3Q GAIN WILD-TYPE 27 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     23   72
  3Q GAIN WILD-TYPE   27   92
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              23                27
  MALE                72                92
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       8                         5    77
  3Q GAIN WILD-TYPE    14                         6    93
D6V11, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   8                14
  BLACK OR AFRICAN AMERICAN               5                 6
  WHITE                                  77                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"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    19   5
  4P GAIN WILD-TYPE 132  52
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               24               184 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                52 
$`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        31.40 
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-GU-A42P TCGA-GV-A6ZA TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-MV-A51V 
       61.94         6.41        11.54         1.81         4.27        13.48 

$`4P GAIN WILD-TYPE`
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        48.53        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.22        12.89        15.68         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        11.93        15.88        24.30        22.45        16.47 
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-A5BX TCGA-FD-A5BY 
       13.38        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-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       50.66         6.71         2.66         2.20         4.01        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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        0.85         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-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
        3.12        20.98         2.20         7.66        11.31         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-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.67         6.41        19.07         1.51         6.74        38.60 
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-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.74         6.38         6.35         3.45        12.23        16.67 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        97.45        56.19        15.35 

  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 
           10.420             8.315 
[1] "0.1 - 130.9 (10.4)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1.8"
D7V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED          1       0        9         8        6
  4P GAIN WILD-TYPE        0       2       59        64       61
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II                9                59
  STAGE III               8                64
  STAGE IV                6                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
  4P GAIN MUTATED         10 12  1
  4P GAIN WILD-TYPE       52 89 31
D7V4, multiclass
          clus
vv         4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1+T2              10                52
  T3                    12                89
  T4                     1                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
  4P GAIN MUTATED    18   4   1   1
  4P GAIN WILD-TYPE 112  18  37   6
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              18               112
  N1               4                18
  N2               1                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
  4P GAIN MUTATED   15  0  9
  4P GAIN WILD-TYPE 91  5 93
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0              15                91
  M1               0                 5
  MX               9                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"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     8  16
  4P GAIN WILD-TYPE  42 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8   16
  4P GAIN WILD-TYPE   42  148
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               8                42
  MALE                16               148
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       2                         0    18
  4P GAIN WILD-TYPE    20                        11   152
D7V11, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   2                20
  BLACK OR AFRICAN AMERICAN               0                11
  WHITE                                  18               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"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    11   3
  4Q GAIN WILD-TYPE 140  54
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               194 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                54 
$`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-GU-A42P TCGA-GV-A6ZA 
        6.41        11.54 

$`4Q GAIN WILD-TYPE`
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        31.40        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        48.53        76.60        15.68        32.28 
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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.22        12.89        15.68         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        11.93        15.88        24.30        22.45        16.47 
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-A5BX TCGA-FD-A5BY 
       13.38        37.15        11.01         6.87         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45        49.68         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       50.66         9.30         6.71         2.66         2.20         4.01 
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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12         0.85         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-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20         7.66        11.31 
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-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.67         6.41        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
        3.45        13.48        12.23        16.67        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

  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 
            9.205             8.550 
[1] "0.1 - 67.4 (9.2)"  "0.1 - 140.8 (8.6)"
[1] "hr=" "1.7"
D8V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED          1       0        6         4        3
  4Q GAIN WILD-TYPE        0       2       62        68       64
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II                6                62
  STAGE III               4                68
  STAGE IV                3                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
  4Q GAIN MUTATED          6  7  0
  4Q GAIN WILD-TYPE       56 94 32
D8V4, multiclass
          clus
vv         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1+T2               6                56
  T3                     7                94
  T4                     0                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
  4Q GAIN MUTATED    11   1   2   0
  4Q GAIN WILD-TYPE 119  21  36   7
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              11               119
  N1               1                21
  N2               2                36
  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    9  0  5
  4Q GAIN WILD-TYPE 97  5 97
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               9                97
  M1               0                 5
  MX               5                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"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  11
  4Q GAIN WILD-TYPE  47 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   11
  4Q GAIN WILD-TYPE   47  153
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               3                47
  MALE                11               153
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         0    11
  4Q GAIN WILD-TYPE    21                        11   159
D8V11, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                21
  BLACK OR AFRICAN AMERICAN               0                11
  WHITE                                  11               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"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   56 24
  5P GAIN WILD-TYPE 95 33
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               80               128 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               24                33 
$`5P GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V 
       40.08         6.74        12.39        32.84        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A1HS 
        8.35        17.16        12.82         2.07        28.70         0.43 
TCGA-CF-A47S TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A2I4 
        0.13        12.92         7.20         5.19         2.53       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A6B1 
       87.32         8.22        20.02         9.67        10.55        67.36 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ 
       32.28        30.67        15.35        26.17        24.66         0.49 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 
        0.59         1.22        12.89        15.68         8.94        11.93 
TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BR 
       45.93         5.52        13.18        19.79        12.13        13.38 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        6.87         5.36         6.84        49.68         2.66         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-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
        4.08         3.25         6.48        35.24         7.04        20.12 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42P 
        2.24        15.81         1.12         2.10        20.98         6.41 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E 
        4.41         6.15         7.63         7.79         4.14         6.41 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-LC-A66R TCGA-MV-A51V 
       19.07         6.74         6.48         1.81         6.35        13.48 
TCGA-PQ-A6FN TCGA-XF-A8HF 
       16.67        56.19 

$`5P GAIN WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         2.66         6.58        11.93        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB 
       17.88        19.50         5.06        14.96         8.25         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        3.65         4.67        15.42         9.99        28.41         8.98 
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-A3KJ TCGA-CU-A3YL 
        0.07         0.10         0.10         4.90         5.46        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        31.40        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-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        1.81        10.59         7.79         2.20         3.98         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       10.49        50.27        21.30         8.28       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-E5-A2PC 
       17.98        64.18        48.53        76.60        15.68        43.59 
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-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL 
        6.87         4.01        12.43        15.88        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       16.47        12.82        46.78         1.97        22.98        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       14.96        14.93         3.62        37.15        11.01         5.69 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 
       27.45         6.87        50.66         6.71         4.01        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        7.13         3.48        61.94        30.61         5.69        26.93 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       17.26         0.85         2.89         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       17.75         2.66         7.73         3.12         2.20         7.66 
TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO 
       11.31         6.41         5.69         6.67        11.54         1.51 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
       38.60         8.75         3.45         4.67         2.50        10.52 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-XF-A8HD 
        1.74         4.27         6.38         3.45        12.23        88.93 
TCGA-XF-A8HE TCGA-XF-A8HG 
       97.45        15.35 

  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 
            8.005             8.945 
[1] "0.1 - 123.8 (8.0)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED          0       1       27        31       23
  5P GAIN WILD-TYPE        1       1       41        41       44
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 1                 1
  STAGE II               27                41
  STAGE III              31                41
  STAGE IV               23                44
[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         24 36 13
  5P GAIN WILD-TYPE       38 65 19
D9V4, multiclass
          clus
vv         5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1+T2              24                38
  T3                    36                65
  T4                    13                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
  5P GAIN MUTATED   48  8 14  2
  5P GAIN WILD-TYPE 82 14 24  5
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              48                82
  N1               8                14
  N2              14                24
  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   35  1 47
  5P GAIN WILD-TYPE 71  4 55
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              35                71
  M1               1                 4
  MX              47                55
[1] 3 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   18 65
  5P GAIN WILD-TYPE 32 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     18   65
  5P GAIN WILD-TYPE   32   99
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              18                32
  MALE                65                99
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       7                         8    65
  5P GAIN WILD-TYPE    15                         3   105
D9V11, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   7                15
  BLACK OR AFRICAN AMERICAN               8                 3
  WHITE                                  65               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"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    19   8
  5Q GAIN WILD-TYPE 132  49
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               27               181 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                49 
$`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-A62S TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FT-A3EE TCGA-G2-A2EO 
        6.28         6.38         4.11         2.20         3.25        35.24 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E 
        2.24        15.81         4.41         7.79         4.14         6.41 
TCGA-K4-A4AC TCGA-LC-A66R TCGA-MV-A51V 
        6.48         6.35        13.48 

$`5Q GAIN WILD-TYPE`
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        31.40        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        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ 
       76.60        67.36        15.68        32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        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-A3SN TCGA-FD-A3SO 
       45.93        24.30        22.45        16.47        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-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01         5.36         5.69         6.84        27.45         6.87 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG 
        2.66         4.83        50.66         9.30         6.71         2.66 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P 
        4.01        15.19         7.13         3.48         4.08         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61         5.69        26.93        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12         0.85         2.89         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-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW 
       20.98         2.20         6.41         7.66        11.31         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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        2.50        10.52         1.74         1.81         4.27         6.38 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.45        12.23        16.67        88.93        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  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 
             6.74              8.94 
[1] "0.4 - 123.8 (6.7)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED          0       1       10        11        6
  5Q GAIN WILD-TYPE        1       1       58        61       61
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 1                 1
  STAGE II               10                58
  STAGE III              11                61
  STAGE IV                6                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
  5Q GAIN MUTATED          8 15  2
  5Q GAIN WILD-TYPE       54 86 30
D10V4, multiclass
          clus
vv         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1+T2               8                54
  T3                    15                86
  T4                     2                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
  5Q GAIN MUTATED    19   3   3   0
  5Q GAIN WILD-TYPE 111  19  35   7
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              19               111
  N1               3                19
  N2               3                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
  5Q GAIN MUTATED   13  0 16
  5Q GAIN WILD-TYPE 93  5 86
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              13                93
  M1               0                 5
  MX              16                86
[1] 3 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     5  24
  5Q GAIN WILD-TYPE  45 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5   24
  5Q GAIN WILD-TYPE   45  140
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               5                45
  MALE                24               140
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       3                         2    23
  5Q GAIN WILD-TYPE    19                         9   147
D10V11, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   3                19
  BLACK OR AFRICAN AMERICAN               2                 9
  WHITE                                  23               147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    24   7
  6P GAIN WILD-TYPE 127  50
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               31               177 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                50 
$`6P GAIN MUTATED`
TCGA-BT-A0S7 TCGA-CF-A47V TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3WX 
        6.58         0.10       130.88        87.32         7.82        10.55 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A541 TCGA-FD-A3B7 TCGA-FD-A3SR TCGA-FD-A3SS 
       67.36        15.68         0.59         4.01        19.79         1.97 
TCGA-FD-A5BU TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-FT-A3EE 
        6.87        49.68         9.30         2.66         3.48         3.25 
TCGA-FT-A61P TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3YS 
        6.48         2.89         2.24        15.81        15.91         1.12 
TCGA-GD-A2C5 TCGA-GU-A42P TCGA-GV-A6ZA TCGA-K4-A4AC TCGA-LC-A66R TCGA-LT-A5Z6 
        7.73         6.41        11.54         6.48         6.35         3.45 
TCGA-XF-A8HD 
       88.93 

$`6P GAIN 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-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-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-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-A1AD TCGA-DK-A1AE 
       31.40        18.41        19.00         8.91       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-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        2.20         3.98         8.22        10.49        50.27        21.30 
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-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
       64.18        48.53        76.60        32.28        30.67        43.59 
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-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.56         0.66         1.38         0.82         1.22        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-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       45.93        24.30        22.45        16.47        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       13.18        46.78        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-A5BV 
        3.62        12.13        13.38        37.15        11.01         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-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
        6.28         6.38        50.66         6.71         4.11         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EJ 
        4.01        15.19         7.13         4.08        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-A3VY TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP 
        0.85         4.50        14.07        17.75         2.66         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
        3.12        20.98         2.20         7.66        11.31         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-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.67         6.41        19.07         1.51         6.74        38.60 
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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.81         4.27         6.38        13.48        12.23        16.67 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       97.45        56.19        15.35 

  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 
             6.58              8.98 
[1] "0.1 - 130.9 (6.6)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED          1       0        9        10       11
  6P GAIN WILD-TYPE        0       2       59        62       56
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II                9                59
  STAGE III              10                62
  STAGE IV               11                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
  6P GAIN MUTATED         10 13  6
  6P GAIN WILD-TYPE       52 88 26
D11V4, multiclass
          clus
vv         6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1+T2              10                52
  T3                    13                88
  T4                     6                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
  6P GAIN MUTATED    19   4   5   2
  6P GAIN WILD-TYPE 111  18  33   5
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              19               111
  N1               4                18
  N2               5                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
  6P GAIN MUTATED   12  1 18
  6P GAIN WILD-TYPE 94  4 84
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              12                94
  M1               1                 4
  MX              18                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"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     6  25
  6P GAIN WILD-TYPE  44 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6   25
  6P GAIN WILD-TYPE   44  139
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               6                44
  MALE                25               139
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
D11V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         2    27
  6P GAIN WILD-TYPE    21                         9   143
D11V11, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                21
  BLACK OR AFRICAN AMERICAN               2                 9
  WHITE                                  27               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"

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    14   4
  6Q GAIN WILD-TYPE 137  53
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               18               190 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                53 
$`6Q GAIN MUTATED`
TCGA-BT-A0S7 TCGA-BT-A2LA TCGA-CF-A47V TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IM 
        6.58        17.16         0.10       130.88        87.32         7.82 
TCGA-DK-A3WX TCGA-DK-A6B1 TCGA-FD-A3SS TCGA-FD-A5C1 TCGA-FJ-A3ZE TCGA-GC-A3BM 
       10.55        67.36         1.97        49.68         3.48         2.89 
TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GU-A42P TCGA-K4-A4AC TCGA-LC-A66R TCGA-XF-A8HD 
       15.81         1.12         6.41         6.48         6.35        88.93 

$`6Q GAIN 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-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-A47X 
        0.43         0.69         0.13         0.07         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        31.40 
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-A6AV 
        9.67         8.28       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
       48.53        76.60        15.68        32.28        30.67        43.59 
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-A7DV 
        0.59         0.56         0.66         1.38         0.82         1.22 
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        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       12.82         5.52        13.18        46.78        19.79        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-A5BY 
       37.15        11.01         6.87         5.36         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45         6.87         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       50.66         9.30         6.71         4.11         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        4.01        15.19         7.13         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-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC 
        7.04        20.12         0.85         2.24         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-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
       20.98         2.20         7.66        11.31         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-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-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        1.81         4.27         6.38         3.45        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        97.45        56.19        15.35 

  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              8.83 
[1] "0.1 - 130.9 (7.2)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED          0       0        5         7        6
  6Q GAIN WILD-TYPE        1       2       63        65       61
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                5                63
  STAGE III               7                65
  STAGE IV                6                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
  6Q GAIN MUTATED          6  8  3
  6Q GAIN WILD-TYPE       56 93 29
D12V4, multiclass
          clus
vv         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1+T2               6                56
  T3                     8                93
  T4                     3                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
  6Q GAIN MUTATED    12   3   1   2
  6Q GAIN WILD-TYPE 118  19  37   5
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              12               118
  N1               3                19
  N2               1                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
  6Q GAIN MUTATED   10  1  7
  6Q GAIN WILD-TYPE 96  4 95
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              10                96
  M1               1                 4
  MX               7                95
[1] 3 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     2  16
  6Q GAIN WILD-TYPE  48 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   16
  6Q GAIN WILD-TYPE   48  148
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               2                48
  MALE                16               148
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       1                         0    17
  6Q GAIN WILD-TYPE    21                        11   153
D12V11, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                21
  BLACK OR AFRICAN AMERICAN               0                11
  WHITE                                  17               153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   66 25
  7P GAIN WILD-TYPE 85 32
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               91               117 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               25                32 
$`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-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E 
       17.16         5.59         3.65        12.82        28.70         9.99 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
       28.41        23.01         0.46        12.92         4.90         5.46 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
        9.34         2.53       130.88        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
       87.32         2.20         3.98         7.82         8.22        50.27 
TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 
       20.02        48.00        17.98        64.18        67.36        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B3 
       43.59        15.35         0.49         0.59         1.22        12.89 
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-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TE 
        6.87        49.68         4.83         6.28         6.71         4.11 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.66         4.01        15.19         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC 
        6.48        35.24         0.85         2.89         2.24        15.91 
TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
       14.07         7.73        20.98         2.20         6.41         7.66 
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-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HF 
        1.81         6.38         6.35        13.48        88.93        56.19 
TCGA-XF-A8HG 
       15.35 

$`7P GAIN WILD-TYPE`
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-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS 
        4.67         2.07        15.42         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-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 
        0.10         7.20         5.19        16.31         1.84         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       31.40        18.41        19.00         8.91       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV 
       17.62        15.62         1.81        10.49        21.30         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
        8.28        10.55       140.81        48.53        76.60        15.68 
TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE 
       32.28        26.17        24.66         0.10         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 
        0.66         1.38         0.82        15.68         6.87        12.43 
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        16.47        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS 
        5.52        13.18        19.79        14.96        12.13        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S 
       11.01         6.87         5.69         6.84         2.66         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FJ-A3Z9 TCGA-G2-A2EF TCGA-G2-A2EJ 
       50.66         9.30         2.20         7.13        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3OO 
        5.69        26.93        17.26         7.04        20.12        15.81 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
        4.50        17.75         1.12         2.66         2.10         3.12 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
       11.31         4.41         6.41         6.15         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        4.14        19.07         1.51         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LT-A5Z6 
        2.50         6.48        10.52         1.74         4.27         3.45 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
       12.23        16.67        97.45 

  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 
             8.94              8.35 
[1] "0.5 - 130.9 (8.9)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED          1       1       21        35       33
  7P GAIN WILD-TYPE        0       1       47        37       34
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 1                 1
  STAGE II               21                47
  STAGE III              35                37
  STAGE IV               33                34
[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         22 47 16
  7P GAIN WILD-TYPE       40 54 16
D13V4, multiclass
          clus
vv         7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1+T2              22                40
  T3                    47                54
  T4                    16                16
[1] 3 2
[1] 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   51  9 20  6
  7P GAIN WILD-TYPE 79 13 18  1
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              51                79
  N1               9                13
  N2              20                18
  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   43  2 47
  7P GAIN WILD-TYPE 63  3 55
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              43                63
  M1               2                 3
  MX              47                55
[1] 3 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   21 72
  7P GAIN WILD-TYPE 29 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     21   72
  7P GAIN WILD-TYPE   29   92
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              21                29
  MALE                72                92
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       6                         5    79
  7P GAIN WILD-TYPE    16                         6    91
D13V11, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   6                16
  BLACK OR AFRICAN AMERICAN               5                 6
  WHITE                                  79                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"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   58 24
  7Q GAIN WILD-TYPE 93 33
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               82               126 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               24                33 
$`7Q GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A2LA 
       40.08         2.66        12.39         6.58        32.84        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
        5.59         3.65        12.82         9.99        28.41        23.01 
TCGA-CF-A1HR TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AD 
        0.46        12.92         4.90         5.46         9.34       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN 
        1.81        10.59         7.79        87.32         3.98         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A2PC 
       50.27        20.02        17.98        67.36        30.67        43.59 
TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 
       15.35         0.49         0.59         1.22        15.68         8.94 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        4.01        11.93        46.78         1.97        22.98        14.93 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C1 
       14.93         3.62        13.38         5.36        27.45        49.68 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE 
        4.83         6.28         6.71         2.20         4.01         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM 
        4.08         3.25         6.48        35.24         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GV-A3JZ 
        2.24        15.91        14.07         7.73        20.98         5.69 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
        7.63         6.67         6.41        19.07        11.54         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V 
       38.60         4.67         1.81         6.38         6.35        13.48 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        97.45        56.19        15.35 

$`7Q GAIN WILD-TYPE`
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-A20X TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ 
        8.25         4.67         2.07        15.42        28.70         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94         0.43         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
        0.07         0.10         0.10         7.20         5.19        16.31 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84         2.53         2.14        31.40        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 
        8.91       130.88        16.14        17.62        15.62       123.85 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
        2.20         7.82        10.49        21.30         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        48.53        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.68        32.28        26.17        24.66         0.10         0.53 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B6 
        0.56         0.66         1.38         0.82        12.89         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        16.47 
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-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        2.66         6.38        50.66         9.30         4.11         2.66 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       15.19         7.13        61.94        30.61         5.69        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC 
       17.26         7.04        20.12        15.81         4.50        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P 
        1.12         2.66         2.10         3.12         2.20         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        7.66        11.31         4.41         6.41         6.15         7.79 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
        4.14         1.51         8.75         3.45         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN 
       10.52         1.74         4.27         3.45        12.23        16.67 

  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 
            9.140             8.315 
[1] "0.5 - 112.4 (9.1)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED          1       1       20        29       31
  7Q GAIN WILD-TYPE        0       1       48        43       36
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 1                 1
  STAGE II               20                48
  STAGE III              29                43
  STAGE IV               31                36
[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         22 39 16
  7Q GAIN WILD-TYPE       40 62 16
D14V4, multiclass
          clus
vv         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1+T2              22                40
  T3                    39                62
  T4                    16                16
[1] 3 2
[1] 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   44  8 18  7
  7Q GAIN WILD-TYPE 86 14 20  0
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              44                86
  N1               8                14
  N2              18                20
  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   34  2 47
  7Q GAIN WILD-TYPE 72  3 55
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              34                72
  M1               2                 3
  MX              47                55
[1] 3 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    21  63
  7Q GAIN WILD-TYPE  29 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     21   63
  7Q GAIN WILD-TYPE   29  101
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              21                29
  MALE                63               101
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
D14V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       4                         6    70
  7Q GAIN WILD-TYPE    18                         5   100
D14V11, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   4                18
  BLACK OR AFRICAN AMERICAN               6                 5
  WHITE                                  70               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    32  11
  8P GAIN WILD-TYPE 119  46
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               43               165 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                46 
$`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-A2LA TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CU-A72E 
       17.16         9.99         1.94        23.01         0.69         9.34 
TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X2 
       31.40        16.14        10.49        50.27        10.55        17.98 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-FD-A3N6 TCGA-FD-A43U 
       15.68        30.67        43.59         0.49        15.88        14.93 
TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TI TCGA-FJ-A3ZE 
       37.15         5.69        49.68         4.83         4.01         3.48 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GV-A3JV TCGA-GV-A3QI 
       17.26         0.85         2.89         2.24         4.41         4.14 
TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A83P TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HF 
       11.54        38.60         6.38        13.48        88.93        56.19 
TCGA-XF-A8HG 
       15.35 

$`8P GAIN WILD-TYPE`
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-A20W TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         8.35         8.25 
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-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
       28.70        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-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-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.53         2.14        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-A2I2 
      112.44        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-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        20.02         9.67         8.28       140.81        48.00 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A4TZ 
       64.18        48.53        76.60        67.36        32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
        8.94         6.87         4.01        12.43        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45        16.47        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-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        6.84        27.45         6.87         2.66         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       50.66         9.30         6.71         4.11         2.66         2.20 
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-A3IB TCGA-G2-A3IE 
       30.61         5.69        26.93        35.24         7.04        20.12 
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-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        6.41         7.66        11.31         6.41         6.15         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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        6.74         8.75         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 
       10.52         1.74         1.81         4.27         6.35         3.45 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
       12.23        16.67        97.45 

  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 
            13.48              7.79 
[1] "0.5 - 88.9 (13.5)" "0.1 - 140.8 (7.8)"
[1] "hr=" "1.4"
D15V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED          1       1       10        18       12
  8P GAIN WILD-TYPE        0       1       58        54       55
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 1                 1
  STAGE II               10                58
  STAGE III              18                54
  STAGE IV               12                55
[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         12 24  5
  8P GAIN WILD-TYPE       50 77 27
D15V4, multiclass
          clus
vv         8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1+T2              12                50
  T3                    24                77
  T4                     5                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
  8P GAIN MUTATED    26   7   6   1
  8P GAIN WILD-TYPE 104  15  32   6
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              26               104
  N1               7                15
  N2               6                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
  8P GAIN MUTATED   23  1 19
  8P GAIN WILD-TYPE 83  4 83
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              23                83
  M1               1                 4
  MX              19                83
[1] 3 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     7  37
  8P GAIN WILD-TYPE  43 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      7   37
  8P GAIN WILD-TYPE   43  127
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               7                43
  MALE                37               127
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       4                         2    34
  8P GAIN WILD-TYPE    18                         9   136
D15V11, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   4                18
  BLACK OR AFRICAN AMERICAN               2                 9
  WHITE                                  34               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"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   70 25
  8Q GAIN WILD-TYPE 81 32
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               95               113 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               25                32 
$`8Q 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-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0EZ 
        8.35         8.25        17.16         5.59         9.99         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47X TCGA-CU-A0YN 
        1.94        23.01         0.69         0.13         0.10        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.46         5.19         1.84         9.34         2.53        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I6 
       18.41       130.88       112.44        16.14        10.59        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X1 
        8.22        10.49        50.27        20.02        10.55        48.00 
TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ 
       17.98        15.68        30.67        43.59        26.17         0.49 
TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3N6 TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43U 
        0.59         6.87        15.88        46.78        22.98        14.93 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 
       13.38        37.15        11.01         5.36         5.69         6.87 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE 
       49.68         4.83         6.28         6.38         6.71         4.11 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EK 
        2.20         4.01         7.13         3.48         3.25         5.69 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3WC 
       17.26         0.85         2.89         2.24         4.50        17.75 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        2.10         3.12        20.98         4.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OE 
        5.69         7.63         7.79         4.14        11.54        38.60 
TCGA-K4-A4AB TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V 
        2.50         1.81         4.27         6.38         6.35        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        16.67        88.93        56.19        15.35 

$`8Q GAIN WILD-TYPE`
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-A2LD TCGA-BT-A3PH 
       19.50         5.06        14.89        14.96         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-CF-A1HR 
       12.82         2.07        15.42        28.70        28.41         0.46 
TCGA-CF-A1HS TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO 
        0.43         0.07         0.10         0.07         0.10         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AF 
        7.20        16.31         2.14        19.00         8.91        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62         1.81         7.79       123.85         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AV 
        7.82        21.30         9.67         8.28       140.81        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E7-A3X6 
       48.53        76.60        67.36        32.28        15.35        24.66 
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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
        1.22        12.89        15.68         8.94         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        45.93        24.30        22.45        16.47        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S 
        5.52        13.18        19.79         1.97        14.93        14.96 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
        3.62        12.13         6.87         6.84        27.45         2.66 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
       50.66         9.30         2.66        15.19         4.08         6.48 
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-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-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3QK TCGA-GV-A40E 
        2.20         6.41         7.66        11.31         6.67         6.41 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       19.07         1.51         6.74         8.75         3.45         4.67 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-XF-A8HE 
        6.48        10.52         1.74         3.45        97.45 

  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 
             8.25              8.91 
[1] "0.1 - 130.9 (8.2)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED          1       2       26        37       29
  8Q GAIN WILD-TYPE        0       0       42        35       38
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 2                 0
  STAGE II               26                42
  STAGE III              37                35
  STAGE IV               29                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
  8Q GAIN MUTATED         28 49 14
  8Q GAIN WILD-TYPE       34 52 18
D16V4, multiclass
          clus
vv         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1+T2              28                34
  T3                    49                52
  T4                    14                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
  8Q GAIN MUTATED   59 12 17  2
  8Q GAIN WILD-TYPE 71 10 21  5
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              59                71
  N1              12                10
  N2              17                21
  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   46  2 48
  8Q GAIN WILD-TYPE 60  3 54
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              46                60
  M1               2                 3
  MX              48                54
[1] 3 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   20 77
  8Q GAIN WILD-TYPE 30 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     20   77
  8Q GAIN WILD-TYPE   30   87
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              20                30
  MALE                77                87
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
D16V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       7                         3    81
  8Q GAIN WILD-TYPE    15                         8    89
D16V11, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   7                15
  BLACK OR AFRICAN AMERICAN               3                 8
  WHITE                                  81                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    29   5
  9P GAIN WILD-TYPE 122  52
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               34               174 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                5                52 
$`9P GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-CU-A0YR 
       40.08         6.74        17.16        12.82        12.92         7.20 
TCGA-CU-A3QU TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A6B6 
        5.19       130.88        10.59        87.32         7.82        30.67 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A5BT 
       12.89         6.87        11.93        22.45        14.93        11.01 
TCGA-FD-A62N TCGA-FD-A6TH TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-GC-A3I6 
        2.66         2.20         3.48        61.94        30.61         2.24 
TCGA-GC-A3RC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40G 
       15.91         7.73         2.10         5.69         4.14        19.07 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-XF-A8HD TCGA-XF-A8HG 
        1.81         6.35        88.93        15.35 

$`9P GAIN WILD-TYPE`
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-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67         2.07        15.42        28.70         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        8.98         1.94        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-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         5.46        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-A1AD 
        2.14        31.40        18.41        19.00         8.91       112.44 
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-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        2.20         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        48.53        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       32.28        43.59        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-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.82         1.22        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        16.47        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-A6TC TCGA-FD-A6TD 
        4.83         6.28         6.38        50.66         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        4.11         2.66         4.01        15.19         7.13         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        3.25         6.48         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
        7.04        20.12         0.85         2.89        15.81         4.50 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07        17.75         1.12         2.66         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        2.20         6.41         7.66        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
        6.15         7.63         7.79         6.67         6.41        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A8HF 
        3.45        13.48        12.23        16.67        97.45        56.19 

  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 
           11.470             8.265 
[1] "1.8 - 130.9 (11.5)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "2.4"
D17V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED          0       1        9        14       10
  9P GAIN WILD-TYPE        1       1       59        58       57
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 1                 1
  STAGE II                9                59
  STAGE III              14                58
  STAGE IV               10                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
  9P GAIN MUTATED         10 16  4
  9P GAIN WILD-TYPE       52 85 28
D17V4, multiclass
          clus
vv         9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1+T2              10                52
  T3                    16                85
  T4                     4                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
  9P GAIN MUTATED    21   2   6   3
  9P GAIN WILD-TYPE 109  20  32   4
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              21               109
  N1               2                20
  N2               6                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
  9P GAIN MUTATED   15  2 17
  9P GAIN WILD-TYPE 91  3 85
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              15                91
  M1               2                 3
  MX              17                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"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     6  28
  9P GAIN WILD-TYPE  44 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6   28
  9P GAIN WILD-TYPE   44  136
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               6                44
  MALE                28               136
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       1                         2    31
  9P GAIN WILD-TYPE    21                         9   139
D17V11, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   1                21
  BLACK OR AFRICAN AMERICAN               2                 9
  WHITE                                  31               139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    24   6
  9Q GAIN WILD-TYPE 127  51
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               30               178 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                6                51 
$`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-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC 
        3.48        61.94        30.61         2.24        15.91        17.75 
TCGA-GC-A3YS TCGA-H4-A2HQ TCGA-K4-A6FZ TCGA-LC-A66R TCGA-XF-A8HD TCGA-XF-A8HG 
        1.12         6.74         1.81         6.35        88.93        15.35 

$`9Q GAIN WILD-TYPE`
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        31.40        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        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       67.36        15.68        32.28        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-A7DV TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.66         1.38         0.82         1.22         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-A3SR 
       16.47        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-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       12.13        13.38        37.15         6.87         5.69         6.84 
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-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
       50.66         9.30         4.11         2.66         4.01        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-GC-A3BM 
       35.24        17.26         7.04        20.12         0.85         2.89 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.81         4.50        14.07         2.66         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20         6.41         7.66        11.31 
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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         8.75         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-MV-A51V 
       10.52         1.74         4.27         6.38         3.45        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A8HF 
       12.23        16.67        97.45        56.19 

  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 
           10.800             8.315 
[1] "1.1 - 130.9 (10.8)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1.6"
D18V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED          0       1        6        17        6
  9Q GAIN WILD-TYPE        1       1       62        55       61
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 1                 1
  STAGE II                6                62
  STAGE III              17                55
  STAGE IV                6                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
  9Q GAIN MUTATED          4 17  4
  9Q GAIN WILD-TYPE       58 84 28
D18V4, multiclass
          clus
vv         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1+T2               4                58
  T3                    17                84
  T4                     4                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
  9Q GAIN MUTATED    22   1   3   1
  9Q GAIN WILD-TYPE 108  21  35   6
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              22               108
  N1               1                21
  N2               3                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
  9Q GAIN MUTATED   13  3 14
  9Q GAIN WILD-TYPE 93  2 88
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              13                93
  M1               3                 2
  MX              14                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"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     8  22
  9Q GAIN WILD-TYPE  42 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      8   22
  9Q GAIN WILD-TYPE   42  142
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               8                42
  MALE                22               142
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       1                         2    26
  9Q GAIN WILD-TYPE    21                         9   144
D18V11, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   1                21
  BLACK OR AFRICAN AMERICAN               2                 9
  WHITE                                  26               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"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    34  22
  10P GAIN WILD-TYPE 117  35
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                56                152 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                 35 
$`10P GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V 
       40.08         2.66         6.58        32.84         5.06         5.06 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42E TCGA-CF-A1HS TCGA-CU-A0YN 
        8.35         5.59        12.82         9.99         0.43        12.92 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IL 
        2.53         2.14        31.40       112.44        87.32         3.98 
TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-FD-A3B6 
        8.22        48.00        15.68        30.67        26.17         6.87 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SS TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BZ 
       45.93        24.30         1.97        13.38        37.15        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FT-A3EE TCGA-FT-A61P 
        6.87        49.68         2.66         4.01         3.25         6.48 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-GC-A3RB TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42P 
       17.26        20.12         4.50         7.73         2.20         6.41 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A6ZA 
        6.41         5.69         7.63         7.79         6.41        11.54 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
       38.60         8.75         6.48        10.52         1.74         1.81 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`10P GAIN WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.74        12.39        11.93        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA 
       17.88        19.50        14.89        14.96         8.25        17.16 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
        3.65         4.67         2.07        15.42        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
        8.98         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-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-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-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
        8.28        10.55       140.81        17.98        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       76.60        67.36        32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.38         0.82         1.22        12.89        15.68         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.43        11.93        15.88        22.45        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       12.82         5.52        13.18        46.78        19.79        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BT 
       14.93        14.96        14.93         3.62        12.13        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62O 
        6.87         5.36         5.69         6.84         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28         6.38        50.66         9.30         6.71         4.11 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EF 
        2.20        15.19         7.13         3.48         4.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3VY 
       30.61         5.69        26.93        35.24         7.04         0.85 
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-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q 
        1.12         2.66         2.10         3.12        20.98         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
       11.31         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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38         6.35         3.45        13.48        12.23        16.67 
TCGA-XF-A8HD TCGA-XF-A8HE 
       88.93        97.45 

  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 
             8.005              8.960 
[1] "0.4 - 112.4 (8.0)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.5"
D19V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED          1       1       17        18       20
  10P GAIN WILD-TYPE        0       1       51        54       47
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  1                  1
  STAGE II                17                 51
  STAGE III               18                 54
  STAGE IV                20                 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
  10P GAIN MUTATED         18 29  8
  10P GAIN WILD-TYPE       44 72 24
D19V4, multiclass
          clus
vv         10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1+T2               18                 44
  T3                     29                 72
  T4                      8                 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
  10P GAIN MUTATED   31  7 12  3
  10P GAIN WILD-TYPE 99 15 26  4
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               31                 99
  N1                7                 15
  N2               12                 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
  10P GAIN MUTATED   27  0 32
  10P GAIN WILD-TYPE 79  5 70
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               27                 79
  M1                0                  5
  MX               32                 70
[1] 3 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    11  48
  10P GAIN WILD-TYPE  39 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     11   48
  10P GAIN WILD-TYPE   39  116
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               11                 39
  MALE                 48                116
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       4                         1    50
  10P GAIN WILD-TYPE    18                        10   120
D19V11, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    4                 18
  BLACK OR AFRICAN AMERICAN                1                 10
  WHITE                                   50                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"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     9   7
  10Q GAIN WILD-TYPE 142  50
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                16                192 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                 50 
$`10Q GAIN MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20V TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A3IN 
        6.58         5.06         5.06         2.53        31.40         8.22 
TCGA-DK-A6B2 TCGA-E5-A4U1 TCGA-FD-A3B6 TCGA-FD-A3SS TCGA-FD-A5BR TCGA-FD-A5BZ 
       15.68        26.17         6.87         1.97        13.38        27.45 
TCGA-FD-A6TI TCGA-GC-A3RB TCGA-HQ-A2OE TCGA-XF-A8HG 
        4.01         4.50        38.60        15.35 

$`10Q GAIN 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-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-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       14.96         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-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-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA 
       16.31         1.84         9.34         2.14        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-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-A6B5 TCGA-DK-A6B6 
       64.18        48.53        76.60        67.36        32.28        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-A7DV 
        0.59         0.56         0.66         1.38         0.82         1.22 
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        16.47        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-A6TC 
        2.66         4.83         6.28         6.38        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.71         4.11         2.66         2.20        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-A3IE 
        5.69        26.93        35.24        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        0.85         2.89         2.24        15.81        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-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
       20.98         2.20         6.41         7.66        11.31         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-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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       13.48        12.23        16.67        88.93        97.45        56.19 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.97               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             38.60             140.81 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             7.545              8.830 
[1] "2.0 - 38.6 (7.5)"  "0.1 - 140.8 (8.8)"
[1] "hr=" "1.7"
D20V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED          0       0        4         5        8
  10Q GAIN WILD-TYPE        1       2       64        67       59
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 4                 64
  STAGE III                5                 67
  STAGE IV                 8                 59
[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          6  7  5
  10Q GAIN WILD-TYPE       56 94 27
D20V4, multiclass
          clus
vv         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1+T2                6                 56
  T3                      7                 94
  T4                      5                 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
  10Q GAIN MUTATED     9   5   3   1
  10Q GAIN WILD-TYPE 121  17  35   6
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                9                121
  N1                5                 17
  N2                3                 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
  10Q GAIN MUTATED   10  0  8
  10Q GAIN WILD-TYPE 96  5 94
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0               10                 96
  M1                0                  5
  MX                8                 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"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3  15
  10Q GAIN WILD-TYPE  47 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3   15
  10Q GAIN WILD-TYPE   47  149
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                3                 47
  MALE                 15                149
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       2                         1    13
  10Q GAIN WILD-TYPE    20                        10   157
D20V11, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    2                 20
  BLACK OR AFRICAN AMERICAN                1                 10
  WHITE                                   13                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"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    14   8
  11P GAIN WILD-TYPE 137  49
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                186 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                 49 
$`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-E5-A2PC TCGA-E7-A5KF TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A5BT TCGA-FD-A62P 
       43.59         0.66         1.22         6.87        11.01         6.28 
TCGA-FD-A6TI TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E 
        4.01         2.24        15.91         5.69         4.14         6.41 
TCGA-K4-A4AC TCGA-LC-A66R TCGA-PQ-A6FI TCGA-XF-A8HF 
        6.48         6.35        12.23        56.19 

$`11P GAIN WILD-TYPE`
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        31.40        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        48.53        76.60        67.36        15.68        32.28 
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-A677 TCGA-E7-A678 TCGA-FD-A3B3 
        0.53         0.59         0.56         1.38         0.82        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        16.47        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-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-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
       49.68         2.66         4.83         6.38        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.71         4.11         2.66         2.20        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-A3IE 
        5.69        26.93        35.24        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
        0.85         2.89        15.81         4.50        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-GV-A3JV TCGA-GV-A3JW 
        2.20         6.41         7.66        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
        6.15         7.63         7.79         6.67        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        2.50        10.52         1.74         1.81         4.27         6.38 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        3.45        13.48        16.67        88.93        97.45        15.35 

  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 
             6.445              8.925 
[1] "0.7 - 56.2 (6.4)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.9"
D21V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED          0       0        8         7        7
  11P GAIN WILD-TYPE        1       2       60        65       60
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 8                 60
  STAGE III                7                 65
  STAGE IV                 7                 60
[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          7  8  5
  11P GAIN WILD-TYPE       55 93 27
D21V4, multiclass
          clus
vv         11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1+T2                7                 55
  T3                      8                 93
  T4                      5                 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 GAIN MUTATED    12   2   3   3
  11P GAIN WILD-TYPE 118  20  35   4
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               12                118
  N1                2                 20
  N2                3                 35
  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 13
  11P GAIN WILD-TYPE 97  5 89
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                9                 97
  M1                0                  5
  MX               13                 89
[1] 3 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  20
  11P GAIN WILD-TYPE  48 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   20
  11P GAIN WILD-TYPE   48  144
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 48
  MALE                 20                144
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       1                         0    21
  11P GAIN WILD-TYPE    21                        11   149
D21V11, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                 21
  BLACK OR AFRICAN AMERICAN                0                 11
  WHITE                                   21                149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    21   9
  11Q GAIN WILD-TYPE 130  48
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                30                178 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                 48 
$`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-E5-A2PC TCGA-E7-A5KF TCGA-E7-A7DV 
        7.82        10.55        17.98        43.59         0.66         1.22 
TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A62P 
        6.87        45.93        14.93        13.38        11.01         6.28 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GV-A3JZ 
        2.66         4.01        15.19         2.24        15.91         5.69 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-K4-A4AC TCGA-LC-A66R TCGA-PQ-A6FI TCGA-XF-A8HF 
        7.63         6.41         6.48         6.35        12.23        56.19 

$`11Q GAIN WILD-TYPE`
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        31.40        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        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 
       67.36        15.68        32.28        30.67        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-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 
        1.38         0.82        12.89        15.68         8.94         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        11.93        15.88        24.30        22.45        16.47 
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-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS 
       22.98        14.96        14.93         3.62        12.13        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-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-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        6.71         4.11         2.20         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-GC-A3BM 
       35.24        17.26         7.04        20.12         0.85         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-GU-A42P 
        7.73         2.10         3.12        20.98         2.20         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        7.66        11.31         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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
       38.60         8.75         3.45         4.67         2.50        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.74         1.81         4.27         6.38         3.45        13.48 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       16.67        88.93        97.45        15.35 

  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 
             7.725              8.830 
[1] "0.7 - 56.2 (7.7)"  "0.1 - 140.8 (8.8)"
[1] "hr=" "1.3"
D22V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED          0       0       10         8       12
  11Q GAIN WILD-TYPE        1       2       58        64       55
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                10                 58
  STAGE III                8                 64
  STAGE IV                12                 55
[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         10 13  6
  11Q GAIN WILD-TYPE       52 88 26
D22V4, multiclass
          clus
vv         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1+T2               10                 52
  T3                     13                 88
  T4                      6                 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
  11Q GAIN MUTATED    16   2   8   3
  11Q GAIN WILD-TYPE 114  20  30   4
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               16                114
  N1                2                 20
  N2                8                 30
  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   12  0 18
  11Q GAIN WILD-TYPE 94  5 84
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0               12                 94
  M1                0                  5
  MX               18                 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"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3  27
  11Q GAIN WILD-TYPE  47 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   27
  11Q GAIN WILD-TYPE   47  137
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 47
  MALE                 27                137
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
D22V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       1                         1    27
  11Q GAIN WILD-TYPE    21                        10   143
D22V11, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    1                 21
  BLACK OR AFRICAN AMERICAN                1                 10
  WHITE                                   27                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"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    39  20
  12P GAIN WILD-TYPE 112  37
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                59                149 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                20                 37 
$`12P GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20R 
       40.08         6.74        19.04        32.84        17.88         5.06 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
        5.06         8.25         5.59         3.65        12.82         2.07 
TCGA-BT-A42E TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A6 
        9.99        12.92         4.90         7.20         1.84        31.40 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 
        7.82        50.27        10.55        48.00        64.18        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-FD-A3B3 TCGA-FD-A3B6 
       15.68        30.67         0.49         0.56        12.89         6.87 
TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BZ 
       45.93         1.97        14.93        37.15         5.36        27.45 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY 
        6.28         6.38        15.19         6.48        35.24         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GV-A3JZ TCGA-GV-A3QH 
        2.89         2.24        15.81        14.07         5.69         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A2OE TCGA-K4-A3WU 
        4.14         6.67         6.41        19.07        38.60         3.45 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A83P TCGA-MV-A51V 
        4.67         6.48         1.81         6.38        13.48 

$`12P GAIN WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        7.33         2.66        12.39         6.58        11.93        12.16 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH 
       19.50        14.89        14.96         8.35        17.16         4.67 
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-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-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
        0.07         0.10         0.10         5.46         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.53         2.14        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-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-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E5-A2PC 
      140.81        17.98        48.53        76.60        32.28        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 
       15.35        26.17        24.66         0.10         0.53         0.59 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.66         1.38         0.82         1.22        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 
       16.47        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-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.66         2.20         4.01         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        3.25        61.94        30.61         5.69        26.93        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
        7.04        20.12         4.50        15.91        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-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        6.41         7.66        11.31         4.41         6.41         6.15 
TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A4AB 
        7.63        11.54         1.51         6.74         8.75         2.50 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       10.52         1.74         4.27         6.35         3.45        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        88.93        97.45        56.19        15.35 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.49               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             67.36             140.81 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              7.79               8.94 
[1] "0.5 - 67.4 (7.8)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED          0       1       22        22       15
  12P GAIN WILD-TYPE        1       1       46        50       52
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                22                 46
  STAGE III               22                 50
  STAGE IV                15                 52
[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         22 26  9
  12P GAIN WILD-TYPE       40 75 23
D23V4, multiclass
          clus
vv         12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1+T2               22                 40
  T3                     26                 75
  T4                      9                 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
  12P GAIN MUTATED   38  6  8  3
  12P GAIN WILD-TYPE 92 16 30  4
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               38                 92
  N1                6                 16
  N2                8                 30
  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   32  0 28
  12P GAIN WILD-TYPE 74  5 74
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               32                 74
  M1                0                  5
  MX               28                 74
[1] 3 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    17  44
  12P GAIN WILD-TYPE  33 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     17   44
  12P GAIN WILD-TYPE   33  120
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               17                 33
  MALE                 44                120
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       6                         3    48
  12P GAIN WILD-TYPE    16                         8   122
D23V11, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    6                 16
  BLACK OR AFRICAN AMERICAN                3                  8
  WHITE                                   48                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"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    27  16
  12Q GAIN WILD-TYPE 124  41
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                43                165 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                 41 
$`12Q GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20X 
       40.08         6.74        19.04        17.88         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42E TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 
        5.59         2.07         9.99         4.90         7.20         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A3IS TCGA-DK-A3WX 
        2.53         2.14        31.40       130.88        50.27        10.55 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-E7-A5KE TCGA-FD-A3NA TCGA-FD-A43Y 
       48.00        64.18        67.36         0.56        45.93        12.13 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A62S TCGA-FJ-A3Z7 TCGA-G2-A2EF 
        5.36        27.45         6.28         6.38        15.19        61.94 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GV-A3QH TCGA-GV-A3QI 
       35.24         0.85         2.89         2.24         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A6FZ TCGA-K4-A83P 
        6.67         6.41        38.60         3.45         1.81         6.38 
TCGA-MV-A51V 
       13.48 

$`12Q GAIN WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        7.33         2.66        12.39         6.58        11.93        32.84 
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       12.16        19.50        14.89        14.96         5.06         8.35 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C 
       17.16         3.65         4.67        12.82        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-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
        0.10        12.92         5.46         5.19        16.31         9.34 
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-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-A3IT 
        2.20         3.98         7.82         8.22        10.49        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
       20.02         9.67         8.28       140.81        17.98        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       76.60        15.68        32.28        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-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        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        16.47        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-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69         6.84         6.87        49.68         2.66         4.83 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       50.66         9.30         6.71         4.11         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        4.01         7.13         3.48         4.08         3.25         6.48 
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-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-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        6.41         7.66        11.31         4.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        5.69         7.63        19.07        11.54         1.51         6.74 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        8.75         4.67         2.50         6.48        10.52         1.74 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        4.27         6.35         3.45        12.23        16.67        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       97.45        56.19        15.35 

  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 
              7.20               8.94 
[1] "0.6 - 130.9 (7.2)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.4"
D24V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED          0       1       16        18       10
  12Q GAIN WILD-TYPE        1       1       52        54       57
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                16                 52
  STAGE III               18                 54
  STAGE IV                10                 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
  12Q GAIN MUTATED         16 19  7
  12Q GAIN WILD-TYPE       46 82 25
D24V4, multiclass
          clus
vv         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1+T2               16                 46
  T3                     19                 82
  T4                      7                 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
  12Q GAIN MUTATED   31  4  7  0
  12Q GAIN WILD-TYPE 99 18 31  7
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               31                 99
  N1                4                 18
  N2                7                 31
  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   28  0 17
  12Q GAIN WILD-TYPE 78  5 85
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               28                 78
  M1                0                  5
  MX               17                 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"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    12  34
  12Q GAIN WILD-TYPE  38 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12   34
  12Q GAIN WILD-TYPE   38  130
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               12                 38
  MALE                 34                130
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       6                         1    37
  12Q GAIN WILD-TYPE    16                        10   133
D24V11, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    6                 16
  BLACK OR AFRICAN AMERICAN                1                 10
  WHITE                                   37                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"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    36  14
  13Q GAIN WILD-TYPE 115  43
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                50                158 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                14                 43 
$`13Q GAIN MUTATED`
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LD 
        6.74         6.58        19.04        19.50        14.96         3.65 
TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU 
       12.82         8.98         0.43        12.92         7.20         5.19 
TCGA-CU-A3YL TCGA-DK-A2HX TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 
       16.31         1.81         3.98        50.27        20.02        48.00 
TCGA-DK-A6B1 TCGA-E5-A2PC TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3SM TCGA-FD-A3SQ 
       67.36        43.59         0.59         6.87        16.47        46.78 
TCGA-FD-A43X TCGA-FD-A5BT TCGA-FD-A62O TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
        3.62        11.01         4.83         4.11         2.66         2.20 
TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-GC-A3OO TCGA-GC-A3WC 
        3.48         6.48        61.94         5.69        15.81        17.75 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        2.10        20.98         6.15         5.69         7.63         7.79 
TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-K4-A54R TCGA-LC-A66R TCGA-MV-A51V TCGA-XF-A8HD 
        6.67         6.74        10.52         6.35        13.48        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`13Q GAIN WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N 
       40.08         7.33         2.66        12.39        11.93        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       12.16        17.88         5.06        14.89         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        8.25        17.16         5.59         4.67         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       28.70         9.99        28.41         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-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-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        31.40        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-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
      123.85        87.32         2.20         7.82         8.22        10.49 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       21.30         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-DK-A6B6 
       64.18        48.53        76.60        15.68        32.28        30.67 
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-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.56         0.66         1.38         0.82         1.22        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-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       45.93        24.30        22.45        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-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       12.13        13.38        37.15         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P 
        6.84        27.45         6.87        49.68         2.66         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 
        6.38        50.66         9.30         6.71         4.01        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
        7.13         4.08         3.25        30.61        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         2.89         2.24 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        14.07         1.12         2.66         7.73 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
        3.12         2.20         6.41         7.66        11.31         4.41 
TCGA-GV-A3JW TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        6.41         4.14         6.41        19.07        11.54         1.51 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         8.75         3.45         4.67         2.50         6.48 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-PQ-A6FI 
        1.74         1.81         4.27         6.38         3.45        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HE 
       16.67        97.45 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.43               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             88.93             140.81 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              7.71               8.83 
[1] "0.4 - 88.9 (7.7)"  "0.1 - 140.8 (8.8)"
[1] "hr=" "1"  
D25V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED          0       0       15        15       22
  13Q GAIN WILD-TYPE        1       2       53        57       45
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                15                 53
  STAGE III               15                 57
  STAGE IV                22                 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
  13Q GAIN MUTATED         14 27  6
  13Q GAIN WILD-TYPE       48 74 26
D25V4, multiclass
          clus
vv         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1+T2               14                 48
  T3                     27                 74
  T4                      6                 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
  13Q GAIN MUTATED    27   4  15   4
  13Q GAIN WILD-TYPE 103  18  23   3
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               27                103
  N1                4                 18
  N2               15                 23
  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   24  4 25
  13Q GAIN WILD-TYPE 82  1 77
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               24                 82
  M1                4                  1
  MX               25                 77
[1] 3 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    13  40
  13Q GAIN WILD-TYPE  37 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     13   40
  13Q GAIN WILD-TYPE   37  124
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               13                 37
  MALE                 40                124
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       3                         1    48
  13Q GAIN WILD-TYPE    19                        10   122
D25V11, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    3                 19
  BLACK OR AFRICAN AMERICAN                1                 10
  WHITE                                   48                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"

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    24  15
  14Q GAIN WILD-TYPE 127  42
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                39                169 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                15                 42 
$`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-GV-A3QH TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A6FZ 
        2.20         6.41         7.79         4.67         6.48         1.81 
TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-XF-A8HG 
        3.45        16.67        15.35 

$`14Q GAIN WILD-TYPE`
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 
       31.40        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        48.53        76.60        67.36        15.68        32.28 
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-A7DV 
        0.59         0.56         0.66         1.38         0.82         1.22 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.68         8.94         6.87        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        16.47        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-A5BU 
       14.93         3.62        12.13        13.38        37.15         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         5.69         6.84         6.87        49.68         2.66 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.28        50.66         9.30         2.66         2.20         4.01 
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-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-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
        7.73         2.10         3.12         7.66        11.31         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
        6.41         6.15         5.69         7.63         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-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-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE 
        6.38         6.35        13.48        12.23        88.93        97.45 
TCGA-XF-A8HF 
       56.19 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.12               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             43.59             140.81 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              7.79               8.91 
[1] "1.1 - 43.6 (7.8)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.7"
D26V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED          0       0       10        20        9
  14Q GAIN WILD-TYPE        1       2       58        52       58
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                10                 58
  STAGE III               20                 52
  STAGE IV                 9                 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
  14Q GAIN MUTATED          6 23  4
  14Q GAIN WILD-TYPE       56 78 28
D26V4, multiclass
          clus
vv         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1+T2                6                 56
  T3                     23                 78
  T4                      4                 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 GAIN MUTATED    25   5   4   1
  14Q GAIN WILD-TYPE 105  17  34   6
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               25                105
  N1                5                 17
  N2                4                 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
  14Q GAIN MUTATED   13  2 24
  14Q GAIN WILD-TYPE 93  3 78
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0               13                 93
  M1                2                  3
  MX               24                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    12  27
  14Q GAIN WILD-TYPE  38 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     12   27
  14Q GAIN WILD-TYPE   38  137
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               12                 38
  MALE                 27                137
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
D26V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         3    31
  14Q GAIN WILD-TYPE    22                         8   139
D26V11, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                 22
  BLACK OR AFRICAN AMERICAN                3                  8
  WHITE                                   31                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    13   6
  15Q GAIN WILD-TYPE 138  51
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                19                189 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                 51 
$`15Q GAIN MUTATED`
TCGA-BT-A20Q TCGA-BT-A20V TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CU-A3YL TCGA-CU-A5W6 
       19.50         5.06        28.41        23.01        16.31         1.84 
TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A6B1 TCGA-E5-A4TZ 
        2.14         1.81        50.27        10.55        67.36        15.35 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EO TCGA-GC-A3BM 
       14.93         3.62         2.66         3.48        35.24         2.89 
TCGA-GC-A3I6 
        2.24 

$`15Q GAIN WILD-TYPE`
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-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-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        9.99         8.98         1.94         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-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-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.53        31.40        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-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-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       10.49        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-A6B2 
       48.00        17.98        64.18        48.53        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       32.28        30.67        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.82         1.22        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        16.47        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-A43Y 
       19.79         1.97        22.98        14.93        14.96        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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28         6.38        50.66         9.30         6.71         4.11 
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-A2ES 
        6.48        61.94        30.61         5.69        26.93        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        7.04        20.12         0.85        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-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20         6.41         7.66        11.31 
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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        6.74        38.60         8.75         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        6.48        10.52         1.74         1.81         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        6.35         3.45        13.48        12.23        16.67        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       97.45        56.19        15.35 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.81               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             67.36             140.81 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             10.55               8.35 
[1] "1.8 - 67.4 (10.6)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED          0       0        6         6        9
  15Q GAIN WILD-TYPE        1       2       62        66       58
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 6                 62
  STAGE III                6                 66
  STAGE IV                 9                 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
  15Q GAIN MUTATED          6  8  6
  15Q GAIN WILD-TYPE       56 93 26
D27V4, multiclass
          clus
vv         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1+T2                6                 56
  T3                      8                 93
  T4                      6                 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
  15Q GAIN MUTATED    12   1   6   2
  15Q GAIN WILD-TYPE 118  21  32   5
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               12                118
  N1                1                 21
  N2                6                 32
  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  6
  15Q GAIN WILD-TYPE 92  4 96
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               14                 92
  M1                1                  4
  MX                6                 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"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     4  17
  15Q GAIN WILD-TYPE  46 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4   17
  15Q GAIN WILD-TYPE   46  147
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                4                 46
  MALE                 17                147
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         1    18
  15Q GAIN WILD-TYPE    21                        10   152
D27V11, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                 21
  BLACK OR AFRICAN AMERICAN                1                 10
  WHITE                                   18                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"

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    21  12
  16P GAIN WILD-TYPE 130  45
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                33                175 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                 45 
$`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-A3IV TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-FD-A3SJ 
        9.67        48.00        15.68        43.59         0.49        24.30 
TCGA-FD-A5BY TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO 
        6.84         2.66         4.01         3.48         3.25        35.24 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GV-A3JV TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU 
        2.89         2.24         4.41         6.74         8.75         3.45 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-LC-A66R 
        2.50         6.38         6.35 

$`16P GAIN WILD-TYPE`
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 
       31.40        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-A3IT TCGA-DK-A3IU 
       87.32         2.20         7.82        10.49        21.30        20.02 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
        8.28        10.55       140.81        17.98        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 
       76.60        67.36        32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.38         0.82         1.22        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-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45        16.47        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-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
        4.83         6.28         6.38        50.66         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A61P 
        4.11         2.20        15.19         7.13         4.08         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61         5.69        26.93        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12         0.85        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-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW 
       20.98         2.20         6.41         7.66        11.31         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-HQ-A2OE TCGA-K4-A3WV 
        6.41        19.07        11.54         1.51        38.60         4.67 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LT-A5Z6 
        6.48        10.52         1.74         1.81         4.27         3.45 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       13.48        12.23        16.67        88.93        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.10               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             50.27             140.81 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              6.58              10.49 
[1] "0.1 - 50.3 (6.6)"   "0.1 - 140.8 (10.5)"
[1] "hr=" "1.8"
D28V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED          0       0        6        11       16
  16P GAIN WILD-TYPE        1       2       62        61       51
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 6                 62
  STAGE III               11                 61
  STAGE IV                16                 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
  16P GAIN MUTATED          6 12 11
  16P GAIN WILD-TYPE       56 89 21
D28V4, multiclass
          clus
vv         16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1+T2                6                 56
  T3                     12                 89
  T4                     11                 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
  16P GAIN MUTATED    15   6   7   2
  16P GAIN WILD-TYPE 115  16  31   5
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               15                115
  N1                6                 16
  N2                7                 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
  16P GAIN MUTATED   17  3 13
  16P GAIN WILD-TYPE 89  2 89
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               17                 89
  M1                3                  2
  MX               13                 89
[1] 3 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     9  24
  16P GAIN WILD-TYPE  41 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9   24
  16P GAIN WILD-TYPE   41  140
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                9                 41
  MALE                 24                140
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       2                         2    26
  16P GAIN WILD-TYPE    20                         9   144
D28V11, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    2                 20
  BLACK OR AFRICAN AMERICAN                2                  9
  WHITE                                   26                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"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    31  11
  16Q GAIN WILD-TYPE 120  46
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                42                166 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                11                 46 
$`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-CU-A3KJ TCGA-DK-A2I2 
       12.82        28.70         8.98         0.10         5.46         7.79 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-E5-A2PC 
        3.98         8.22        50.27        48.00        15.68        43.59 
TCGA-FD-A3B3 TCGA-FD-A43P TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TG 
       12.89        14.93         6.84         6.28         6.38         2.66 
TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM 
        4.01         3.48         3.25        35.24         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GV-A3JW 
        2.24         1.12         2.66         7.73        20.98         6.41 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6MB TCGA-LC-A66R 
        6.74         8.75         3.45         2.50         4.27         6.35 

$`16Q GAIN WILD-TYPE`
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-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-A1A7 TCGA-DK-A1AA 
        9.34         2.53         2.14        31.40        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-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM 
        1.81        10.59       123.85        87.32         2.20         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       10.49        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        48.53        76.60        67.36 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       32.28        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-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        0.82         1.22        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 
       16.47        12.82         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-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-A62N TCGA-FD-A62O TCGA-FD-A6TA 
       27.45         6.87        49.68         2.66         4.83        50.66 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        9.30         6.71         4.11         2.20        15.19         7.13 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        4.08         6.48        61.94        30.61         5.69        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       17.26         7.04        20.12        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P 
       14.07        17.75         2.10         3.12         2.20         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.66        11.31         4.41         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-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        1.51        38.60         4.67         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.81         6.38         3.45        13.48        12.23        16.67 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        97.45        56.19        15.35 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.10               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             50.27             140.81 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             6.395             10.535 
[1] "0.1 - 50.3 (6.4)"   "0.1 - 140.8 (10.5)"
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED          0       0       10        15       17
  16Q GAIN WILD-TYPE        1       2       58        57       50
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                10                 58
  STAGE III               15                 57
  STAGE IV                17                 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
  16Q GAIN MUTATED          8 19 10
  16Q GAIN WILD-TYPE       54 82 22
D29V4, multiclass
          clus
vv         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1+T2                8                 54
  T3                     19                 82
  T4                     10                 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
  16Q GAIN MUTATED    21   7   7   3
  16Q GAIN WILD-TYPE 109  15  31   4
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               21                109
  N1                7                 15
  N2                7                 31
  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   18  3 20
  16Q GAIN WILD-TYPE 88  2 82
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               18                 88
  M1                3                  2
  MX               20                 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"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    15  27
  16Q GAIN WILD-TYPE  35 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     15   27
  16Q GAIN WILD-TYPE   35  137
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               15                 35
  MALE                 27                137
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       2                         4    33
  16Q GAIN WILD-TYPE    20                         7   137
D29V11, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    2                 20
  BLACK OR AFRICAN AMERICAN                4                  7
  WHITE                                   33                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"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    17  14
  17P GAIN WILD-TYPE 134  43
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                31                177 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                 43 
$`17P GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20U 
       40.08         2.66         6.74         6.58         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YR 
        8.35         3.65        12.82        28.70         8.98         7.20 
TCGA-DK-A3IM TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-FD-A3B7 TCGA-FD-A3SP TCGA-FD-A5BT 
        7.82        67.36        30.67         4.01        13.18        11.01 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-GV-A3JV TCGA-GV-A3QH 
        4.11         2.20        15.19         3.25         4.41         7.79 
TCGA-GV-A40E TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-LC-A66R 
        6.41        38.60         3.45         4.67         1.81         6.35 
TCGA-MV-A51V 
       13.48 

$`17P GAIN WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        7.33        12.39        11.93        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       17.88        19.50        14.89         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        5.59         4.67         2.07        15.42         9.99        28.41 
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-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         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        31.40        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-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-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ 
       48.53        76.60        15.68        32.28        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-A7DV TCGA-FD-A3B3 
        0.56         0.66         1.38         0.82         1.22        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-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       45.93        24.30        22.45        16.47        12.82         5.52 
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-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-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-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        6.71         2.66         4.01         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-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         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-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        6.41         7.66        11.31         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.63         4.14         6.67        19.07        11.54         1.51 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        6.74         8.75         2.50         6.48        10.52         1.74 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        4.27         6.38         3.45        12.23        16.67        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       97.45        56.19        15.35 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.81               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             67.36             140.81 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               7.2                9.3 
[1] "1.8 - 67.4 (7.2)"  "0.1 - 140.8 (9.3)"
[1] "hr=" "2.2"
D30V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED          0       1        7        13       10
  17P GAIN WILD-TYPE        1       1       61        59       57
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                 7                 61
  STAGE III               13                 59
  STAGE IV                10                 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
  17P GAIN MUTATED          6 16  6
  17P GAIN WILD-TYPE       56 85 26
D30V4, multiclass
          clus
vv         17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1+T2                6                 56
  T3                     16                 85
  T4                      6                 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
  17P GAIN MUTATED    16   4   7   1
  17P GAIN WILD-TYPE 114  18  31   6
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               16                114
  N1                4                 18
  N2                7                 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
  17P GAIN MUTATED   14  1 17
  17P GAIN WILD-TYPE 92  4 85
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               14                 92
  M1                1                  4
  MX               17                 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"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     7  25
  17P GAIN WILD-TYPE  43 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7   25
  17P GAIN WILD-TYPE   43  139
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                7                 43
  MALE                 25                139
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
D30V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       1                         1    26
  17P GAIN WILD-TYPE    21                        10   144
D30V11, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                 21
  BLACK OR AFRICAN AMERICAN                1                 10
  WHITE                                   26                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"

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    42  28
  17Q GAIN WILD-TYPE 109  29
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                70                138 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                28                 29 
$`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-A0YR TCGA-CU-A3YL 
        3.65        28.70         8.98         0.10         7.20        16.31 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I2 TCGA-DK-A3IM 
        1.84        31.40        18.41       112.44         7.79         7.82 
TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 
       50.27        10.55        48.00        17.98        67.36        30.67 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-FD-A3B5 
       43.59         0.49         0.59         0.56         1.38         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-A6TE TCGA-FD-A6TH 
        5.36        49.68         4.83        50.66         4.11         2.20 
TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-GC-A3BM TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JV 
       15.19         3.25         2.89         6.41        11.31         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-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-LC-A66R 
        6.74        38.60         3.45         4.67         1.81         6.35 
TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        88.93        56.19        15.35 

$`17Q GAIN WILD-TYPE`
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-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A3 
       12.92         4.90         5.46         5.19         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
        2.14        19.00         8.91       130.88        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-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        3.98         8.22        10.49        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
        8.28       140.81        64.18        48.53        76.60        15.68 
TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       32.28        15.35        26.17        24.66         0.10         0.53 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 
        0.66         0.82         1.22        12.89        15.68        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        15.88        45.93        22.45        16.47        12.82 
TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
        5.52        19.79         1.97        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.93         3.62        12.13        37.15        11.01         6.87 
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-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 
        6.38         9.30         6.71         2.66         4.01         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-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-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A6ZA 
        2.20         7.66         6.41         6.15         4.14        11.54 
TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        1.51         8.75         2.50         6.48        10.52         1.74 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        4.27         6.38         3.45        12.23        16.67        97.45 

  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 
              8.30               8.83 
[1] "0.1 - 112.4 (8.3)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1.7"
D31V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED          0       1       19        23       28
  17Q GAIN WILD-TYPE        1       1       49        49       39
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                19                 49
  STAGE III               23                 49
  STAGE IV                28                 39
[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         21 33 12
  17Q GAIN WILD-TYPE       41 68 20
D31V4, multiclass
          clus
vv         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1+T2               21                 41
  T3                     33                 68
  T4                     12                 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
  17Q GAIN MUTATED   36  9 18  2
  17Q GAIN WILD-TYPE 94 13 20  5
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               36                 94
  N1                9                 13
  N2               18                 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
  17Q GAIN MUTATED   35  2 35
  17Q GAIN WILD-TYPE 71  3 67
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               35                 71
  M1                2                  3
  MX               35                 67
[1] 3 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    18  54
  17Q GAIN WILD-TYPE  32 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     18   54
  17Q GAIN WILD-TYPE   32  110
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               18                 32
  MALE                 54                110
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
D31V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       6                         3    58
  17Q GAIN WILD-TYPE    16                         8   112
D31V11, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    6                 16
  BLACK OR AFRICAN AMERICAN                3                  8
  WHITE                                   58                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"

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    43  20
  18P GAIN WILD-TYPE 108  37
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                63                145 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                20                 37 
$`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-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SR TCGA-FD-A3SS 
        8.94         6.87        11.93        45.93        19.79         1.97 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BY 
       14.93        12.13        13.38        11.01         5.36         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       27.45        49.68         4.11         2.20        15.19         4.08 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3RC 
        6.48        61.94        26.93        35.24         0.85        15.91 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
        2.66         7.73         2.10         2.20         6.41         7.66 
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-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 
        6.74         4.67         1.74         1.81         6.35         3.45 
TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HG 
       13.48        88.93        15.35 

$`18P GAIN WILD-TYPE`
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        31.40        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        48.53        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.68        32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.82         1.22        12.89        15.68         4.01        12.43 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        24.30        22.45        16.47        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       13.18        46.78        22.98        14.96        14.93         3.62 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O 
       37.15         6.87         5.69         6.87         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG 
        6.28         6.38        50.66         9.30         6.71         2.66 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.01         7.13         3.48         3.25        30.61         5.69 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.26         7.04        20.12         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GD-A3OS 
        4.50        14.07        17.75         1.12         3.12        20.98 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A6ZA 
       11.31         4.41         6.41         7.63         6.41        11.54 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
        1.51        38.60         8.75         3.45         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
       10.52         4.27         6.38        12.23        16.67        97.45 
TCGA-XF-A8HF 
       56.19 

  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               9.67 
[1] "0.4 - 88.9 (7.8)"  "0.1 - 140.8 (9.7)"
[1] "hr=" "1.3"
D32V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED          0       0       19        23       20
  18P GAIN WILD-TYPE        1       2       49        49       47
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                19                 49
  STAGE III               23                 49
  STAGE IV                20                 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
  18P GAIN MUTATED         14 29 11
  18P GAIN WILD-TYPE       48 72 21
D32V4, multiclass
          clus
vv         18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1+T2               14                 48
  T3                     29                 72
  T4                     11                 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
  18P GAIN MUTATED   39  5 11  3
  18P GAIN WILD-TYPE 91 17 27  4
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               39                 91
  N1                5                 17
  N2               11                 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
  18P GAIN MUTATED   24  2 36
  18P GAIN WILD-TYPE 82  3 66
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               24                 82
  M1                2                  3
  MX               36                 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"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    17  46
  18P GAIN WILD-TYPE  33 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     17   46
  18P GAIN WILD-TYPE   33  118
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               17                 33
  MALE                 46                118
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
D32V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       2                         5    53
  18P GAIN WILD-TYPE    20                         6   117
D32V11, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    2                 20
  BLACK OR AFRICAN AMERICAN                5                  6
  WHITE                                   53                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"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    21  14
  18Q GAIN WILD-TYPE 130  43
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                35                173 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                14                 43 
$`18Q GAIN MUTATED`
TCGA-BL-A3JM TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 
        6.74         5.06         5.59         9.99         8.98         1.94 
TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3IN TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-FD-A3B6 
       16.14         7.79         8.22        30.67        15.35         6.87 
TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ 
       19.79        14.93        12.13        13.38         5.36        27.45 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        9.30         4.11         2.20        15.19         4.08         6.48 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A42Q TCGA-GV-A3QH 
       26.93        35.24         2.10         6.41         7.66         7.79 
TCGA-GV-A3QI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-XF-A8HG 
        4.14         1.74         1.81         3.45        15.35 

$`18Q GAIN WILD-TYPE`
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-A42C TCGA-BT-A42F 
        4.67        12.82         2.07        15.42        28.70        28.41 
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-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        31.40        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88       112.44        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-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        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       67.36        15.68        32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.38         0.82         1.22        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        16.47        12.82         5.52        13.18        46.78 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS 
        1.97        22.98        14.96        14.93         3.62        37.15 
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-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD 
        2.66         4.83         6.28         6.38        50.66         6.71 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF 
        2.66         4.01         7.13         3.48         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-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-A3OQ TCGA-GD-A3OS 
       17.75         1.12         2.66         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        2.20        11.31         4.41         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.63         6.67         6.41        19.07        11.54         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        6.74        38.60         8.75         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V 
        6.48        10.52         4.27         6.38         6.35        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       12.23        16.67        88.93        97.45        56.19 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.74               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             35.24             140.81 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              7.79               8.94 
[1] "1.7 - 35.2 (7.8)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "2"  
D33V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED          0       0        9        14       12
  18Q GAIN WILD-TYPE        1       2       59        58       55
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 9                 59
  STAGE III               14                 58
  STAGE IV                12                 55
[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          5 17  8
  18Q GAIN WILD-TYPE       57 84 24
D33V4, multiclass
          clus
vv         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1+T2                5                 57
  T3                     17                 84
  T4                      8                 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
  18Q GAIN MUTATED    20   3   8   1
  18Q GAIN WILD-TYPE 110  19  30   6
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               20                110
  N1                3                 19
  N2                8                 30
  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   13  1 21
  18Q GAIN WILD-TYPE 93  4 81
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0               13                 93
  M1                1                  4
  MX               21                 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"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     9  26
  18Q GAIN WILD-TYPE  41 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      9   26
  18Q GAIN WILD-TYPE   41  138
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                9                 41
  MALE                 26                138
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
D33V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         2    30
  18Q GAIN WILD-TYPE    22                         9   140
D33V11, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                 22
  BLACK OR AFRICAN AMERICAN                2                  9
  WHITE                                   30                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    31   9
  19P GAIN WILD-TYPE 120  48
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                40                168 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 9                 48 
$`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-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47V TCGA-CF-A47X TCGA-CU-A3KJ 
       23.01         0.46         0.43         0.10         0.10         5.46 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A6AV 
       16.31         2.53        18.41         1.81       123.85        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-FD-A3SR 
       67.36        15.68        30.67        26.17         0.56        19.79 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A3EE 
       14.93         3.62         2.66         2.20        15.19         3.25 
TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH 
        0.85         1.12         7.73         4.41         6.41         7.79 
TCGA-GV-A40G TCGA-HQ-A2OE TCGA-XF-A8HF TCGA-XF-A8HG 
       19.07        38.60        56.19        15.35 

$`19P GAIN WILD-TYPE`
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-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN 
        0.69         0.13         0.07         0.07         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
        4.90         7.20         5.19         1.84         9.34         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       31.40        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
       17.62        15.62        10.59         7.79        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-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ 
       17.98        48.53        76.60        32.28        43.59        15.35 
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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.38         0.82         1.22        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        16.47        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43Y 
       46.78         1.97        22.98        14.93        14.96        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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28         6.38        50.66         9.30         6.71         4.11 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        4.01         7.13         3.48         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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       20.12         2.89         2.24        15.81         4.50        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-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A3JZ 
        2.20         6.41         7.66        11.31         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.63         4.14         6.67         6.41        11.54         1.51 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        6.74         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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
        3.45        13.48        12.23        16.67        88.93        97.45 

  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 
             7.760              8.925 
[1] "0.1 - 123.8 (7.8)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED          0       0       14        11       14
  19P GAIN WILD-TYPE        1       2       54        61       53
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                14                 54
  STAGE III               11                 61
  STAGE IV                14                 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
  19P GAIN MUTATED         12 20  7
  19P GAIN WILD-TYPE       50 81 25
D34V4, multiclass
          clus
vv         19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1+T2               12                 50
  T3                     20                 81
  T4                      7                 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
  19P GAIN MUTATED    23   3  12   0
  19P GAIN WILD-TYPE 107  19  26   7
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               23                107
  N1                3                 19
  N2               12                 26
  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
  19P GAIN MUTATED   24  0 17
  19P GAIN WILD-TYPE 82  5 85
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               24                 82
  M1                0                  5
  MX               17                 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"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     8  34
  19P GAIN WILD-TYPE  42 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      8   34
  19P GAIN WILD-TYPE   42  130
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                8                 42
  MALE                 34                130
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
D34V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       9                         0    28
  19P GAIN WILD-TYPE    13                        11   142
D34V11, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    9                 13
  BLACK OR AFRICAN AMERICAN                0                 11
  WHITE                                   28                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"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    48  18
  19Q GAIN WILD-TYPE 103  39
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                66                142 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                18                 39 
$`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-A1HR TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 
        0.46         0.43         0.10         5.46        16.31         2.53 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 
       31.40        18.41         8.91         1.81       123.85        87.32 
TCGA-DK-A3IL TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
        3.98        48.00        64.18        67.36        15.68        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-FD-A3SJ 
       43.59        15.35        26.17         0.59         0.56        24.30 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BZ 
       19.79         1.97        22.98        14.93         3.62        27.45 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
        2.66         2.20        15.19         4.08         3.25        61.94 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 
       35.24         0.85        15.91        14.07         1.12         7.73 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       11.31         4.41         6.41         5.69         7.63         7.79 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-XF-A8HF TCGA-XF-A8HG 
        6.74        38.60         8.75         2.50        56.19        15.35 

$`19Q GAIN WILD-TYPE`
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-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        8.98         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-A5W6 
        0.10        12.92         4.90         7.20         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
        9.34         2.14        19.00       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM 
       17.62        15.62        10.59         7.79         2.20         7.82 
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-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        17.98        48.53        76.60 
TCGA-DK-A6B5 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KF 
       32.28        24.66         0.10         0.49         0.53         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.38         0.82         1.22        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-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45        16.47        12.82         5.52        13.18        46.78 
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-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-A6TC 
        2.66         4.83         6.28         6.38        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A61P 
        6.71         4.11         4.01         7.13         3.48         6.48 
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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A6I1 
        2.89         2.24        15.81         4.50        17.75         2.66 
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         7.66 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        6.15         4.14         6.67         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        1.51         3.45         4.67         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.81         4.27         6.38         6.35         3.45        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
       12.23        16.67        88.93        97.45 

  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 
              9.45               8.25 
[1] "0.1 - 123.8 (9.4)" "0.1 - 140.8 (8.2)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED          0       0       18        20       27
  19Q GAIN WILD-TYPE        1       2       50        52       40
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                18                 50
  STAGE III               20                 52
  STAGE IV                27                 40
[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         17 30 13
  19Q GAIN WILD-TYPE       45 71 19
D35V4, multiclass
          clus
vv         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1+T2               17                 45
  T3                     30                 71
  T4                     13                 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
  19Q GAIN MUTATED   35  7 17  2
  19Q GAIN WILD-TYPE 95 15 21  5
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               35                 95
  N1                7                 15
  N2               17                 21
  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
  19Q GAIN MUTATED   37  1 29
  19Q GAIN WILD-TYPE 69  4 73
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               37                 69
  M1                1                  4
  MX               29                 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"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    17  51
  19Q GAIN WILD-TYPE  33 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     17   51
  19Q GAIN WILD-TYPE   33  113
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               17                 33
  MALE                 51                113
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
D35V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       8                         2    52
  19Q GAIN WILD-TYPE    14                         9   118
D35V11, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    8                 14
  BLACK OR AFRICAN AMERICAN                2                  9
  WHITE                                   52                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"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   71 34
  20P GAIN WILD-TYPE 80 23
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               105                103 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                34                 23 
$`20P GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20T 
       40.08         2.66         6.74         6.58         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C 
        5.06         8.35         8.25         3.65         2.07        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-A47T TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.43         0.07         0.10        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A1AD 
        5.46         1.84         2.14        31.40       130.88       112.44 
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-A3IU TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 
        8.22        20.02        10.55        17.98        67.36        15.68 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A7DV 
       30.67        43.59        15.35        26.17         0.59         1.22 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
       12.89         6.87         4.01        11.93        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       22.45        13.18        46.78        19.79         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A62O 
       14.93         3.62        13.38        11.01        27.45         4.83 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI 
        6.38         9.30         6.71         4.11         2.20         4.01 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         3.25         6.48        61.94        30.61         5.69 
TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       35.24         2.89         2.24        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GV-A3JV TCGA-GV-A3JW 
        2.66         7.73         2.10         2.20         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HQ 
        6.15         7.63         7.79         4.14        19.07         6.74 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A6FZ TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        8.75         3.45         1.81        13.48        12.23        16.67 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        56.19        15.35 

$`20P GAIN WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        7.33        12.39        11.93        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       17.88        19.50        14.96        17.16         5.59         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W 
       12.82        15.42         0.69         0.13         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 
        0.10         5.19        16.31         9.34         2.53        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 
       19.00         8.91        16.14        17.62        15.62        87.32 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
        7.82        10.49        50.27        21.30         9.67         8.28 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
      140.81        48.00        64.18        48.53        76.60        32.28 
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-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
        1.38         0.82        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 
       16.47        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-A6TG TCGA-FJ-A3Z7 
       49.68         2.66         6.28        50.66         2.66        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        7.13         4.08        26.93        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GD-A3OS 
        0.85         4.50        17.75         1.12         3.12        20.98 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E 
        6.41         7.66        11.31         5.69         6.67         6.41 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       11.54         1.51        38.60         4.67         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-XF-A8HE 
       97.45 

  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 
              8.22               9.34 
[1] "0.1 - 130.9 (8.2)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.5"
D36V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED          0       1       32        36       38
  20P GAIN WILD-TYPE        1       1       36        36       29
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                32                 36
  STAGE III               36                 36
  STAGE IV                38                 29
[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         31 53 17
  20P GAIN WILD-TYPE       31 48 15
D36V4, multiclass
          clus
vv         20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1+T2               31                 31
  T3                     53                 48
  T4                     17                 15
[1] 3 2
[1] 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   66 11 22  5
  20P GAIN WILD-TYPE 64 11 16  2
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               66                 64
  N1               11                 11
  N2               22                 16
  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
  20P GAIN MUTATED   52  4 53
  20P GAIN WILD-TYPE 54  1 49
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               52                 54
  M1                4                  1
  MX               53                 49
[1] 3 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   26 83
  20P GAIN WILD-TYPE 24 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     26   83
  20P GAIN WILD-TYPE   24   81
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               26                 24
  MALE                 83                 81
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
D36V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       7                         6    89
  20P GAIN WILD-TYPE    15                         5    81
D36V11, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    7                 15
  BLACK OR AFRICAN AMERICAN                6                  5
  WHITE                                   89                 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"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   84 36
  20Q GAIN WILD-TYPE 67 21
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               120                 88 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                36                 21 
$`20Q GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N 
       40.08         2.66         6.74         6.58        19.04        32.84 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK 
       19.50        14.89         8.35         8.25         3.65         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-A47X TCGA-CU-A0YN 
        0.46         0.43         0.13         0.07         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 
        4.90         7.20         5.46         1.84         2.14        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       18.41       130.88       112.44         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU 
      123.85         3.98         7.82         8.22        50.27        20.02 
TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       10.55        17.98        64.18        67.36        15.68        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV 
       43.59        15.35        26.17         0.49         0.59         1.22 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
       12.89         6.87         4.01        11.93        45.93        24.30 
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-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        3.62        13.38        11.01        27.45         6.87        49.68 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
        4.83         6.38         9.30         6.71         4.11         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        4.01        15.19         3.48         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       30.61         5.69        35.24         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81         4.50        15.91        14.07         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        7.73         2.10         7.66        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-H4-A2HQ 
        6.15         7.63         7.79         4.14         6.41         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-LT-A5Z6 
       38.60         8.75         3.45         6.48         1.81         3.45 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        12.23        16.67        88.93        56.19        15.35 

$`20Q GAIN WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R 
        7.33        12.39        11.93        12.16        17.88         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         5.06        17.16         5.59         4.67        12.82 
TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A3QU 
       15.42         0.69         0.10         0.07         0.10         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
       16.31         9.34         2.53        19.00         8.91        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IT 
       17.62        15.62        87.32         2.20        10.49        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67         8.28       140.81        48.00        48.53        76.60 
TCGA-DK-A6B5 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF 
       32.28        24.66         0.10         0.53         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
        1.38         0.82        15.68         8.94        12.43        15.88 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U 
       22.45        16.47        12.82         5.52        14.96        14.93 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       12.13        37.15         6.87         5.36         5.69         6.84 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        2.66         6.28        50.66         2.66         7.13         4.08 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3WC TCGA-GD-A3OQ 
       26.93        17.26         7.04        20.12        17.75         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40G 
       20.98         2.20         6.41         5.69         6.67        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ 
       11.54         1.51         4.67         2.50        10.52         1.74 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-XF-A8HE 
        4.27         6.38         6.35        97.45 

  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 
             8.235              9.140 
[1] "0.1 - 130.9 (8.2)" "0.1 - 140.8 (9.1)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED          0       1       41        40       39
  20Q GAIN WILD-TYPE        1       1       27        32       28
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                41                 27
  STAGE III               40                 32
  STAGE IV                39                 28
[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         37 59 16
  20Q GAIN WILD-TYPE       25 42 16
D37V4, multiclass
          clus
vv         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1+T2               37                 25
  T3                     59                 42
  T4                     16                 16
[1] 3 2
[1] 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   74 11 24  5
  20Q GAIN WILD-TYPE 56 11 14  2
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               74                 56
  N1               11                 11
  N2               24                 14
  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
  20Q GAIN MUTATED   58  3 62
  20Q GAIN WILD-TYPE 48  2 40
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               58                 48
  M1                3                  2
  MX               62                 40
[1] 3 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   27 97
  20Q GAIN WILD-TYPE 23 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     27   97
  20Q GAIN WILD-TYPE   23   67
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               27                 23
  MALE                 97                 67
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
D37V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED      11                         5    99
  20Q GAIN WILD-TYPE    11                         6    71
D37V11, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                   11                 11
  BLACK OR AFRICAN AMERICAN                5                  6
  WHITE                                   99                 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"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    49  18
  21Q GAIN WILD-TYPE 102  39
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                67                141 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                18                 39 
$`21Q GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LA 
       40.08         2.66        12.39        32.84         8.35        17.16 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS 
        3.65         2.07        28.70         8.98         1.94         0.43 
TCGA-CF-A27C TCGA-CF-A47V TCGA-CU-A3KJ TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2I1 
        0.69         0.10         5.46         2.53        18.41        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS 
      123.85        87.32         2.20         3.98         7.82        50.27 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E5-A4TZ 
        9.67        48.00        17.98        67.36        15.68        15.35 
TCGA-E7-A4IJ TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN 
        0.49         6.87         4.01        45.93        24.30        12.82 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62O 
       13.18        19.79        22.98        27.45         6.87         4.83 
TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF 
        6.28         9.30         4.11         2.66         2.20         4.08 
TCGA-G2-A2EK TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P 
        5.69         0.85         2.89         7.73         2.10         6.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ 
        6.41         6.15         7.63         6.41        19.07         6.74 
TCGA-K4-A3WU TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-XF-A8HD 
        3.45         1.81         4.27         6.35        13.48        88.93 
TCGA-XF-A8HF 
       56.19 

$`21Q GAIN WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.74         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-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E 
        8.25         5.59         4.67        12.82        15.42         9.99 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       28.41        23.01         0.46         0.13         0.07         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
        0.10         0.10        12.92         4.90         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
       16.31         1.84         9.34         2.14        31.40        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-A2I2 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        1.81         7.79         8.22        10.49        21.30        20.02 
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        48.53        76.60 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       32.28        30.67        43.59        26.17        24.66         0.10 
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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        1.22        12.89        15.68         8.94        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS 
       15.88        22.45        16.47         5.52        46.78         1.97 
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-A5BY 
       37.15        11.01         6.87         5.36         5.69         6.84 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TI 
       49.68         2.66         6.38        50.66         6.71         4.01 
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-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61        26.93        35.24        17.26         7.04        20.12 
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-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
        1.12         2.66         3.12        20.98         2.20         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       11.31         4.41         5.69         7.79         4.14         6.67 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB 
       11.54         1.51        38.60         8.75         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-PQ-A6FI 
        6.48        10.52         1.74         6.38         3.45        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A8HG 
       16.67        97.45        15.35 

  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 
              6.87               9.99 
[1] "0.1 - 123.8 (6.9)"  "0.1 - 140.8 (10.0)"
[1] "hr=" "1"  
D38V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED          0       1       20        19       26
  21Q GAIN WILD-TYPE        1       1       48        53       41
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                20                 48
  STAGE III               19                 53
  STAGE IV                26                 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
  21Q GAIN MUTATED         18 35  8
  21Q GAIN WILD-TYPE       44 66 24
D38V4, multiclass
          clus
vv         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1+T2               18                 44
  T3                     35                 66
  T4                      8                 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
  21Q GAIN MUTATED   36  7 18  0
  21Q GAIN WILD-TYPE 94 15 20  7
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               36                 94
  N1                7                 15
  N2               18                 20
  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   33  2 32
  21Q GAIN WILD-TYPE 73  3 70
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0               33                 73
  M1                2                  3
  MX               32                 70
[1] 3 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    14  54
  21Q GAIN WILD-TYPE  36 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     14   54
  21Q GAIN WILD-TYPE   36  110
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               14                 36
  MALE                 54                110
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
D38V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       6                         2    55
  21Q GAIN WILD-TYPE    16                         9   115
D38V11, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    6                 16
  BLACK OR AFRICAN AMERICAN                2                  9
  WHITE                                   55                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"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    19   9
  22Q GAIN WILD-TYPE 132  48
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                28                180 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                 48 
$`22Q GAIN MUTATED`
TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-C4-A0F6 
       40.08         6.58         8.35         5.59        12.82        23.01 
TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX 
       31.40       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-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QH 
        2.89         2.24        14.07         4.41         5.69         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A2OE 
        4.14         6.67         6.41        38.60 

$`22Q GAIN WILD-TYPE`
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-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16         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-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-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-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.53         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-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        48.53        76.60        67.36        15.68        32.28 
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-A7DV 
        0.53         0.56         0.66         1.38         0.82         1.22 
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        16.47        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-A5BY 
       37.15        11.01         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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       50.66         9.30         6.71         4.11         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.01        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-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
       20.12         0.85        15.81         4.50        15.91        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-GV-A3JW TCGA-GV-A3JX 
        2.20         6.41         7.66        11.31         6.41         6.15 
TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS 
        7.63        19.07        11.54         1.51         6.74         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-MV-A51V 
        1.81         4.27         6.38         6.35         3.45        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        16.67        88.93        97.45        56.19        15.35 

  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 
              8.07               8.83 
[1] "0.5 - 112.4 (8.1)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED          0       1        9        11        6
  22Q GAIN WILD-TYPE        1       1       59        61       61
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                 9                 59
  STAGE III               11                 61
  STAGE IV                 6                 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
  22Q GAIN MUTATED         10 13  3
  22Q GAIN WILD-TYPE       52 88 29
D39V4, multiclass
          clus
vv         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1+T2               10                 52
  T3                     13                 88
  T4                      3                 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
  22Q GAIN MUTATED    15   3   4   2
  22Q GAIN WILD-TYPE 115  19  34   5
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               15                115
  N1                3                 19
  N2                4                 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
  22Q GAIN MUTATED   18  0 10
  22Q GAIN WILD-TYPE 88  5 92
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               18                 88
  M1                0                  5
  MX               10                 92
[1] 3 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     5  23
  22Q GAIN WILD-TYPE  45 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5   23
  22Q GAIN WILD-TYPE   45  141
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                5                 45
  MALE                 23                141
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
D39V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       1                         1    24
  22Q GAIN WILD-TYPE    21                        10   146
D39V11, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    1                 21
  BLACK OR AFRICAN AMERICAN                1                 10
  WHITE                                   24                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"

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    14  10
  XQ GAIN WILD-TYPE 137  47
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               24               184 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               10                47 
$`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-A1AC TCGA-DK-A1AE 
       28.70         0.43        12.92        31.40       130.88        16.14 
TCGA-FD-A3B6 TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A6TC TCGA-FD-A6TI TCGA-FT-A3EE 
        6.87        19.79        14.93         9.30         4.01         3.25 
TCGA-GC-A3I6 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-MV-A51V 
        2.24         7.73        20.98         5.69         7.79        13.48 

$`XQ GAIN WILD-TYPE`
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-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       19.00         8.91       112.44        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-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-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        48.53        76.60        67.36        15.68        32.28 
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-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 
        0.82         1.22        12.89        15.68         8.94         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-A3SS 
       16.47        12.82         5.52        13.18        46.78         1.97 
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-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-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45         6.87        49.68         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
        6.38        50.66         6.71         4.11         2.66         2.20 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
       15.19         7.13         3.48         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-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       20.12         0.85         2.89        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        17.75         1.12         2.66         2.10         3.12 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        2.20         6.41         7.66        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        6.15         7.63         4.14         6.67         6.41        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       11.54         1.51         6.74        38.60         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-PQ-A6FI TCGA-PQ-A6FN 
        4.27         6.38         6.35         3.45        12.23        16.67 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        97.45        56.19        15.35 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.43              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           130.88            140.81 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           11.110             8.315 
[1] "0.4 - 130.9 (11.1)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1.4"
D40V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED          0       0        5        11        7
  XQ GAIN WILD-TYPE        1       2       63        61       60
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                5                63
  STAGE III              11                61
  STAGE IV                7                60
[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          3 11  7
  XQ GAIN WILD-TYPE       59 90 25
D40V4, multiclass
          clus
vv         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1+T2               3                59
  T3                    11                90
  T4                     7                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
  XQ GAIN MUTATED    15   2   4   1
  XQ GAIN WILD-TYPE 115  20  34   6
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              15               115
  N1               2                20
  N2               4                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
  XQ GAIN MUTATED   12  0 12
  XQ GAIN WILD-TYPE 94  5 90
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              12                94
  M1               0                 5
  MX              12                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"
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     6  18
  XQ GAIN WILD-TYPE  44 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6   18
  XQ GAIN WILD-TYPE   44  146
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               6                44
  MALE                18               146
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
D40V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       1                         1    20
  XQ GAIN WILD-TYPE    21                        10   150
D40V11, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   1                21
  BLACK OR AFRICAN AMERICAN               1                10
  WHITE                                  20               150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    10   6
  1P LOSS WILD-TYPE 141  51
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16               192 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                51 
$`1P LOSS MUTATED`
TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A3IQ 
        2.07         8.98         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-K4-A3WS TCGA-PQ-A6FI TCGA-XF-A8HF TCGA-XF-A8HG 
        8.75        12.23        56.19        15.35 

$`1P LOSS WILD-TYPE`
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-A42B 
       17.16         5.59         3.65         4.67        12.82        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       28.70         9.99        28.41         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        31.40        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 
       48.53        76.60        67.36        15.68        32.28        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-A7DV TCGA-FD-A3B3 
        0.56         0.66         1.38         0.82         1.22        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        16.47        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-A5BY 
       37.15        11.01         6.87         5.36         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       27.45         6.87        49.68         2.66         4.83         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       50.66         9.30         6.71         2.66         2.20         4.01 
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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12         0.85         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-GU-A42P TCGA-GU-A42Q 
        2.10         3.12        20.98         2.20         6.41         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.31         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-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        1.51         6.74        38.60         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        6.48        10.52         1.74         1.81         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
        6.35         3.45        13.48        16.67        88.93        97.45 

  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 
            8.865             8.315 
[1] "0.1 - 56.2 (8.9)"  "0.1 - 140.8 (8.3)"
[1] "hr=" "1.4"
D41V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED          0       0        5         5        6
  1P LOSS WILD-TYPE        1       2       63        67       61
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                5                63
  STAGE III               5                67
  STAGE IV                6                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
  1P LOSS MUTATED          6  8  0
  1P LOSS WILD-TYPE       56 93 32
D41V4, multiclass
          clus
vv         1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1+T2               6                56
  T3                     8                93
  T4                     0                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
  1P LOSS MUTATED     9   2   3   1
  1P LOSS WILD-TYPE 121  20  35   6
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0               9               121
  N1               2                20
  N2               3                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
  1P LOSS MUTATED     5   2   9
  1P LOSS WILD-TYPE 101   3  93
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               5               101
  M1               2                 3
  MX               9                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"
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2  14
  1P LOSS WILD-TYPE  48 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   14
  1P LOSS WILD-TYPE   48  150
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               2                48
  MALE                14               150
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
D41V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         0    13
  1P LOSS WILD-TYPE    21                        11   157
D41V11, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                21
  BLACK OR AFRICAN AMERICAN               0                11
  WHITE                                  13               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"

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    11   6
  1Q LOSS WILD-TYPE 140  51
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               191 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                51 
$`1Q LOSS MUTATED`
TCGA-BT-A3PK TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT 
        2.07         4.90         7.20         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-GV-A3QH TCGA-XF-A8HF 
        4.11        20.12        15.91         7.79        56.19 

$`1Q LOSS WILD-TYPE`
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-A42B 
       17.16         5.59         3.65         4.67        12.82        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-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-A3KJ TCGA-CU-A3QU 
        0.07         0.10         0.10        12.92         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        31.40 
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 
       48.53        76.60        67.36        15.68        32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        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-A3SN TCGA-FD-A3SO 
       45.93        24.30        22.45        16.47        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-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-A6TA TCGA-FD-A6TC 
        6.87        49.68         2.66         4.83        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.71         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-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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
        2.89         2.24        15.81         4.50        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-GV-A3JV TCGA-GV-A3JW 
        2.20         6.41         7.66        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        6.15         5.69         7.63         4.14         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
       19.07        11.54         1.51         6.74        38.60         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-MV-A51V 
        1.81         4.27         6.38         6.35         3.45        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       12.23        16.67        88.93        97.45        15.35 

  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 
             7.79              8.75 
[1] "0.5 - 56.2 (7.8)"  "0.1 - 140.8 (8.8)"
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED          0       0        7         5        5
  1Q LOSS WILD-TYPE        1       2       61        67       62
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                7                61
  STAGE III               5                67
  STAGE IV                5                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
  1Q LOSS MUTATED          6  8  0
  1Q LOSS WILD-TYPE       56 93 32
D42V4, multiclass
          clus
vv         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1+T2               6                56
  T3                     8                93
  T4                     0                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
  1Q LOSS MUTATED     8   1   4   0
  1Q LOSS WILD-TYPE 122  21  34   7
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               8               122
  N1               1                21
  N2               4                34
  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  9
  1Q LOSS WILD-TYPE 98  5 93
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               8                98
  M1               0                 5
  MX               9                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"
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     4  13
  1Q LOSS WILD-TYPE  46 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4   13
  1Q LOSS WILD-TYPE   46  151
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               4                46
  MALE                13               151
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
D42V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       1                         1    15
  1Q LOSS WILD-TYPE    21                        10   155
D42V11, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   1                21
  BLACK OR AFRICAN AMERICAN               1                10
  WHITE                                  15               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"

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    13   7
  2P LOSS WILD-TYPE 138  50
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               20               188 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7                50 
$`2P LOSS MUTATED`
TCGA-BT-A20N TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3IV 
       32.84         5.46         5.19         1.81        50.27         9.67 
TCGA-E5-A4U1 TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A5BR TCGA-FJ-A3ZE TCGA-G2-A2EL 
       26.17         8.94        24.30        13.38         3.48        26.93 
TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GV-A3JV TCGA-GV-A3JW TCGA-K4-A3WU TCGA-K4-A5RJ 
       15.81         1.12         4.41         6.41         3.45         1.74 
TCGA-MV-A51V TCGA-XF-A8HG 
       13.48        15.35 

$`2P LOSS WILD-TYPE`
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-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        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-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-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        31.40 
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-A3IQ TCGA-DK-A3IT 
        2.20         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-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        48.53        76.60        67.36        15.68        32.28 
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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        1.22        12.89        15.68         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        15.88        45.93        22.45        16.47        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-A5BS 
       14.93        14.96        14.93         3.62        12.13        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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       50.66         9.30         6.71         4.11         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        4.01        15.19         7.13         4.08         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61         5.69        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC 
       20.12         0.85         2.89         2.24         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-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JX 
       20.98         2.20         6.41         7.66        11.31         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-K4-A3WS 
       19.07        11.54         1.51         6.74        38.60         8.75 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB 
        4.67         2.50         6.48        10.52         1.81         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        6.38         6.35         3.45        12.23        16.67        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF 
       97.45        56.19 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1.12              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            50.27            140.81 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            9.305             8.315 
[1] "1.1 - 50.3 (9.3)"  "0.1 - 140.8 (8.3)"
[1] "hr=" "1.3"
D43V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED          0       0        9         6        7
  2P LOSS WILD-TYPE        1       2       59        66       60
D43V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                9                59
  STAGE III               6                66
  STAGE IV                7                60
[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         10  8  1
  2P LOSS WILD-TYPE       52 93 31
D43V4, multiclass
          clus
vv         2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1+T2              10                52
  T3                     8                93
  T4                     1                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
  2P LOSS MUTATED    13   4   2   1
  2P LOSS WILD-TYPE 117  18  36   6
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              13               117
  N1               4                18
  N2               2                36
  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   11  1 10
  2P LOSS WILD-TYPE 95  4 92
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0              11                95
  M1               1                 4
  MX              10                92
[1] 3 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     1  21
  2P LOSS WILD-TYPE  49 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   21
  2P LOSS WILD-TYPE   49  143
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               1                49
  MALE                21               143
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
D43V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       2                         1    16
  2P LOSS WILD-TYPE    20                        10   154
D43V11, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   2                20
  BLACK OR AFRICAN AMERICAN               1                10
  WHITE                                  16               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"

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    30  16
  2Q LOSS WILD-TYPE 121  41
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               46               162 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16                41 
$`2Q LOSS MUTATED`
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH TCGA-C4-A0EZ 
       32.84        14.89         5.06        17.16         4.67         8.98 
TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A2HX 
        0.43         0.10        12.92         5.46         5.19         1.81 
TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
        2.20        50.27         9.67        17.98        64.18        67.36 
TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A541 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3SJ 
       30.67        26.17         0.59        15.68         8.94        24.30 
TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TE 
       19.79        13.38         5.36        27.45         2.66         4.11 
TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2EL TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GD-A3OP 
        2.20         6.48        26.93        15.81        14.07         2.10 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QK TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AC 
        4.41         6.41         6.67        38.60         3.45         6.48 
TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HG 
        1.74         3.45        13.48        15.35 

$`2Q LOSS WILD-TYPE`
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-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ 
       14.96         8.35         8.25         5.59         3.65        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        2.07        15.42        28.70         9.99        28.41         1.94 
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-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 
        0.07         0.10         4.90         7.20        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        31.40        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-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59         7.79       123.85        87.32         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        10.49        21.30        20.02         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        48.53        76.60        15.68        32.28 
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-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.56         0.66         1.38         0.82         1.22        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        16.47        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-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        9.30         6.71         2.66         4.01        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-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
       35.24        17.26         7.04        20.12         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        2.24         4.50        15.91        17.75         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
        7.73         3.12        20.98         2.20         6.41         7.66 
TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       11.31         6.15         5.69         7.63         7.79         4.14 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS 
        6.41        19.07        11.54         1.51         6.74         8.75 
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-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        6.35        12.23        16.67        88.93        97.45        56.19 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.10              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            67.36            140.81 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            8.960             8.315 
[1] "0.1 - 67.4 (9.0)"  "0.1 - 140.8 (8.3)"
[1] "hr=" "1.4"
D44V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED          0       0       16        12       18
  2Q LOSS WILD-TYPE        1       2       52        60       49
D44V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               16                52
  STAGE III              12                60
  STAGE IV               18                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
  2Q LOSS MUTATED         16 22  6
  2Q LOSS WILD-TYPE       46 79 26
D44V4, multiclass
          clus
vv         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1+T2              16                46
  T3                    22                79
  T4                     6                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
  2Q LOSS MUTATED    25   6  13   0
  2Q LOSS WILD-TYPE 105  16  25   7
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              25               105
  N1               6                16
  N2              13                25
  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   23  1 24
  2Q LOSS WILD-TYPE 83  4 78
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              23                83
  M1               1                 4
  MX              24                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    11  37
  2Q LOSS WILD-TYPE  39 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11   37
  2Q LOSS WILD-TYPE   39  127
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              11                39
  MALE                37               127
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
D44V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       6                         3    34
  2Q LOSS WILD-TYPE    16                         8   136
D44V11, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   6                16
  BLACK OR AFRICAN AMERICAN               3                 8
  WHITE                                  34               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"

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    20   7
  3P LOSS WILD-TYPE 131  50
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               27               181 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                50 
$`3P LOSS MUTATED`
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS 
        5.06         8.25        28.70         8.98         1.94         0.43 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A2I2 TCGA-DK-A3IM 
       12.92         5.46        31.40         8.91         7.79         7.82 
TCGA-DK-A3WX TCGA-DK-A6B5 TCGA-E7-A4IJ TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 
       10.55        32.28         0.49         1.22        15.68         6.87 
TCGA-FD-A3N5 TCGA-FD-A43Y TCGA-FD-A5C1 TCGA-G2-A3IB TCGA-GC-A3RB TCGA-GC-A3WC 
       11.93        12.13        49.68         7.04         4.50        17.75 
TCGA-GC-A3YS TCGA-K4-A4AC TCGA-XF-A8HD 
        1.12         6.48        88.93 

$`3P LOSS WILD-TYPE`
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-A20W TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.89        14.96         8.35        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
        3.65         4.67        12.82         2.07        15.42         9.99 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       28.41        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-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-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-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81        10.59       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-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67         8.28       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC 
       48.53        76.60        67.36        15.68        30.67        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 
       15.35        26.17        24.66         0.10         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B5 
        0.56         0.66         1.38         0.82        12.89         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        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-A3SR 
       16.47        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-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-A62N TCGA-FD-A62O TCGA-FD-A62P 
        6.84        27.45         6.87         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.38        50.66         9.30         6.71         4.11         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.20         4.01        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-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       35.24        17.26        20.12         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.81        15.91        14.07         2.66         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20         6.41         7.66        11.31 
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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        6.74        38.60         8.75         3.45         4.67         2.50 
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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A8HF 
        3.45        13.48        12.23        16.67        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.43              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            88.93            140.81 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             8.25              8.75 
[1] "0.4 - 88.9 (8.2)"  "0.1 - 140.8 (8.8)"
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED          0       0        7        10        9
  3P LOSS WILD-TYPE        1       2       61        62       58
D45V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                7                61
  STAGE III              10                62
  STAGE IV                9                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
  3P LOSS MUTATED          6 12  7
  3P LOSS WILD-TYPE       56 89 25
D45V4, multiclass
          clus
vv         3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1+T2               6                56
  T3                    12                89
  T4                     7                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
  3P LOSS MUTATED    16   3   3   2
  3P LOSS WILD-TYPE 114  19  35   5
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              16               114
  N1               3                19
  N2               3                35
  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   15  1 11
  3P LOSS WILD-TYPE 91  4 91
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              15                91
  M1               1                 4
  MX              11                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"
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     9  18
  3P LOSS WILD-TYPE  41 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      9   18
  3P LOSS WILD-TYPE   41  146
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               9                41
  MALE                18               146
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
D45V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       2                         4    19
  3P LOSS WILD-TYPE    20                         7   151
D45V11, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   2                20
  BLACK OR AFRICAN AMERICAN               4                 7
  WHITE                                  19               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"

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     7   3
  3Q LOSS WILD-TYPE 144  54
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               198 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                54 
$`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        32.28         1.22 
TCGA-FD-A43Y TCGA-FD-A5C1 TCGA-K4-A4AC TCGA-XF-A8HD 
       12.13        49.68         6.48        88.93 

$`3Q LOSS WILD-TYPE`
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        31.40 
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        48.53        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-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.38         0.82        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        16.47        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-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-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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28         6.38        50.66         9.30         6.71         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.66         2.20         4.01        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-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        17.26         7.04        20.12         0.85 
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-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
       20.98         2.20         6.41         7.66        11.31         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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
       38.60         8.75         3.45         4.67         2.50        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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        12.23        16.67        97.45        56.19        15.35 

  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             8.265 
[1] "1.2 - 88.9 (11.3)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.1"
D46V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED          0       0        2         5        3
  3Q LOSS WILD-TYPE        1       2       66        67       64
D46V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                2                66
  STAGE III               5                67
  STAGE IV                3                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
  3Q LOSS MUTATED          2  5  3
  3Q LOSS WILD-TYPE       60 96 29
D46V4, multiclass
          clus
vv         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1+T2               2                60
  T3                     5                96
  T4                     3                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
  3Q LOSS MUTATED     7   1   1   1
  3Q LOSS WILD-TYPE 123  21  37   6
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               7               123
  N1               1                21
  N2               1                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
  3Q LOSS MUTATED     4   1   5
  3Q LOSS WILD-TYPE 102   4  97
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               4               102
  M1               1                 4
  MX               5                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"
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3   7
  3Q LOSS WILD-TYPE  47 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    7
  3Q LOSS WILD-TYPE   47  157
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               3                47
  MALE                 7               157
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
D46V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         0     8
  3Q LOSS WILD-TYPE    22                        11   162
D46V11, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                22
  BLACK OR AFRICAN AMERICAN               0                11
  WHITE                                   8               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"

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    48  22
  4P LOSS WILD-TYPE 103  35
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               70               138 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               22                35 
$`4P LOSS MUTATED`
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.04        32.84         5.06         5.06         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A1HR 
        5.59         3.65         4.67        15.42         9.99         0.46 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX 
        0.43        12.92         4.90        18.41       112.44         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV 
       10.59        87.32         7.82         8.22        21.30         9.67 
TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E7-A3X6 
       17.98        15.68        32.28        30.67        15.35        24.66 
TCGA-E7-A4IJ TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SO 
        0.49        12.89         8.94         4.01        22.45         5.52 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C1 
        1.97        22.98        13.38         6.87         6.84        49.68 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TH 
        2.66         4.83         6.28         6.38         2.66         2.20 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
       15.19         4.08         7.04         2.89        15.81         4.50 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JV TCGA-GV-A40G 
        1.12         7.73         2.20         7.66         4.41        19.07 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        6.74         8.75         4.67         6.48        10.52         1.74 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        16.67        56.19        15.35 

$`4P LOSS WILD-TYPE`
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-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       11.93        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ 
       17.16        12.82         2.07        28.70        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94        23.01         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.07         0.10         0.10         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        31.40 
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-A3IQ TCGA-DK-A3IS 
        7.79       123.85         2.20         3.98        10.49        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-A6B1 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 
       48.53        76.60        67.36        43.59        26.17         0.10 
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-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        1.22        15.68         6.87        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        16.47        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-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-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         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-GC-A3I6 
       26.93        35.24        17.26        20.12         0.85         2.24 
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-GU-A42P TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       20.98         6.41        11.31         6.41         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-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6FZ TCGA-K4-A6MB 
        1.51        38.60         3.45         2.50         1.81         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HE 
        6.38         6.35         3.45        13.48        88.93        97.45 

  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 
             8.02              9.32 
[1] "0.4 - 112.4 (8.0)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.4"
D47V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED          0       0       21        23       26
  4P LOSS WILD-TYPE        1       2       47        49       41
D47V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               21                47
  STAGE III              23                49
  STAGE IV               26                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
  4P LOSS MUTATED         20 39  8
  4P LOSS WILD-TYPE       42 62 24
D47V4, multiclass
          clus
vv         4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1+T2              20                42
  T3                    39                62
  T4                     8                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
  4P LOSS MUTATED   40  9 16  1
  4P LOSS WILD-TYPE 90 13 22  6
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              40                90
  N1               9                13
  N2              16                22
  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   32  2 38
  4P LOSS WILD-TYPE 74  3 64
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              32                74
  M1               2                 3
  MX              38                64
[1] 3 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    17  55
  4P LOSS WILD-TYPE  33 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     17   55
  4P LOSS WILD-TYPE   33  109
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              17                33
  MALE                55               109
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       6                         7    56
  4P LOSS WILD-TYPE    16                         4   114
D47V11, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   6                16
  BLACK OR AFRICAN AMERICAN               7                 4
  WHITE                                  56               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"

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   55 19
  4Q LOSS WILD-TYPE 96 38
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               74               134 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               19                38 
$`4Q LOSS MUTATED`
TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       32.84         5.06         5.06         5.59         3.65         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
       15.42         9.99        28.41         1.94         0.46         0.43 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX 
       12.92         4.90         7.20        18.41       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        32.28        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-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q 
       15.81         4.50         1.12         7.73         2.20         7.66 
TCGA-GV-A3JV TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC 
        4.41        19.07         6.74         8.75         4.67         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       10.52         1.74         1.81        13.48        12.23        16.67 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`4Q LOSS WILD-TYPE`
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-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       11.93        19.04        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.96         8.35         8.25        17.16        12.82         2.07 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       28.70         8.98        23.01         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.10         0.07         0.10         0.10         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        31.40 
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        48.53 
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-A7DV TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        1.22        15.68        12.43        11.93        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        16.47        12.82        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS 
        1.97        14.93        14.96        14.93         3.62        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TA 
       11.01         6.87         5.36         5.69         6.87        50.66 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        9.30         6.71         4.11         4.01         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-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
       17.26        20.12         0.85         2.24        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P 
       17.75         2.66         2.10         3.12        20.98         6.41 
TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       11.31         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
        4.14         6.67         6.41        11.54         1.51        38.60 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        3.45         2.50         4.27         6.38         6.35         3.45 
TCGA-XF-A8HD TCGA-XF-A8HE 
       88.93        97.45 

  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 
             7.76              9.32 
[1] "0.4 - 112.4 (7.8)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1"  
D48V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED          0       0       20        26       28
  4Q LOSS WILD-TYPE        1       2       48        46       39
D48V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               20                48
  STAGE III              26                46
  STAGE IV               28                39
[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         20 43  8
  4Q LOSS WILD-TYPE       42 58 24
D48V4, multiclass
          clus
vv         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1+T2              20                42
  T3                    43                58
  T4                     8                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
  4Q LOSS MUTATED   45 11 16  1
  4Q LOSS WILD-TYPE 85 11 22  6
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              45                85
  N1              11                11
  N2              16                22
  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   33  2 41
  4Q LOSS WILD-TYPE 73  3 61
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              33                73
  M1               2                 3
  MX              41                61
[1] 3 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    20  56
  4Q LOSS WILD-TYPE  30 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     20   56
  4Q LOSS WILD-TYPE   30  108
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              20                30
  MALE                56               108
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
D48V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       6                         6    60
  4Q LOSS WILD-TYPE    16                         5   110
D48V11, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   6                16
  BLACK OR AFRICAN AMERICAN               6                 5
  WHITE                                  60               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"

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    23   9
  5P LOSS WILD-TYPE 128  48
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               32               176 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                48 
$`5P LOSS MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-C4-A0F6 
        6.58        19.04         5.59         3.65         4.67        23.01 
TCGA-CF-A1HR TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IM 
        0.46        18.41       112.44        10.59         3.98         7.82 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-FD-A3B6 TCGA-FD-A3SJ 
       50.27        21.30        48.00        43.59         6.87        24.30 
TCGA-FD-A3SL TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A3VY 
       22.45        14.93        27.45         3.48        61.94         0.85 
TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GV-A3JW TCGA-GV-A6ZA TCGA-K4-A3WU TCGA-K4-A3WV 
        2.66         2.20         6.41        11.54         3.45         4.67 
TCGA-K4-A4AB TCGA-XF-A8HG 
        2.50        15.35 

$`5P 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-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-A3PJ 
       14.96         5.06         8.35         8.25        17.16        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-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94         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-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
        2.14        31.40        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        2.20         8.22        10.49        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        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 
       67.36        15.68        32.28        30.67        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        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 
       16.47        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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.38        50.66         9.30         6.71         4.11         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-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        6.48        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        7.04        20.12         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-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
        3.12        20.98         6.41         7.66        11.31         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-K4-A3WS 
        6.41        19.07         1.51         6.74        38.60         8.75 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        6.48        10.52         1.74         1.81         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        6.35         3.45        13.48        12.23        16.67        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF 
       97.45        56.19 

  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 
            9.205             8.550 
[1] "0.5 - 112.4 (9.2)" "0.1 - 140.8 (8.6)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED          1       0       10        10       12
  5P LOSS WILD-TYPE        0       2       58        62       55
D49V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               10                58
  STAGE III              10                62
  STAGE IV               12                55
[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         11 15  5
  5P LOSS WILD-TYPE       51 86 27
D49V4, multiclass
          clus
vv         5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1+T2              11                51
  T3                    15                86
  T4                     5                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
  5P LOSS MUTATED    20   3   7   2
  5P LOSS WILD-TYPE 110  19  31   5
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              20               110
  N1               3                19
  N2               7                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
  5P LOSS MUTATED   14  2 17
  5P LOSS WILD-TYPE 92  3 85
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0              14                92
  M1               2                 3
  MX              17                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"
D49V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    11  23
  5P LOSS WILD-TYPE  39 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     11   23
  5P LOSS WILD-TYPE   39  141
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              11                39
  MALE                23               141
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
D49V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       3                         0    28
  5P LOSS WILD-TYPE    19                        11   142
D49V11, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   3                19
  BLACK OR AFRICAN AMERICAN               0                11
  WHITE                                  28               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"

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   56 23
  5Q LOSS WILD-TYPE 95 34
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               79               129 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23                34 
$`5Q LOSS MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LD TCGA-BT-A3PH 
        6.58        19.04         5.06         5.06         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CU-A3QU 
       12.82        15.42         9.99        23.01         0.46         5.19 
TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        2.14       112.44        10.59         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X1 
       10.49        50.27        21.30        20.02        10.55        48.00 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       64.18        15.68        32.28        43.59        15.35        24.66 
TCGA-E7-A4IJ TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL 
        0.49         8.94         6.87        11.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43U 
       16.47        12.82        13.18        19.79         1.97        14.93 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62O 
       13.38         5.36         6.84        27.45         6.87         4.83 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       50.66         9.30         6.71         2.66         3.48         4.08 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3YS 
        6.48        61.94         7.04        20.12         0.85         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JW 
        2.66         7.73         2.10         2.20         6.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
        6.15         5.69         7.63        19.07        11.54         6.74 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ TCGA-PQ-A6FN TCGA-XF-A8HF 
        3.45         2.50        10.52         1.81        16.67        56.19 
TCGA-XF-A8HG 
       15.35 

$`5Q 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-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-A2LB TCGA-BT-A3PK TCGA-BT-A42C 
        8.35         8.25        17.16         5.59         2.07        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       28.41         8.98         1.94         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-A5W6 TCGA-CU-A72E 
        4.90         7.20         5.46        16.31         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.53        31.40        18.41        19.00         8.91       130.88 
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-A2I6 TCGA-DK-A3IK TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X2 
       87.32         2.20         9.67         8.28       140.81        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3Y1 
       48.53        76.60        67.36        30.67        26.17         0.10 
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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
        1.22        12.89        15.68         4.01        12.43        15.88 
TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       45.93         5.52        46.78        22.98        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-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TE TCGA-FD-A6TH 
       49.68         2.66         6.28         6.38         4.11         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.01        15.19         7.13         3.25        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       26.93        35.24        17.26         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS 
        4.50        15.91        14.07        17.75         3.12        20.98 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        7.66        11.31         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-A4AC 
        6.41         1.51        38.60         8.75         4.67         6.48 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.74         4.27         6.38         6.35         3.45        13.48 
TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE 
       12.23        88.93        97.45 

  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 
             8.94              8.35 
[1] "0.5 - 112.4 (8.9)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED          1       0       20        25       34
  5Q LOSS WILD-TYPE        0       2       48        47       33
D50V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               20                48
  STAGE III              25                47
  STAGE IV               34                33
[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         21 39 14
  5Q LOSS WILD-TYPE       41 62 18
D50V4, multiclass
          clus
vv         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1+T2              21                41
  T3                    39                62
  T4                    14                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
  5Q LOSS MUTATED   40 10 19  5
  5Q LOSS WILD-TYPE 90 12 19  2
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              40                90
  N1              10                12
  N2              19                19
  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   30  4 46
  5Q LOSS WILD-TYPE 76  1 56
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              30                76
  M1               4                 1
  MX              46                56
[1] 3 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    20  61
  5Q LOSS WILD-TYPE  30 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     20   61
  5Q LOSS WILD-TYPE   30  103
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              20                30
  MALE                61               103
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
D50V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       5                         5    67
  5Q LOSS WILD-TYPE    17                         6   103
D50V11, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   5                17
  BLACK OR AFRICAN AMERICAN               5                 6
  WHITE                                  67               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"

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    35  15
  6P LOSS WILD-TYPE 116  42
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               50               158 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               15                42 
$`6P LOSS MUTATED`
TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       32.84         5.06         8.25         5.59         3.65         4.67 
TCGA-BT-A42C TCGA-CF-A1HR TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AB 
       28.70         0.46         0.10         5.19         1.84         8.91 
TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        1.81       123.85         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        32.28        30.67        43.59        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-GC-A3RB TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GV-A3JW 
       35.24        20.12         4.50        14.07         2.10         6.41 
TCGA-GV-A3JZ TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A4AB TCGA-K4-A6FZ TCGA-MV-A51V 
        5.69         6.74        38.60         2.50         1.81        13.48 
TCGA-PQ-A6FN TCGA-XF-A8HG 
       16.67        15.35 

$`6P LOSS WILD-TYPE`
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-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.89        14.96         8.35        17.16        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-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-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        9.34         2.53         2.14        31.40        18.41        19.00 
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-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU 
        7.79        87.32         2.20         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        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       76.60        67.36        15.68        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV 
        0.53         0.59         0.66         1.38         0.82         1.22 
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-A3SM TCGA-FD-A3SO 
       11.93        15.88        45.93        24.30        16.47         5.52 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       13.18        19.79         1.97        22.98        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-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P 
        6.84        27.45         6.87        49.68         2.66         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH 
        6.38        50.66         9.30         6.71         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        4.01         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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
        2.89         2.24        15.81        15.91        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        2.66         7.73         3.12        20.98         2.20         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
        7.66        11.31         4.41         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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        8.75         3.45         4.67         6.48        10.52         1.74 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-XF-A8HD 
        4.27         6.38         6.35         3.45        12.23        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF 
       97.45        56.19 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.10              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           123.85            140.81 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            11.31              8.25 
[1] "0.1 - 123.8 (11.3)" "0.1 - 140.8 (8.2)" 
[1] "hr=" "1"  
D51V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED          0       0       10        18       21
  6P LOSS WILD-TYPE        1       2       58        54       46
D51V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               10                58
  STAGE III              18                54
  STAGE IV               21                46
[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         10 23 13
  6P LOSS WILD-TYPE       52 78 19
D51V4, multiclass
          clus
vv         6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1+T2              10                52
  T3                    23                78
  T4                    13                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
  6P LOSS MUTATED    26   3  16   1
  6P LOSS WILD-TYPE 104  19  22   6
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              26               104
  N1               3                19
  N2              16                22
  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   27  2 22
  6P LOSS WILD-TYPE 79  3 80
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              27                79
  M1               2                 3
  MX              22                80
[1] 3 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    15  36
  6P LOSS WILD-TYPE  35 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     15   36
  6P LOSS WILD-TYPE   35  128
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              15                35
  MALE                36               128
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
D51V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       5                         2    41
  6P LOSS WILD-TYPE    17                         9   129
D51V11, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   5                17
  BLACK OR AFRICAN AMERICAN               2                 9
  WHITE                                  41               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"

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   56 22
  6Q LOSS WILD-TYPE 95 35
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               78               130 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22                35 
$`6Q LOSS MUTATED`
TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42C 
       32.84         5.06         5.59         3.65         4.67        28.70 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A6 
        1.94         0.46         0.10         5.19         1.84        31.40 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
        8.91         1.81        10.59         7.79       123.85         2.20 
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-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ 
       32.28        30.67        43.59        15.35        26.17         0.49 
TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ 
        0.56         1.22         8.94        22.45        12.82        46.78 
TCGA-FD-A3SR TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BV 
       19.79        14.93        12.13        13.38         6.87         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        6.84        27.45         6.87         4.83         6.28         6.38 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        9.30         4.11         2.66         2.20        15.19         4.08 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GC-A3RB 
        6.48        35.24        17.26        20.12         2.24         4.50 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX 
       14.07         2.66         2.10        11.31         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-K4-A4AB TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HG 
        2.50         1.81         3.45        13.48        16.67        15.35 

$`6Q LOSS WILD-TYPE`
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-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        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-A3PJ 
       14.89        14.96         8.35         8.25        17.16        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
        2.07        15.42         9.99        28.41         8.98        23.01 
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-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC 
        9.34         2.53         2.14        18.41        19.00       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IM 
      112.44        16.14        17.62        15.62        87.32         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-A6B2 TCGA-E7-A3X6 
       48.00        48.53        76.60        67.36        15.68        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         0.53         0.59         0.66         1.38         0.82 
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-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       15.88        45.93        24.30        16.47         5.52        13.18 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BS 
        1.97        22.98        14.93        14.96         3.62        37.15 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TD 
       11.01         5.69        49.68         2.66        50.66         6.71 
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-A3IB TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3OO 
        5.69        26.93         7.04         0.85         2.89        15.81 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        17.75         1.12         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A3QK 
        2.20         6.41         7.66         4.41         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        6.41        19.07         1.51         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-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       12.23        88.93        97.45        56.19 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.10              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           123.85            140.81 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             7.71              9.16 
[1] "0.1 - 123.8 (7.7)" "0.1 - 140.8 (9.2)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED          1       0       22        23       32
  6Q LOSS WILD-TYPE        0       2       46        49       35
D52V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               22                46
  STAGE III              23                49
  STAGE IV               32                35
[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         21 36 15
  6Q LOSS WILD-TYPE       41 65 17
D52V4, multiclass
          clus
vv         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1+T2              21                41
  T3                    36                65
  T4                    15                17
[1] 3 2
[1] 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   40  6 22  3
  6Q LOSS WILD-TYPE 90 16 16  4
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              40                90
  N1               6                16
  N2              22                16
  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   35  2 43
  6Q LOSS WILD-TYPE 71  3 59
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              35                71
  M1               2                 3
  MX              43                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"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    23  57
  6Q LOSS WILD-TYPE  27 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     23   57
  6Q LOSS WILD-TYPE   27  107
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              23                27
  MALE                57               107
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
D52V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       7                         5    63
  6Q LOSS WILD-TYPE    15                         6   107
D52V11, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   7                15
  BLACK OR AFRICAN AMERICAN               5                 6
  WHITE                                  63               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"

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     6   3
  7P LOSS WILD-TYPE 145  54
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                9               199 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                54 
$`7P LOSS MUTATED`
TCGA-BT-A20X TCGA-CF-A47X TCGA-DK-A1A5 TCGA-DK-A6B5 TCGA-FD-A5BY TCGA-FD-A6TA 
        8.25         0.10         2.14        32.28         6.84        50.66 
TCGA-FD-A6TC TCGA-GV-A3QF TCGA-K4-A3WS 
        9.30         7.63         8.75 

$`7P LOSS WILD-TYPE`
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-A2LA 
        5.06        14.89        14.96         5.06         8.35        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-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-A1A6 
        5.19        16.31         1.84         9.34         2.53        31.40 
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-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        48.53        76.60 
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-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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        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-A3SN TCGA-FD-A3SO 
       45.93        24.30        22.45        16.47        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-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-A6TD 
       49.68         2.66         4.83         6.28         6.38         6.71 
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-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-A3IE 
        5.69        26.93        35.24        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        0.85         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-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20         6.41         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI 
        4.41         6.41         6.15         5.69         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-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       38.60         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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       13.48        12.23        16.67        88.93        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  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 
             8.25              8.91 
[1] "0.1 - 50.7 (8.2)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.3"
D53V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED          0       0        2         3        5
  7P LOSS WILD-TYPE        1       2       66        69       62
D53V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                2                66
  STAGE III               3                69
  STAGE IV                5                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
  7P LOSS MUTATED          2  5  3
  7P LOSS WILD-TYPE       60 96 29
D53V4, multiclass
          clus
vv         7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1+T2               2                60
  T3                     5                96
  T4                     3                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
  7P LOSS MUTATED     5   0   4   1
  7P LOSS WILD-TYPE 125  22  34   6
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               5               125
  N1               0                22
  N2               4                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
  7P LOSS MUTATED     4   0   6
  7P LOSS WILD-TYPE 102   5  96
D53V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               4               102
  M1               0                 5
  MX               6                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"
D53V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   8
  7P LOSS WILD-TYPE  48 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    8
  7P LOSS WILD-TYPE   48  156
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               2                48
  MALE                 8               156
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
D53V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         0     6
  7P LOSS WILD-TYPE    21                        11   164
D53V11, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                21
  BLACK OR AFRICAN AMERICAN               0                11
  WHITE                                   6               164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     9   2
  7Q LOSS WILD-TYPE 142  55
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               197 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                55 
$`7Q LOSS MUTATED`
TCGA-BT-A20X TCGA-CF-A47X TCGA-DK-A1A5 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
        8.25         0.10         2.14       123.85         2.20         7.82 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TC TCGA-FD-A6TE TCGA-K4-A3WS 
        6.84         6.87         9.30         4.11         8.75 

$`7Q LOSS WILD-TYPE`
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-A2LA 
        5.06        14.89        14.96         5.06         8.35        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-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-A1A6 
        5.19        16.31         1.84         9.34         2.53        31.40 
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-A2I6 
       17.62        15.62         1.81        10.59         7.79        87.32 
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-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        48.53        76.60        67.36        15.68        32.28 
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-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.82         1.22        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        16.47        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-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.36         5.69        27.45        49.68         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH 
        6.28         6.38        50.66         6.71         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.01        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-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         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-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        6.41         7.66        11.31         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-K4-A3WU 
       19.07        11.54         1.51         6.74        38.60         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-MV-A51V TCGA-PQ-A6FI 
        4.27         6.38         6.35         3.45        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        88.93        97.45        56.19        15.35 

  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              8.98 
[1] "0.1 - 123.8 (6.9)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1"  
D54V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED          0       0        2         5        4
  7Q LOSS WILD-TYPE        1       2       66        67       63
D54V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                2                66
  STAGE III               5                67
  STAGE IV                4                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
  7Q LOSS MUTATED          2  7  2
  7Q LOSS WILD-TYPE       60 94 30
D54V4, multiclass
          clus
vv         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1+T2               2                60
  T3                     7                94
  T4                     2                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
  7Q LOSS MUTATED     7   0   4   0
  7Q LOSS WILD-TYPE 123  22  34   7
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               7               123
  N1               0                22
  N2               4                34
  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   5
  7Q LOSS WILD-TYPE 100   5  97
D54V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               6               100
  M1               0                 5
  MX               5                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"
D54V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2   9
  7Q LOSS WILD-TYPE  48 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    9
  7Q LOSS WILD-TYPE   48  155
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               2                48
  MALE                 9               155
[1] 2 2
[1] FALSE
D54V8, continuous
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                59 
       TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CF-A3MF        TCGA-CF-A3MG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CF-A3MH        TCGA-CF-A3MI        TCGA-CF-A47S        TCGA-CF-A47T 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CF-A47V        TCGA-CF-A47W        TCGA-CF-A47Y        TCGA-DK-A2HX 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A3IN        TCGA-DK-A3IV        TCGA-DK-A3WX        TCGA-DK-A3X2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A6B2        TCGA-DK-A6B5        TCGA-DK-A6B6        TCGA-E5-A2PC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-E5-A4TZ        TCGA-E5-A4U1        TCGA-E7-A519        TCGA-E7-A541 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-E7-A7DV        TCGA-FT-A61P        TCGA-G2-A2EF        TCGA-G2-A2EJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO        TCGA-G2-A2ES 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A3IB        TCGA-G2-A3IE        TCGA-G2-A3VY        TCGA-GC-A3BM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GC-A3I6        TCGA-GC-A3OO        TCGA-GC-A3RC        TCGA-GC-A3RD 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GC-A3YS        TCGA-GC-A6I1        TCGA-GD-A3OS        TCGA-GD-A6C6 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GV-A3JV        TCGA-GV-A3JW        TCGA-GV-A3JX        TCGA-GV-A3JZ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GV-A3QF        TCGA-GV-A3QH        TCGA-GV-A3QI        TCGA-GV-A3QK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GV-A40E        TCGA-GV-A40G        TCGA-GV-A6ZA        TCGA-XF-A8HD 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-XF-A8HE        TCGA-XF-A8HF        TCGA-XF-A8HG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D54V9, continuous
D54V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       1                         0     8
  7Q LOSS WILD-TYPE    21                        11   162
D54V11, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   1                21
  BLACK OR AFRICAN AMERICAN               0                11
  WHITE                                   8               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"

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   71 22
  8P LOSS WILD-TYPE 80 35
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               93               115 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               22                35 
$`8P LOSS MUTATED`
TCGA-BL-A13J TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ 
        2.66         5.59         2.07        28.70        28.41         8.98 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 
        0.43         0.13        12.92         5.46         5.19         2.53 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
       18.41       130.88       112.44         1.81        10.59       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-A3IV TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 
        9.67        64.18        32.28        15.35        26.17         0.59 
TCGA-E7-A677 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.38         1.22        15.68         8.94         6.87         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SR 
       11.93        24.30        22.45        16.47         5.52        19.79 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BY 
       22.98        14.93        12.13        13.38         6.87         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       27.45         6.87         2.66         6.28         6.38        50.66 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        6.71         4.11         2.20        15.19         4.08         6.48 
TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IE TCGA-GC-A3RB TCGA-GC-A3RC 
       61.94         5.69        35.24        20.12         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        17.75         1.12         7.73         2.10         3.12 
TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        6.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        6.41        19.07         6.74         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-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN 
        3.45        12.23        16.67 

$`8P LOSS WILD-TYPE`
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-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 
        3.65         4.67        12.82        15.42         9.99         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-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 
        0.10         0.10         4.90         7.20        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
        9.34         2.14        31.40        19.00         8.91        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
       17.62        15.62         7.79        10.49        50.27        20.02 
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        48.53 
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-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 
        0.10         0.49         0.53         0.56         0.66         0.82 
TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SP 
       12.89        12.43        15.88        45.93        12.82        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS 
       46.78         1.97        14.96        14.93         3.62        37.15 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TC 
       11.01         5.36         5.69        49.68         4.83         9.30 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EJ 
        2.66         4.01         7.13         3.48         3.25        30.61 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       26.93        17.26         7.04         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       15.81         2.66        20.98         2.20         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
        4.41         4.14         6.67        11.54         1.51        38.60 
TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        6.38         6.35        13.48        88.93        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  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 
             6.87             10.55 
[1] "0.1 - 130.9 (6.9)"  "0.1 - 140.8 (10.6)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED          0       0       29        27       37
  8P LOSS WILD-TYPE        1       2       39        45       30
D55V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               29                39
  STAGE III              27                45
  STAGE IV               37                30
[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         25 43 16
  8P LOSS WILD-TYPE       37 58 16
D55V4, multiclass
          clus
vv         8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1+T2              25                37
  T3                    43                58
  T4                    16                16
[1] 3 2
[1] 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   51 11 22  3
  8P LOSS WILD-TYPE 79 11 16  4
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              51                79
  N1              11                11
  N2              22                16
  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   34  4 56
  8P LOSS WILD-TYPE 72  1 46
D55V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              34                72
  M1               4                 1
  MX              56                46
[1] 3 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   21 73
  8P LOSS WILD-TYPE 29 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     21   73
  8P LOSS WILD-TYPE   29   91
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              21                29
  MALE                73                91
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
D55V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       5                         8    75
  8P LOSS WILD-TYPE    17                         3    95
D55V11, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   5                17
  BLACK OR AFRICAN AMERICAN               8                 3
  WHITE                                  75                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    17   5
  8Q LOSS WILD-TYPE 134  52
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               186 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                52 
$`8Q LOSS MUTATED`
TCGA-BT-A42F TCGA-CF-A1HS TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM 
       28.41         0.43         1.81       123.85         3.98         7.82 
TCGA-DK-A6B5 TCGA-E7-A677 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SR 
       32.28         1.38         1.22         4.01        22.45        19.79 
TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FJ-A3Z7 TCGA-G2-A2EO TCGA-GU-A42P TCGA-H4-A2HQ 
        6.87        27.45        15.19        35.24         6.41         6.74 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A5RJ TCGA-LT-A5Z6 
        8.75         3.45         1.74         3.45 

$`8Q LOSS WILD-TYPE`
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-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       15.42        28.70         9.99         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-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-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 
       31.40        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-A2I6 
       16.14        17.62        15.62        10.59         7.79        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        48.53        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-FD-A3B3 
        0.53         0.59         0.56         0.66         0.82        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-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       45.93        24.30        16.47        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       46.78         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-A5BV 
        3.62        12.13        13.38        37.15        11.01         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69         6.84         6.87        49.68         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28         6.38        50.66         9.30         6.71         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.66         2.20         4.01         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-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         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-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        7.66        11.31         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-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       11.54         1.51        38.60         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V 
       10.52         1.81         4.27         6.38         6.35        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        16.67        88.93        97.45        56.19        15.35 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.43              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           123.85            140.81 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            6.805             8.960 
[1] "0.4 - 123.8 (6.8)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.2"
D56V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED          0       0        4         6       11
  8Q LOSS WILD-TYPE        1       2       64        66       56
D56V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II                4                64
  STAGE III               6                66
  STAGE IV               11                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
  8Q LOSS MUTATED          3 10  7
  8Q LOSS WILD-TYPE       59 91 25
D56V4, multiclass
          clus
vv         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1+T2               3                59
  T3                    10                91
  T4                     7                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
  8Q LOSS MUTATED    10   3   6   1
  8Q LOSS WILD-TYPE 120  19  32   6
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              10               120
  N1               3                19
  N2               6                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
  8Q LOSS MUTATED    9  2 11
  8Q LOSS WILD-TYPE 97  3 91
D56V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               9                97
  M1               2                 3
  MX              11                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"
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6  16
  8Q LOSS WILD-TYPE  44 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   16
  8Q LOSS WILD-TYPE   44  148
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               6                44
  MALE                16               148
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       2                         3    15
  8Q LOSS WILD-TYPE    20                         8   155
D56V11, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   2                20
  BLACK OR AFRICAN AMERICAN               3                 8
  WHITE                                  15               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"

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   64 23
  9P LOSS WILD-TYPE 87 34
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               87               121 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               23                34 
$`9P LOSS MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
        6.58        19.04        32.84        17.88        19.50        14.89 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        8.35         5.59         9.99         1.94        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A5W6 
        0.69         0.10         0.10         4.90         5.46         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
        9.34         2.53         2.14        19.00         8.91       112.44 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       17.62        15.62         2.20         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 
       21.30        10.55        48.00        17.98        64.18        15.68 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE 
       32.28        43.59        26.17        24.66         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        0.66         1.22         8.94        16.47        12.82        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-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        5.36        27.45         6.87        49.68         4.83         6.28 
TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3IB 
       50.66         6.71         2.66         6.48        35.24         7.04 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A6C6 
        0.85         2.89        14.07         1.12         2.66         2.20 
TCGA-GU-A42Q TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ 
        7.66         6.41         7.79         6.67        11.54         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB 
       38.60         8.75         3.45         4.67         2.50         4.27 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HF 
       12.23        16.67        56.19 

$`9P 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-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       12.16         5.06        14.96         5.06         8.25        17.16 
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-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       28.41         8.98         0.43         0.13         0.07         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 
        0.10        12.92         7.20         5.19        16.31        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       18.41       130.88        16.14         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV 
      123.85        87.32         3.98         7.82        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
        8.28       140.81        48.53        76.60        67.36        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-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-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.20         4.01        15.19         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        3.25        61.94        30.61         5.69        26.93        17.26 
TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
       20.12         2.24        15.81         4.50        15.91        17.75 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42R 
        7.73         2.10         3.12        20.98         6.41        11.31 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E 
        4.41         6.15         5.69         7.63         4.14         6.41 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
       19.07         1.51         6.48        10.52         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HE 
        6.38         6.35         3.45        13.48        88.93        97.45 
TCGA-XF-A8HG 
       15.35 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.10              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           112.44            140.81 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             8.75              8.28 
[1] "0.1 - 112.4 (8.8)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED          1       0       27        31       29
  9P LOSS WILD-TYPE        0       2       41        41       38
D57V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               27                41
  STAGE III              31                41
  STAGE IV               29                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
  9P LOSS MUTATED         28 47 12
  9P LOSS WILD-TYPE       34 54 20
D57V4, multiclass
          clus
vv         9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1+T2              28                34
  T3                    47                54
  T4                    12                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
  9P LOSS MUTATED   56  7 19  2
  9P LOSS WILD-TYPE 74 15 19  5
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              56                74
  N1               7                15
  N2              19                19
  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   47  2 41
  9P LOSS WILD-TYPE 59  3 61
D57V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              47                59
  M1               2                 3
  MX              41                61
[1] 3 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   19 72
  9P LOSS WILD-TYPE 31 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     19   72
  9P LOSS WILD-TYPE   31   92
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              19                31
  MALE                72                92
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
D57V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED      12                         3    67
  9P LOSS WILD-TYPE    10                         8   103
D57V11, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                  12                10
  BLACK OR AFRICAN AMERICAN               3                 8
  WHITE                                  67               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"

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   57 21
  9Q LOSS WILD-TYPE 94 36
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               78               130 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               21                36 
$`9Q LOSS MUTATED`
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 
       32.28        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        16.47        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-A6TG TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY 
        2.66         6.48         5.69        26.93        35.24         0.85 
TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
        2.89        14.07         2.66         7.73         2.10         2.20 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE 
        4.41         6.41         7.79        19.07        11.54        38.60 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-PQ-A6FN TCGA-XF-A8HF 
        8.75         3.45         4.67         2.50        16.67        56.19 

$`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 
       31.40        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        48.53        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-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       12.89        15.68         4.01        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       45.93        24.30        22.45        12.82         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-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TC 
        5.36         5.69         6.84         2.66         6.38         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.71         4.11         2.20         4.01        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES 
        3.48         4.08         3.25        61.94        30.61        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        7.04        20.12         2.24        15.81         4.50        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q 
       17.75         1.12         3.12        20.98         6.41         7.66 
TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
       11.31         6.15         5.69         7.63         4.14         6.67 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        6.41         1.51         6.74         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.81         4.27         6.38         6.35         3.45        13.48 
TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       12.23        88.93        97.45        15.35 

  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 
            9.140             8.265 
[1] "0.1 - 112.4 (9.1)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED          1       0       28        26       24
  9Q LOSS WILD-TYPE        0       2       40        46       43
D58V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE 0A                1                 0
  STAGE I                 0                 2
  STAGE II               28                40
  STAGE III              26                46
  STAGE IV               24                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
  9Q LOSS MUTATED         28 39 10
  9Q LOSS WILD-TYPE       34 62 22
D58V4, multiclass
          clus
vv         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1+T2              28                34
  T3                    39                62
  T4                    10                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
  9Q LOSS MUTATED   51  6 18  2
  9Q LOSS WILD-TYPE 79 16 20  5
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              51                79
  N1               6                16
  N2              18                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
  9Q LOSS MUTATED   42  1 38
  9Q LOSS WILD-TYPE 64  4 64
D58V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              42                64
  M1               1                 4
  MX              38                64
[1] 3 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   16 66
  9Q LOSS WILD-TYPE 34 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     16   66
  9Q LOSS WILD-TYPE   34   98
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              16                34
  MALE                66                98
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
D58V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED      12                         1    61
  9Q LOSS WILD-TYPE    10                        10   109
D58V11, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                  12                10
  BLACK OR AFRICAN AMERICAN               1                10
  WHITE                                  61               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    32   9
  10P LOSS WILD-TYPE 119  48
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                41                167 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 9                 48 
$`10P LOSS MUTATED`
TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F6 
       14.96        17.16         3.65        28.70         1.94        23.01 
TCGA-CF-A27C TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A2I2 TCGA-DK-A3IS TCGA-DK-A6B1 
        0.69         7.20         5.46         7.79        50.27        67.36 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 
       43.59        15.35         0.59        15.68         8.94         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A6TD 
       11.93        19.79        22.98        12.13         6.84         6.71 
TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3IB 
        4.11        15.19         3.48         4.08        26.93         7.04 
TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HQ 
        2.89        15.91         6.15         4.14        19.07         6.74 
TCGA-K4-A3WU TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HE 
        3.45         3.45        13.48        12.23        97.45 

$`10P LOSS WILD-TYPE`
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-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB 
        5.06        14.89         5.06         8.35         8.25         5.59 
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-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        8.98         0.46         0.43         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU 
        0.07         0.10         0.10        12.92         4.90         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        31.40 
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-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81        10.59       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
        2.20         3.98         7.82         8.22        10.49        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-A6B2 TCGA-DK-A6B5 
       17.98        64.18        48.53        76.60        15.68        32.28 
TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       30.67        26.17        24.66         0.10         0.49         0.53 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.56         0.66         1.38         0.82         1.22        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 
       16.47        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-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FT-A3EE 
        9.30         2.66         2.20         4.01         7.13         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES 
        6.48        61.94        30.61         5.69        35.24        17.26 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
       20.12         0.85         2.24        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-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
       20.98         2.20         6.41         7.66        11.31         4.41 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
        6.41         5.69         7.63         7.79         6.67         6.41 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB 
       11.54         1.51        38.60         8.75         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        6.48        10.52         1.74         1.81         4.27         6.38 
TCGA-LC-A66R TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
        6.35        16.67        88.93        56.19        15.35 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.59               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             97.45             140.81 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              8.94               8.35 
[1] "0.6 - 97.5 (8.9)"  "0.1 - 140.8 (8.3)"
[1] "hr=" "1.3"
D59V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED          0       0       13        16       11
  10P LOSS WILD-TYPE        1       2       55        56       56
D59V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                13                 55
  STAGE III               16                 56
  STAGE IV                11                 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
  10P LOSS MUTATED         12 16  6
  10P LOSS WILD-TYPE       50 85 26
D59V4, multiclass
          clus
vv         10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1+T2               12                 50
  T3                     16                 85
  T4                      6                 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
  10P LOSS MUTATED    28   3   5   2
  10P LOSS WILD-TYPE 102  19  33   5
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               28                102
  N1                3                 19
  N2                5                 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
  10P LOSS MUTATED   17  2 22
  10P LOSS WILD-TYPE 89  3 80
D59V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               17                 89
  M1                2                  3
  MX               22                 80
[1] 3 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     8  33
  10P LOSS WILD-TYPE  42 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8   33
  10P LOSS WILD-TYPE   42  131
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                8                 42
  MALE                 33                131
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
D59V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       1                         6    31
  10P LOSS WILD-TYPE    21                         5   139
D59V11, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    1                 21
  BLACK OR AFRICAN AMERICAN                6                  5
  WHITE                                   31                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   56 15
  10Q LOSS WILD-TYPE 95 42
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                71                137 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                 42 
$`10Q LOSS MUTATED`
TCGA-BT-A20N TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A42B 
       32.84        14.96         8.35        17.16         3.65        15.42 
TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CU-A0YR TCGA-CU-A3KJ 
       28.70         1.94        23.01         0.69         7.20         5.46 
TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I6 
        5.19         2.14       112.44         1.81         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6B1 
        2.20         3.98         7.82        50.27        48.00        67.36 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 
       30.67        43.59        15.35        24.66         0.49         0.59 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P 
        1.22         4.01        11.93        19.79        22.98        14.93 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-FD-A6TE 
       14.93        12.13         6.84        49.68         6.71         4.11 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3IB TCGA-G2-A3IE 
       15.19         3.48         4.08         6.48         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OP 
        0.85         2.89        15.91        14.07        17.75         2.10 
TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        6.41         6.41         6.15         7.63         7.79         4.14 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC 
       19.07        11.54         6.74         8.75         3.45         6.48 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HF 
        1.81         3.45        13.48        12.23        56.19 

$`10Q LOSS WILD-TYPE`
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-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.89         5.06         8.25         5.59         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS 
        2.07         9.99        28.41         8.98         0.46         0.43 
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-A0YO TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       12.92         4.90        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 
       31.40        18.41        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IQ 
       17.62        15.62        10.59       123.85         8.22        10.49 
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        48.53        76.60        15.68        32.28 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       26.17         0.10         0.53         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 
        0.82        12.89        15.68         8.94         6.87        12.43 
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        16.47        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43X 
        5.52        13.18        46.78         1.97        14.96         3.62 
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-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45         6.87         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
       50.66         9.30         2.66         2.20         4.01         7.13 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I1 
       17.26         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         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OE 
        4.41         5.69         6.67         6.41         1.51        38.60 
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-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        6.35        16.67        88.93        97.45        15.35 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.49               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            112.44             140.81 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              7.79               8.98 
[1] "0.5 - 112.4 (7.8)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.4"
D60V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED          1       0       23        23       23
  10Q LOSS WILD-TYPE        0       2       45        49       44
D60V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                23                 45
  STAGE III               23                 49
  STAGE IV                23                 44
[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         21 32  8
  10Q LOSS WILD-TYPE       41 69 24
D60V4, multiclass
          clus
vv         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1+T2               21                 41
  T3                     32                 69
  T4                      8                 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
  10Q LOSS MUTATED   39  6 13  3
  10Q LOSS WILD-TYPE 91 16 25  4
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               39                 91
  N1                6                 16
  N2               13                 25
  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   31  2 37
  10Q LOSS WILD-TYPE 75  3 65
D60V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               31                 75
  M1                2                  3
  MX               37                 65
[1] 3 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    15  56
  10Q LOSS WILD-TYPE  35 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     15   56
  10Q LOSS WILD-TYPE   35  108
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               15                 35
  MALE                 56                108
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
D60V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       3                         5    58
  10Q LOSS WILD-TYPE    19                         6   112
D60V11, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    3                 19
  BLACK OR AFRICAN AMERICAN                5                  6
  WHITE                                   58                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"

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   58 20
  11P LOSS WILD-TYPE 93 37
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                78                130 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                20                 37 
$`11P LOSS MUTATED`
TCGA-BL-A0C8 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA 
       40.08        32.84        14.89         5.06         8.35        17.16 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR 
        4.67        15.42        28.70         8.98        23.01         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E 
        0.43         0.69         0.10         5.46         1.84         9.34 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 
        2.14        31.40         8.91       112.44         1.81        10.59 
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-A3X2 TCGA-DK-A6AV TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       21.30        17.98        64.18        15.35        26.17        24.66 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SL 
        0.49         0.59         0.56         8.94        24.30        22.45 
TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BZ 
       12.82         1.97        22.98        12.13        13.38        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC 
        6.87        49.68         2.66         4.83        50.66         9.30 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EO 
        2.66         2.20        15.19         3.48         6.48        35.24 
TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.26         2.89        14.07         1.12         7.73         2.10 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF 
        2.20         7.66        11.31         4.41         6.41         7.63 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A6MB TCGA-XF-A8HG 
       19.07        11.54         6.74        38.60         4.27        15.35 

$`11P LOSS WILD-TYPE`
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-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E 
        8.25         5.59         3.65        12.82         2.07         9.99 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       28.41         1.94         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-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-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV 
       15.62         7.79       123.85         8.22        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        48.00        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3Y1 
       67.36        15.68        32.28        30.67        43.59         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.53         0.66         1.38         0.82         1.22        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-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       45.93        16.47         5.52        13.18        46.78        19.79 
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-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A62S 
        6.87         5.36         5.69         6.84         6.28         6.38 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE 
        6.71         4.11         4.01         7.13         4.08         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        30.61         5.69        26.93         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
        0.85         2.24        15.81         4.50        15.91        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3JZ 
        2.66         3.12        20.98         6.41         6.15         5.69 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-K4-A3WS 
        7.79         4.14         6.67         6.41         1.51         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-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        1.81         6.38         6.35         3.45        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       16.67        88.93        97.45        56.19 

  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 
             9.140              8.005 
[1] "0.1 - 112.4 (9.1)" "0.1 - 140.8 (8.0)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED          1       1       21        20       35
  11P LOSS WILD-TYPE        0       1       47        52       32
D61V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  1                  1
  STAGE II                21                 47
  STAGE III               20                 52
  STAGE IV                35                 32
[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         25 43 10
  11P LOSS WILD-TYPE       37 58 22
D61V4, multiclass
          clus
vv         11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1+T2               25                 37
  T3                     43                 58
  T4                     10                 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
  11P LOSS MUTATED   41 10 22  2
  11P LOSS WILD-TYPE 89 12 16  5
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               41                 89
  N1               10                 12
  N2               22                 16
  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   42  4 36
  11P LOSS WILD-TYPE 64  1 66
D61V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               42                 64
  M1                4                  1
  MX               36                 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"
D61V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   17 65
  11P LOSS WILD-TYPE 33 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     17   65
  11P LOSS WILD-TYPE   33   99
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               17                 33
  MALE                 65                 99
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
D61V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED      12                         3    60
  11P LOSS WILD-TYPE    10                         8   110
D61V11, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                   12                 10
  BLACK OR AFRICAN AMERICAN                3                  8
  WHITE                                   60                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"

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    42  18
  11Q LOSS WILD-TYPE 109  39
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                60                148 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                18                 39 
$`11Q LOSS MUTATED`
TCGA-BL-A0C8 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA 
       40.08        32.84        14.89         5.06         8.35        17.16 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A27C 
        4.67        15.42        28.70         8.98         0.43         0.69 
TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB 
        0.10         5.46         1.84         2.14        31.40         8.91 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ 
      112.44        10.59        87.32         3.98         8.22        10.49 
TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 
       50.27        64.18        30.67        15.35         0.49         0.59 
TCGA-E7-A5KE TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BV 
        0.56         8.94        24.30        22.98        12.13         5.36 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TC 
        6.84         6.87        49.68         2.66         4.83         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-GU-A42Q TCGA-GV-A3JV 
        2.66         7.73         2.10         2.20         7.66         4.41 
TCGA-GV-A3JW TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-XF-A8HG 
        6.41         6.67        19.07         6.74        38.60        15.35 

$`11Q LOSS WILD-TYPE`
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-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E 
        8.25         5.59         3.65        12.82         2.07         9.99 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T 
       28.41         1.94        23.01         0.46         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-A1A7 TCGA-DK-A1AA 
        5.19        16.31         9.34         2.53        18.41        19.00 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 
      130.88        16.14        17.62        15.62         1.81         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
      123.85         2.20         7.82        21.30        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        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 
       76.60        67.36        15.68        32.28        43.59        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       24.66         0.10         0.53         0.66         1.38         0.82 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        1.22        12.89        15.68         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        15.88        45.93        22.45        16.47        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
        5.52        13.18        46.78        19.79         1.97        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        14.93         3.62        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        6.87         5.69        27.45         6.28         6.38        50.66 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.71         4.11         2.66         4.01        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-GC-A3I6 TCGA-GC-A3OO 
       26.93         7.04        20.12         0.85         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS 
        4.50        15.91        14.07        17.75         3.12        20.98 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        6.41        11.31         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU 
        4.14         6.41        11.54         1.51         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-MV-A51V TCGA-PQ-A6FI 
        4.27         6.38         6.35         3.45        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       16.67        88.93        97.45        56.19 

  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 
             7.975              9.505 
[1] "0.1 - 112.4 (8.0)" "0.1 - 140.8 (9.5)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED          0       1       18        19       22
  11Q LOSS WILD-TYPE        1       1       50        53       45
D62V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  1                  1
  STAGE II                18                 50
  STAGE III               19                 53
  STAGE IV                22                 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
  11Q LOSS MUTATED         21 30  9
  11Q LOSS WILD-TYPE       41 71 23
D62V4, multiclass
          clus
vv         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1+T2               21                 41
  T3                     30                 71
  T4                      9                 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
  11Q LOSS MUTATED   35  8 14  0
  11Q LOSS WILD-TYPE 95 14 24  7
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               35                 95
  N1                8                 14
  N2               14                 24
  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   32  2 29
  11Q LOSS WILD-TYPE 74  3 73
D62V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               32                 74
  M1                2                  3
  MX               29                 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"
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    17  46
  11Q LOSS WILD-TYPE  33 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     17   46
  11Q LOSS WILD-TYPE   33  118
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               17                 33
  MALE                 46                118
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED      10                         3    46
  11Q LOSS WILD-TYPE    12                         8   124
D62V11, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                   10                 12
  BLACK OR AFRICAN AMERICAN                3                  8
  WHITE                                   46                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"

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    17   5
  12P LOSS WILD-TYPE 134  52
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                22                186 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 52 
$`12P LOSS MUTATED`
TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1AC TCGA-DK-A3IV 
       17.16         1.94         0.10         5.19       130.88         9.67 
TCGA-E5-A2PC TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43X 
       43.59        22.45        46.78        19.79        22.98         3.62 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-FD-A6TH TCGA-GC-A3YS TCGA-GV-A3JW 
        5.69         6.87         4.11         2.20         1.12         6.41 
TCGA-LC-A66R TCGA-PQ-A6FN TCGA-XF-A8HF TCGA-XF-A8HG 
        6.35        16.67        56.19        15.35 

$`12P LOSS WILD-TYPE`
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-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-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        31.40        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-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-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        48.53        76.60        67.36        15.68        32.28 
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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.22        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-A3SM 
       12.43        11.93        15.88        45.93        24.30        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S 
       12.82         5.52        13.18         1.97        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.93        12.13        13.38        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.36         6.84        27.45        49.68         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG 
        6.28         6.38        50.66         9.30         6.71         2.66 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.01        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-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         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-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.66        11.31         4.41         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-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         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-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE 
        6.38         3.45        13.48        12.23        88.93        97.45 

  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 
              8.27               8.55 
[1] "0.1 - 130.9 (8.3)" "0.1 - 140.8 (8.6)"
[1] "hr=" "1.4"
D63V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED          0       0        6         6       11
  12P LOSS WILD-TYPE        1       2       62        66       56
D63V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 6                 62
  STAGE III                6                 66
  STAGE IV                11                 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
  12P LOSS MUTATED          7 12  3
  12P LOSS WILD-TYPE       55 89 29
D63V4, multiclass
          clus
vv         12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1+T2                7                 55
  T3                     12                 89
  T4                      3                 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 LOSS MUTATED    10   4   7   0
  12P LOSS WILD-TYPE 120  18  31   7
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               10                120
  N1                4                 18
  N2                7                 31
  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    8  1 14
  12P LOSS WILD-TYPE 98  4 88
D63V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                8                 98
  M1                1                  4
  MX               14                 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"
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2  21
  12P LOSS WILD-TYPE  48 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   21
  12P LOSS WILD-TYPE   48  143
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 48
  MALE                 21                143
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
D63V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       2                         0    20
  12P LOSS WILD-TYPE    20                        11   150
D63V11, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    2                 20
  BLACK OR AFRICAN AMERICAN                0                 11
  WHITE                                   20                150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    19   7
  12Q LOSS WILD-TYPE 132  50
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                26                182 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 7                 50 
$`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-GC-A3RD 
        3.62         5.69         4.11         2.20         6.48        14.07 
TCGA-GC-A3YS TCGA-GV-A3JW TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-LC-A66R TCGA-PQ-A6FN 
        1.12         6.41         6.48         1.74         6.35        16.67 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`12Q LOSS WILD-TYPE`
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        31.40        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        48.53        76.60        67.36        15.68        32.28 
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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.22        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-A3SM 
       12.43        11.93        15.88        45.93        24.30        16.47 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       12.82        13.18        19.79        14.93        14.96        14.93 
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-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-A6TC TCGA-FD-A6TD TCGA-FD-A6TG 
        6.28         6.38        50.66         9.30         6.71         2.66 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.01        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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.04        20.12         0.85         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
        4.50        15.91        17.75         2.66         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20         6.41         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        4.41         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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
       38.60         8.75         3.45         4.67         2.50        10.52 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        1.81         4.27         6.38         3.45        13.48        12.23 
TCGA-XF-A8HD TCGA-XF-A8HE 
       88.93        97.45 

  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 
              6.38               8.96 
[1] "0.1 - 87.3 (6.4)"  "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED          0       0        8         5       14
  12Q LOSS WILD-TYPE        1       2       60        67       53
D64V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 8                 60
  STAGE III                5                 67
  STAGE IV                14                 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
  12Q LOSS MUTATED         10 13  3
  12Q LOSS WILD-TYPE       52 88 29
D64V4, multiclass
          clus
vv         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1+T2               10                 52
  T3                     13                 88
  T4                      3                 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
  12Q LOSS MUTATED    11   7   6   1
  12Q LOSS WILD-TYPE 119  15  32   6
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               11                119
  N1                7                 15
  N2                6                 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
  12Q LOSS MUTATED    9  1 17
  12Q LOSS WILD-TYPE 97  4 85
D64V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                9                 97
  M1                1                  4
  MX               17                 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"
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     4  23
  12Q LOSS WILD-TYPE  46 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4   23
  12Q LOSS WILD-TYPE   46  141
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                4                 46
  MALE                 23                141
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
D64V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       2                         0    24
  12Q LOSS WILD-TYPE    20                        11   146
D64V11, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    2                 20
  BLACK OR AFRICAN AMERICAN                0                 11
  WHITE                                   24                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"

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    31  15
  13Q LOSS WILD-TYPE 120  42
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                46                162 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                15                 42 
$`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-GC-A3BM 
       49.68         2.66         4.08        35.24        17.26         2.89 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JW TCGA-GV-A3QI 
        1.12         2.66         2.20         7.66         6.41         4.14 
TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A6FZ 
       38.60         4.67         6.48         1.81 

$`13Q LOSS WILD-TYPE`
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 
       31.40        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 
       48.53        76.60        67.36        15.68        32.28        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-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 
        1.38         0.82        12.89        15.68         6.87        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
       11.93        15.88        45.93        22.45        16.47         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-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-A5C0 TCGA-FD-A62O 
        6.87         5.69         6.84        27.45         6.87         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28         6.38        50.66         9.30         6.71         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.66         2.20         4.01        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-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        7.04        20.12         0.85         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-GU-A42P TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
       20.98         6.41        11.31         4.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        7.63         7.79         6.67         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R 
        1.51         6.74         8.75         3.45         2.50        10.52 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.74         4.27         6.38         6.35         3.45        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        16.67        88.93        97.45        56.19        15.35 

  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 
             7.070              9.505 
[1] "0.5 - 130.9 (7.1)" "0.1 - 140.8 (9.5)"
[1] "hr=" "1.5"
D65V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED          0       0       14        17       14
  13Q LOSS WILD-TYPE        1       2       54        55       53
D65V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                14                 54
  STAGE III               17                 55
  STAGE IV                14                 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
  13Q LOSS MUTATED         15 22  6
  13Q LOSS WILD-TYPE       47 79 26
D65V4, multiclass
          clus
vv         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1+T2               15                 47
  T3                     22                 79
  T4                      6                 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
  13Q LOSS MUTATED    28   5   7   2
  13Q LOSS WILD-TYPE 102  17  31   5
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               28                102
  N1                5                 17
  N2                7                 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
  13Q LOSS MUTATED   24  0 22
  13Q LOSS WILD-TYPE 82  5 80
D65V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               24                 82
  M1                0                  5
  MX               22                 80
[1] 3 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     8  38
  13Q LOSS WILD-TYPE  42 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8   38
  13Q LOSS WILD-TYPE   42  126
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                8                 42
  MALE                 38                126
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
D65V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       3                         4    35
  13Q LOSS WILD-TYPE    19                         7   135
D65V11, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    3                 19
  BLACK OR AFRICAN AMERICAN                4                  7
  WHITE                                   35                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"

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    42  15
  14Q LOSS WILD-TYPE 109  42
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                57                151 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                15                 42 
$`14Q LOSS MUTATED`
TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A3PK TCGA-CF-A1HR 
       19.04        14.89         5.06         5.59         2.07         0.46 
TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 
        0.43         0.10         4.90         7.20         1.84         2.53 
TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IQ 
        2.14       130.88       112.44        10.59        87.32        10.49 
TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 
       50.27        48.00        64.18        32.28        15.35        26.17 
TCGA-E7-A4IJ TCGA-E7-A7DV TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N 
        0.49         1.22        12.82        13.18        46.78        22.98 
TCGA-FD-A43U TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC 
       14.93         6.87        49.68         6.28        50.66         9.30 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        2.66         2.20        15.19         4.08         6.48        61.94 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GU-A42Q TCGA-GV-A3JZ 
       20.12         0.85         4.50        14.07         7.66         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-K4-A3WU TCGA-K4-A6MB TCGA-PQ-A6FI 
        3.45         4.27        12.23 

$`14Q LOSS WILD-TYPE`
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-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         8.35         8.25        17.16         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82        15.42        28.70         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94        23.01         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
        0.07         0.10        12.92         5.46         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
        9.34        31.40        18.41        19.00         8.91        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62         1.81         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        3.98         7.82         8.22        21.30        20.02         9.67 
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        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       67.36        15.68        30.67        43.59        24.66         0.10 
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-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        16.47 
TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
        5.52        19.79         1.97        14.93        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-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
        5.69         6.84        27.45         2.66         4.83         6.38 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        6.71         4.11         4.01         7.13         3.48         3.25 
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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
        2.89         2.24        15.81        15.91        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-A42P TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        6.41        11.31         4.41         6.41         6.15         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB 
        4.14         6.67         1.51         8.75         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
        6.48        10.52         1.74         1.81         6.38         6.35 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.45        13.48        16.67        88.93        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  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 
              9.30               8.35 
[1] "0.1 - 130.9 (9.3)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED          1       0       17        14       23
  14Q LOSS WILD-TYPE        0       2       51        58       44
D66V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                17                 51
  STAGE III               14                 58
  STAGE IV                23                 44
[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         17 25 10
  14Q LOSS WILD-TYPE       45 76 22
D66V4, multiclass
          clus
vv         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1+T2               17                 45
  T3                     25                 76
  T4                     10                 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
  14Q LOSS MUTATED   31  3 17  2
  14Q LOSS WILD-TYPE 99 19 21  5
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               31                 99
  N1                3                 19
  N2               17                 21
  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
  14Q LOSS MUTATED   27  1 29
  14Q LOSS WILD-TYPE 79  4 73
D66V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               27                 79
  M1                1                  4
  MX               29                 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"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    10  48
  14Q LOSS WILD-TYPE  40 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   48
  14Q LOSS WILD-TYPE   40  116
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               10                 40
  MALE                 48                116
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
D66V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       7                         2    44
  14Q LOSS WILD-TYPE    15                         9   126
D66V11, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    7                 15
  BLACK OR AFRICAN AMERICAN                2                  9
  WHITE                                   44                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"

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   54 19
  15Q LOSS WILD-TYPE 97 38
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                73                135 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                19                 38 
$`15Q LOSS MUTATED`
TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A20X 
       40.08         6.58        19.04        32.84         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
        5.59         3.65        15.42        28.70         9.99         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A3KJ TCGA-DK-A1A7 TCGA-DK-A2I2 
        1.94         0.43         0.10         5.46        18.41         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A6B2 TCGA-DK-A6B5 
      123.85        87.32         7.82         8.22        15.68        32.28 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3NA 
       43.59         0.49         0.59         1.22        12.89        45.93 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       12.82        13.18        22.98         5.36         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TH 
        6.87        49.68         2.66         6.38         6.71         2.20 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IE 
       15.19         4.08         6.48        61.94        26.93        20.12 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 
       15.81         4.50         1.12         2.66         2.10         2.20 
TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G 
        6.41         6.15         7.63         7.79         6.41        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A5RJ 
       11.54         6.74        38.60         8.75         2.50         1.74 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF 
        6.35         3.45        13.48        16.67        88.93        56.19 
TCGA-XF-A8HG 
       15.35 

$`15Q LOSS WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O 
        7.33         2.66         6.74        12.39        11.93        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-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F6 
       17.16         4.67        12.82         2.07        28.41        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-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-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
        1.84         9.34         2.53         2.14        31.40        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-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS 
        1.81        10.59         2.20         3.98        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        48.53        76.60        67.36 
TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       30.67        15.35        26.17        24.66         0.10         0.53 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.56         0.66         1.38         0.82        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-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       22.45        16.47         5.52        46.78        19.79         1.97 
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-A5BX TCGA-FD-A62O TCGA-FD-A62P 
       37.15        11.01         6.87         5.69         4.83         6.28 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 
       50.66         9.30         4.11         2.66         4.01         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES 
        3.48         3.25        30.61         5.69        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
        7.04         0.85         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         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO 
        4.41         6.41         5.69         4.14         6.67         1.51 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB 
        3.45         4.67         6.48        10.52         1.81         4.27 
TCGA-K4-A83P TCGA-PQ-A6FI TCGA-XF-A8HE 
        6.38        12.23        97.45 

  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               9.30 
[1] "0.1 - 123.8 (8.2)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED          1       1       18        28       23
  15Q LOSS WILD-TYPE        0       1       50        44       44
D67V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  1                  1
  STAGE II                18                 50
  STAGE III               28                 44
  STAGE IV                23                 44
[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         16 39  9
  15Q LOSS WILD-TYPE       46 62 23
D67V4, multiclass
          clus
vv         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1+T2               16                 46
  T3                     39                 62
  T4                      9                 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
  15Q LOSS MUTATED   44  9 11  2
  15Q LOSS WILD-TYPE 86 13 27  5
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               44                 86
  N1                9                 13
  N2               11                 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
  15Q LOSS MUTATED   28  2 43
  15Q LOSS WILD-TYPE 78  3 59
D67V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               28                 78
  M1                2                  3
  MX               43                 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"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    17  56
  15Q LOSS WILD-TYPE  33 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     17   56
  15Q LOSS WILD-TYPE   33  108
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               17                 33
  MALE                 56                108
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
D67V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       4                         2    62
  15Q LOSS WILD-TYPE    18                         9   108
D67V11, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    4                 18
  BLACK OR AFRICAN AMERICAN                2                  9
  WHITE                                   62                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    47  13
  16P LOSS WILD-TYPE 104  44
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                60                148 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                13                 44 
$`16P LOSS MUTATED`
TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A3PJ TCGA-BT-A42E TCGA-CF-A1HS TCGA-CU-A0YN 
       32.84         5.06        12.82         9.99         0.43        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AC TCGA-DK-A2HX 
        5.46         5.19         1.84         2.53       130.88         1.81 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B1 
      123.85        87.32        21.30        10.55        17.98        67.36 
TCGA-DK-A6B6 TCGA-E7-A541 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3SO TCGA-FD-A3SP 
       30.67         0.59        12.89         6.87         5.52        13.18 
TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       22.98        12.13        13.38         5.36        27.45         2.66 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 
        4.83         6.38         6.71         4.11         2.20        15.19 
TCGA-G2-A2EF TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
       61.94        20.12        15.91        14.07         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3JZ 
        7.73         2.10         2.20         6.41         6.15         5.69 
TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        7.79        11.54        38.60         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HF TCGA-XF-A8HG 
        1.81         3.45        13.48        12.23        56.19        15.35 

$`16P LOSS WILD-TYPE`
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-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       11.93        19.04        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-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
        3.65         4.67         2.07        15.42        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
        8.98         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-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        7.20        16.31         9.34         2.14        31.40        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-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-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       10.49        50.27        20.02         9.67         8.28       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
       48.00        64.18        48.53        76.60        15.68        32.28 
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-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV 
        0.53         0.56         0.66         1.38         0.82         1.22 
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-A3SQ 
       45.93        24.30        22.45        16.47        12.82        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-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-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI 
       49.68         6.28        50.66         9.30         2.66         4.01 
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-A3VY 
        5.69        26.93        35.24        17.26         7.04         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GD-A3OQ 
        2.89         2.24        15.81         4.50        17.75         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF 
       20.98         7.66        11.31         4.41         6.41         7.63 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.67         6.41        19.07         1.51         6.74 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P 
        8.75         3.45         4.67         2.50         4.27         6.38 
TCGA-LC-A66R TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
        6.35        16.67        88.93        97.45 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.43               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            130.88             140.81 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              8.89               8.55 
[1] "0.4 - 130.9 (8.9)" "0.1 - 140.8 (8.6)"
[1] "hr=" "1.3"
D68V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED          1       0       15        26       16
  16P LOSS WILD-TYPE        0       2       53        46       51
D68V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                15                 53
  STAGE III               26                 46
  STAGE IV                16                 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
  16P LOSS MUTATED         14 36  5
  16P LOSS WILD-TYPE       48 65 27
D68V4, multiclass
          clus
vv         16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1+T2               14                 48
  T3                     36                 65
  T4                      5                 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
  16P LOSS MUTATED   37  7 10  2
  16P LOSS WILD-TYPE 93 15 28  5
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               37                 93
  N1                7                 15
  N2               10                 28
  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 37
  16P LOSS WILD-TYPE 83  5 65
D68V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               23                 83
  M1                0                  5
  MX               37                 65
[1] 3 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    13  47
  16P LOSS WILD-TYPE  37 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     13   47
  16P LOSS WILD-TYPE   37  117
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               13                 37
  MALE                 47                117
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
D68V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       2                         1    55
  16P LOSS WILD-TYPE    20                        10   115
D68V11, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    2                 20
  BLACK OR AFRICAN AMERICAN                1                 10
  WHITE                                   55                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"

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    39  14
  16Q LOSS WILD-TYPE 112  43
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                53                155 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                 43 
$`16Q LOSS MUTATED`
TCGA-BT-A42E TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 
        9.99         0.43        12.92         5.19         1.84         2.53 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IT TCGA-DK-A3IV 
      130.88         1.81       123.85        87.32        21.30         9.67 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 
       17.98        67.36        30.67        15.35         0.49         0.59 
TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR 
        5.52         1.97        22.98        14.93        12.13        13.38 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TD TCGA-FD-A6TE 
        5.36        27.45         2.66         4.83         6.71         4.11 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OP 
       15.19         6.48        20.12        15.91        14.07         2.10 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH 
        2.20         6.41         4.41         6.15         5.69         7.79 
TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 
       38.60         4.67         6.48         1.74         1.81         3.45 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        12.23        97.45        56.19        15.35 

$`16Q LOSS WILD-TYPE`
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-A3KJ TCGA-CU-A3YL 
        0.10         0.10         4.90         7.20         5.46        16.31 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.14        31.40        18.41        19.00         8.91 
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-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-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 
       48.53        76.60        15.68        32.28        43.59        26.17 
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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.82         1.22        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-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       22.45        16.47        12.82        13.18        46.78        19.79 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.93        14.96         3.62        37.15        11.01         6.87 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A62S 
        5.69         6.84         6.87        49.68         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
       50.66         9.30         2.66         2.20         4.01         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-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3BM 
       26.93        35.24        17.26         7.04         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        2.24        15.81         4.50        17.75         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW 
        7.73         3.12        20.98         7.66        11.31         6.41 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        7.63         4.14         6.67         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R 
        1.51         6.74         8.75         3.45         2.50        10.52 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FN TCGA-XF-A8HD 
        4.27         6.38         6.35        16.67        88.93 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.43               0.07 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            130.88             140.81 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              7.79               8.75 
[1] "0.4 - 130.9 (7.8)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1"  
D69V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED          0       0       14        20       17
  16Q LOSS WILD-TYPE        1       2       54        52       50
D69V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                14                 54
  STAGE III               20                 52
  STAGE IV                17                 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
  16Q LOSS MUTATED         12 28  8
  16Q LOSS WILD-TYPE       50 73 24
D69V4, multiclass
          clus
vv         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1+T2               12                 50
  T3                     28                 73
  T4                      8                 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
  16Q LOSS MUTATED    28   6  11   2
  16Q LOSS WILD-TYPE 102  16  27   5
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               28                102
  N1                6                 16
  N2               11                 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
  16Q LOSS MUTATED   20  0 33
  16Q LOSS WILD-TYPE 86  5 69
D69V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               20                 86
  M1                0                  5
  MX               33                 69
[1] 3 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     8  45
  16Q LOSS WILD-TYPE  42 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8   45
  16Q LOSS WILD-TYPE   42  119
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                8                 42
  MALE                 45                119
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
D69V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       3                         0    48
  16Q LOSS WILD-TYPE    19                        11   122
D69V11, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    3                 19
  BLACK OR AFRICAN AMERICAN                0                 11
  WHITE                                   48                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"

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   61 27
  17P LOSS WILD-TYPE 90 30
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                88                120 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                27                 30 
$`17P LOSS MUTATED`
TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       12.39        19.04        32.84        17.88        19.50        14.89 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42E 
        8.25        17.16         5.59         4.67         2.07         9.99 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3KJ 
        1.94         0.46         0.43         0.69         0.10         5.46 
TCGA-CU-A5W6 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IL 
        1.84         8.91       112.44         1.81        87.32         3.98 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 
        8.22        10.49        50.27        21.30         9.67        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       17.98        64.18        32.28        43.59        15.35        26.17 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.49         0.59         0.56         1.38        15.68         8.94 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS 
       45.93        24.30        12.82         5.52        46.78         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV 
       22.98        14.93        14.93         3.62        13.38         5.36 
TCGA-FD-A5BY TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD 
        6.84         4.83         6.28         6.38        50.66         6.71 
TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
        2.66         3.48        61.94        30.61        26.93        35.24 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS 
        7.04        20.12         0.85         2.89        14.07         1.12 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3QF 
        2.10         2.20         7.66        11.31         6.41         7.63 
TCGA-H4-A2HQ TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.74         6.48         1.74         4.27        12.23        16.67 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        97.45        56.19        15.35 

$`17P LOSS WILD-TYPE`
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-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LD 
       12.16         5.06        14.96         5.06         8.35         3.65 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
       12.82        15.42        28.70        28.41         8.98        23.01 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN 
        0.13         0.07         0.10         0.07         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         7.20         5.19        16.31         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE 
        2.14        31.40        18.41        19.00       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        10.59         7.79       123.85         2.20 
TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW 
        7.82        20.02         8.28        10.55       140.81        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       76.60        67.36        15.68        30.67        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B6 
        0.53         0.66         0.82         1.22        12.89         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.43        11.93        15.88        22.45        16.47 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       13.18        19.79        14.96        12.13        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        6.87         5.69        27.45         6.87        49.68         2.66 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        9.30         4.11         2.20         4.01        15.19         7.13 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2ES TCGA-GC-A3I6 
        4.08         3.25         6.48         5.69        17.26         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.81         4.50        15.91        17.75         2.66         7.73 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
        3.12        20.98         6.41         4.41         6.15         5.69 
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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        1.51        38.60         8.75         3.45         4.67         2.50 
TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       10.52         1.81         6.38         6.35         3.45        13.48 

  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 
             9.305              8.050 
[1] "0.1 - 112.4 (9.3)" "0.1 - 140.8 (8.1)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED          0       0       31        28       28
  17P LOSS WILD-TYPE        1       2       37        44       39
D70V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                31                 37
  STAGE III               28                 44
  STAGE IV                28                 39
[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         27 42 11
  17P LOSS WILD-TYPE       35 59 21
D70V4, multiclass
          clus
vv         17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1+T2               27                 35
  T3                     42                 59
  T4                     11                 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
  17P LOSS MUTATED   55  7 17  2
  17P LOSS WILD-TYPE 75 15 21  5
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               55                 75
  N1                7                 15
  N2               17                 21
  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   42  2 45
  17P LOSS WILD-TYPE 64  3 57
D70V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               42                 64
  M1                2                  3
  MX               45                 57
[1] 3 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   20 70
  17P LOSS WILD-TYPE 30 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     20   70
  17P LOSS WILD-TYPE   30   94
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               20                 30
  MALE                 70                 94
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, continuous
D70V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED      11                         6    69
  17P LOSS WILD-TYPE    11                         5   101
D70V11, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                   11                 11
  BLACK OR AFRICAN AMERICAN                6                  5
  WHITE                                   69                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    19   5
  17Q LOSS WILD-TYPE 132  52
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                184 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 52 
$`17Q LOSS MUTATED`
TCGA-BT-A20P TCGA-BT-A2LA TCGA-CF-A1HR TCGA-CF-A1HS TCGA-DK-A1AB TCGA-DK-A3IN 
       17.88        17.16         0.46         0.43         8.91         8.22 
TCGA-DK-A6AV TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A43N 
       64.18        15.35        26.17        45.93         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A62S TCGA-FJ-A3ZE TCGA-G2-A3IB 
       14.93        14.93         3.62         6.38         3.48         7.04 
TCGA-G2-A3IE TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GV-A3JW TCGA-K4-A4AC TCGA-PQ-A6FN 
       20.12         1.12         2.10         6.41         6.48        16.67 

$`17Q LOSS WILD-TYPE`
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-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-A27C 
        9.99        28.41         8.98         1.94        23.01         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-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        31.40        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-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-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-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       48.53        76.60        67.36        15.68        32.28        30.67 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       43.59        24.66         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.56         0.66         1.38         0.82         1.22        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-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        24.30        22.45        16.47        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR 
       13.18        46.78        19.79        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-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45         6.87        49.68         2.66         4.83         6.28 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       50.66         9.30         6.71         4.11         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        4.01        15.19         7.13         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-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        0.85         2.89         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07        17.75         2.66         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX 
        2.20         6.41         7.66        11.31         4.41         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-K4-A3WS 
       19.07        11.54         1.51         6.74        38.60         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-MV-A51V TCGA-PQ-A6FI 
        4.27         6.38         6.35         3.45        13.48        12.23 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        97.45        56.19        15.35 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.43               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             64.18             140.81 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             8.565              8.550 
[1] "0.4 - 64.2 (8.6)"  "0.1 - 140.8 (8.6)"
[1] "hr=" "1.3"
D71V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED          0       0       10         6        7
  17Q LOSS WILD-TYPE        1       2       58        66       60
D71V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                10                 58
  STAGE III                6                 66
  STAGE IV                 7                 60
[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          8  8  6
  17Q LOSS WILD-TYPE       54 93 26
D71V4, multiclass
          clus
vv         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1+T2                8                 54
  T3                      8                 93
  T4                      6                 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
  17Q LOSS MUTATED    15   1   3   2
  17Q LOSS WILD-TYPE 115  21  35   5
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               15                115
  N1                1                 21
  N2                3                 35
  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 15
  17Q LOSS WILD-TYPE 97  4 87
D71V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                9                 97
  M1                1                  4
  MX               15                 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"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     7  18
  17Q LOSS WILD-TYPE  43 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   18
  17Q LOSS WILD-TYPE   43  146
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                7                 43
  MALE                 18                146
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, continuous
D71V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       4                         3    17
  17Q LOSS WILD-TYPE    18                         8   153
D71V11, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    4                 18
  BLACK OR AFRICAN AMERICAN                3                  8
  WHITE                                   17                153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    33  14
  18P LOSS WILD-TYPE 118  43
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                47                161 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                14                 43 
$`18P LOSS MUTATED`
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20X TCGA-BT-A2LA 
       19.04        32.84         5.06        14.89         8.25        17.16 
TCGA-BT-A42B TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CU-A5W6 TCGA-CU-A72E 
       15.42         0.46         0.13         0.07         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF 
        2.53         2.14        18.41         8.91       112.44        17.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 
        1.81        10.59        10.49        50.27        21.30        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A5KE 
       64.18        15.68        32.28        43.59        24.66         0.56 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A62O 
        1.22         4.01        24.30        12.82        46.78         4.83 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS 
        6.38        50.66        20.12         2.89        14.07         1.12 
TCGA-GV-A3JW TCGA-GV-A40E TCGA-HQ-A2OE TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.41         6.41        38.60        12.23        16.67 

$`18P LOSS WILD-TYPE`
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-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V 
       11.93        12.16        17.88        19.50        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         5.59         3.65         4.67        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-A1HS TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.43         0.69         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-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I2 
       31.40        19.00       130.88        16.14        15.62         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-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-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 
       48.53        76.60        67.36        30.67        15.35        26.17 
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-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 
        0.82        12.89        15.68         8.94         6.87        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
       11.93        15.88        45.93        22.45        16.47         5.52 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       13.18        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-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-A62P TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       49.68         2.66         6.28         9.30         6.71         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.66         2.20         4.01        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-A3IB TCGA-G2-A3VY TCGA-GC-A3I6 
       26.93        35.24        17.26         7.04         0.85         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.81         4.50        15.91        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         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       11.31         4.41         6.15         5.69         7.63         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-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-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        88.93        97.45        56.19        15.35 

  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 
             12.82               7.79 
[1] "0.1 - 112.4 (12.8)" "0.1 - 140.8 (7.8)" 
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED          0       0       17        10       21
  18P LOSS WILD-TYPE        1       2       51        62       46
D72V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                17                 51
  STAGE III               10                 62
  STAGE IV                21                 46
[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         18 25  5
  18P LOSS WILD-TYPE       44 76 27
D72V4, multiclass
          clus
vv         18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1+T2               18                 44
  T3                     25                 76
  T4                      5                 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
  18P LOSS MUTATED    24   6  14   1
  18P LOSS WILD-TYPE 106  16  24   6
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               24                106
  N1                6                 16
  N2               14                 24
  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   31  0 19
  18P LOSS WILD-TYPE 75  5 83
D72V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               31                 75
  M1                0                  5
  MX               19                 83
[1] 3 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    13  37
  18P LOSS WILD-TYPE  37 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     13   37
  18P LOSS WILD-TYPE   37  127
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               13                 37
  MALE                 37                127
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, continuous
D72V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       8                         2    37
  18P LOSS WILD-TYPE    14                         9   133
D72V11, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    8                 14
  BLACK OR AFRICAN AMERICAN                2                  9
  WHITE                                   37                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"

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   57 17
  18Q LOSS WILD-TYPE 94 40
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                74                134 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                17                 40 
$`18Q LOSS MUTATED`
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A20X 
       19.04        32.84         5.06        14.89         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42C TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
       17.16        15.42        28.70         0.46         0.43         0.13 
TCGA-CF-A47T TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
        0.07        12.92         7.20         1.84         9.34         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-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32         2.20         3.98        10.49        50.27        21.30 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 
       48.00        64.18        15.68        32.28        43.59        24.66 
TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SN 
        0.56         1.22        15.68         4.01        45.93        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A62N 
        5.52        13.18        46.78         1.97        22.98         2.66 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-G2-A2EF TCGA-G2-A3IE TCGA-GC-A3BM 
        4.83         6.38        50.66        61.94        20.12         2.89 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GD-A6C6 
       15.91        14.07         1.12         2.66        20.98         2.20 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
        6.41         6.15         6.41        19.07        11.54         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
       38.60         8.75         4.67         6.35        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HF 
       16.67        56.19 

$`18Q LOSS WILD-TYPE`
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-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V 
       11.93        12.16        17.88        19.50        14.96         5.06 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E 
        5.59         3.65         4.67        12.82         2.07         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47V 
       28.41         8.98         1.94        23.01         0.69         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.07         0.10         0.10         4.90         5.46         5.19 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE 
       16.31         2.53        31.40        19.00       130.88        16.14 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU 
       15.62         7.79       123.85         7.82         8.22        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        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 
       76.60        67.36        30.67        15.35        26.17         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-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        16.47        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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       49.68         6.28         9.30         6.71         4.11         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.20         4.01        15.19         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25         6.48        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       17.26         7.04         0.85         2.24        15.81         4.50 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42P TCGA-GU-A42Q 
       17.75         7.73         2.10         3.12         6.41         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       11.31         4.41         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        6.67         1.51         3.45         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-XF-A8HD 
        1.74         1.81         4.27         6.38         3.45        88.93 
TCGA-XF-A8HE TCGA-XF-A8HG 
       97.45        15.35 

  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 
            11.885              7.695 
[1] "0.1 - 112.4 (11.9)" "0.1 - 140.8 (7.7)" 
[1] "hr=" "1.6"
D73V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED          1       0       25        21       26
  18Q LOSS WILD-TYPE        0       2       43        51       41
D73V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                25                 43
  STAGE III               21                 51
  STAGE IV                26                 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
  18Q LOSS MUTATED         25 37  8
  18Q LOSS WILD-TYPE       37 64 24
D73V4, multiclass
          clus
vv         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1+T2               25                 37
  T3                     37                 64
  T4                      8                 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
  18Q LOSS MUTATED   44  8 15  2
  18Q LOSS WILD-TYPE 86 14 23  5
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               44                 86
  N1                8                 14
  N2               15                 23
  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   41  1 34
  18Q LOSS WILD-TYPE 65  4 68
D73V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               41                 65
  M1                1                  4
  MX               34                 68
[1] 3 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    21  55
  18Q LOSS WILD-TYPE  29 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     21   55
  18Q LOSS WILD-TYPE   29  109
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               21                 29
  MALE                 55                109
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, continuous
D73V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       9                         4    58
  18Q LOSS WILD-TYPE    13                         7   112
D73V11, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    9                 13
  BLACK OR AFRICAN AMERICAN                4                  7
  WHITE                                   58                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"

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    33  22
  19P LOSS WILD-TYPE 118  35
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                55                153 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                 35 
$`19P LOSS MUTATED`
TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       19.04         5.06         5.06         5.59         3.65         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A1A5 
        2.07        15.42         9.99         8.98        12.92         2.14 
TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
      112.44        87.32         3.98         8.22        10.49        21.30 
TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A7DV TCGA-FD-A3SJ TCGA-FD-A3SM 
       17.98        43.59         0.49         1.22        24.30        16.47 
TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A5BV TCGA-FD-A5BY 
        5.52         1.97        22.98        14.93         5.36         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       27.45         6.87        49.68         4.11         3.48         4.08 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GC-A3RB 
        6.48        17.26         7.04        20.12         2.24         4.50 
TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GV-A3JZ TCGA-H4-A2HQ 
        2.66         2.20         6.41         7.66         5.69         6.74 
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 
       16.67 

$`19P LOSS WILD-TYPE`
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-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       11.93        32.84        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42C 
       14.96         8.35         8.25        17.16        12.82        28.70 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         1.94        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-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.53        31.40        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IU 
        7.79       123.85         2.20         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 
       48.53        76.60        67.36        15.68        32.28        30.67 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 
       15.35        26.17        24.66         0.10         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.56         0.66         1.38         0.82        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-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       45.93        22.45        12.82        13.18        46.78        19.79 
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-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       11.01         6.87         5.69         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH 
        6.38        50.66         9.30         6.71         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
        4.01        15.19         7.13         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3OO 
        5.69        26.93        35.24         0.85         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-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        3.12        20.98        11.31         4.41         6.41         6.15 
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-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       11.54         1.51        38.60         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-XF-A8HD 
        6.48         1.81         4.27         6.38         3.45        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       97.45        56.19        15.35 

  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 
              6.87               9.34 
[1] "0.5 - 112.4 (6.9)" "0.1 - 140.8 (9.3)"
[1] "hr=" "2.1"
D74V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED          0       0       12        18       25
  19P LOSS WILD-TYPE        1       2       56        54       42
D74V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                12                 56
  STAGE III               18                 54
  STAGE IV                25                 42
[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         12 32  6
  19P LOSS WILD-TYPE       50 69 26
D74V4, multiclass
          clus
vv         19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1+T2               12                 50
  T3                     32                 69
  T4                      6                 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
  19P LOSS MUTATED    27   9  11   4
  19P LOSS WILD-TYPE 103  13  27   3
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               27                103
  N1                9                 13
  N2               11                 27
  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
  19P LOSS MUTATED   22  4 29
  19P LOSS WILD-TYPE 84  1 73
D74V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               22                 84
  M1                4                  1
  MX               29                 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"
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    14  41
  19P LOSS WILD-TYPE  36 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     14   41
  19P LOSS WILD-TYPE   36  123
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               14                 36
  MALE                 41                123
[1] 2 2
[1] FALSE
D74V8, continuous
D74V9, continuous
D74V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         4    48
  19P LOSS WILD-TYPE    21                         7   122
D74V11, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                 21
  BLACK OR AFRICAN AMERICAN                4                  7
  WHITE                                   48                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"

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    21  13
  19Q LOSS WILD-TYPE 130  44
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                34                174 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                 44 
$`19Q LOSS MUTATED`
TCGA-BT-A20R TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-C4-A0EZ 
        5.06         3.65         4.67         2.07        15.42         8.98 
TCGA-CU-A0YN TCGA-DK-A1AD TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X2 
       12.92       112.44         8.22        10.49        21.30        17.98 
TCGA-E7-A4IJ TCGA-FD-A3SO TCGA-FD-A43P TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 
        0.49         5.52        14.93         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-K4-A54R TCGA-K4-A5RJ TCGA-LC-A66R 
        2.24         4.50         2.20        10.52         1.74         6.35 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        3.45        13.48        12.23        16.67 

$`19Q LOSS WILD-TYPE`
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-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        5.59        12.82        28.70         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-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-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        31.40        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-A3IS 
      123.85        87.32         2.20         3.98         7.82        50.27 
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-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        48.53        76.60        67.36        15.68        32.28 
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-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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.22        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-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       16.47        12.82        13.18        46.78        19.79         1.97 
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-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       37.15        11.01         6.87         5.69        27.45         6.87 
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-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.71         2.66         2.20         4.01        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-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       35.24         0.85         2.89        15.81        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-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
       20.98         6.41         7.66        11.31         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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A6FZ 
        8.75         3.45         4.67         2.50         6.48         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        4.27         6.38        88.93        97.45        56.19        15.35 

  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              8.925 
[1] "0.5 - 112.4 (6.9)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.9"
D75V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED          0       0       10        12       12
  19Q LOSS WILD-TYPE        1       2       58        60       55
D75V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                10                 58
  STAGE III               12                 60
  STAGE IV                12                 55
[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 22  2
  19Q LOSS WILD-TYPE       56 79 30
D75V4, multiclass
          clus
vv         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1+T2                6                 56
  T3                     22                 79
  T4                      2                 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
  19Q LOSS MUTATED    18   5   6   1
  19Q LOSS WILD-TYPE 112  17  32   6
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               18                112
  N1                5                 17
  N2                6                 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
  19Q LOSS MUTATED   13  2 19
  19Q LOSS WILD-TYPE 93  3 83
D75V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               13                 93
  M1                2                  3
  MX               19                 83
[1] 3 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     7  27
  19Q LOSS WILD-TYPE  43 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      7   27
  19Q LOSS WILD-TYPE   43  137
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                7                 43
  MALE                 27                137
[1] 2 2
[1] FALSE
D75V8, continuous
D75V9, continuous
D75V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         2    30
  19Q LOSS WILD-TYPE    21                         9   140
D75V11, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                 21
  BLACK OR AFRICAN AMERICAN                2                  9
  WHITE                                   30                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    12   4
  20P LOSS WILD-TYPE 139  53
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                16                192 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                 53 
$`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-A3X1 TCGA-DK-A6AV TCGA-FD-A5C0 TCGA-G2-A3VY TCGA-GU-A42R TCGA-GV-A3JZ 
       48.00        64.18         6.87         0.85        11.31         5.69 
TCGA-GV-A40E TCGA-HQ-A2OE TCGA-K4-A4AC TCGA-XF-A8HE 
        6.41        38.60         6.48        97.45 

$`20P LOSS WILD-TYPE`
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        31.40        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-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        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
       76.60        67.36        15.68        32.28        30.67        43.59 
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-A7DV 
        0.59         0.56         0.66         1.38         0.82         1.22 
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        16.47 
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-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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.38        50.66         9.30         6.71         4.11         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.20         4.01        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-GC-A3BM TCGA-GC-A3I6 
       35.24        17.26         7.04        20.12         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-A42P TCGA-GU-A42Q TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF 
        6.41         7.66         4.41         6.41         6.15         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-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        6.74         8.75         3.45         4.67         2.50        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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        12.23        16.67        88.93        56.19        15.35 

  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 
             9.565              8.550 
[1] "0.1 - 97.5 (9.6)"  "0.1 - 140.8 (8.6)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED          0       0        7         5        3
  20P LOSS WILD-TYPE        1       2       61        67       64
D76V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 7                 61
  STAGE III                5                 67
  STAGE IV                 3                 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
  20P LOSS MUTATED          5  7  1
  20P LOSS WILD-TYPE       57 94 31
D76V4, multiclass
          clus
vv         20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1+T2                5                 57
  T3                      7                 94
  T4                      1                 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
  20P LOSS MUTATED     9   0   3   1
  20P LOSS WILD-TYPE 121  22  35   6
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                9                121
  N1                0                 22
  N2                3                 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
  20P LOSS MUTATED     6   0   9
  20P LOSS WILD-TYPE 100   5  93
D76V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                6                100
  M1                0                  5
  MX                9                 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"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3  13
  20P LOSS WILD-TYPE  47 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3   13
  20P LOSS WILD-TYPE   47  151
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                 47
  MALE                 13                151
[1] 2 2
[1] FALSE
D76V8, continuous
D76V9, continuous
D76V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       3                         0    11
  20P LOSS WILD-TYPE    19                        11   159
D76V11, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    3                 19
  BLACK OR AFRICAN AMERICAN                0                 11
  WHITE                                   11                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"

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     3   2
  20Q LOSS WILD-TYPE 148  55
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                203 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 55 
$`20Q LOSS MUTATED`
TCGA-BT-A20P TCGA-BT-A20V TCGA-DK-A1A3 TCGA-DK-A2I6 TCGA-GV-A3JZ 
       17.88         5.06         2.53        87.32         5.69 

$`20Q LOSS WILD-TYPE`
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        31.40 
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-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        48.53        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       15.68        32.28        30.67        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        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-A3SN TCGA-FD-A3SO 
       45.93        24.30        22.45        16.47        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-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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       50.66         9.30         6.71         4.11         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.01        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-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         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-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        6.41         7.66        11.31         4.41         6.41         6.15 
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-K4-A3WS TCGA-K4-A3WU 
       11.54         1.51         6.74        38.60         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-MV-A51V TCGA-PQ-A6FI 
        4.27         6.38         6.35         3.45        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        88.93        97.45        56.19        15.35 

  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 
              5.69               8.75 
[1] "2.5 - 87.3 (5.7)"  "0.1 - 140.8 (8.8)"
[1] "hr=" "1.5"
D77V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED          0       0        0         1        4
  20Q LOSS WILD-TYPE        1       2       68        71       63
D77V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE 0A                 0                  1
  STAGE I                  0                  2
  STAGE II                 0                 68
  STAGE III                1                 71
  STAGE IV                 4                 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
  20Q LOSS MUTATED          1  2  2
  20Q LOSS WILD-TYPE       61 99 30
D77V4, multiclass
          clus
vv         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1+T2                1                 61
  T3                      2                 99
  T4                      2                 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
  20Q LOSS MUTATED     1   1   2   1
  20Q LOSS WILD-TYPE 129  21  36   6
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                1                129
  N1                1                 21
  N2                2                 36
  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
  20Q LOSS MUTATED     4   0   1
  20Q LOSS WILD-TYPE 102   5 101
D77V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                4                102
  M1                0                  5
  MX                1                101
[1] 3 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     2   3
  20Q LOSS WILD-TYPE  48 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    3
  20Q LOSS WILD-TYPE   48  161
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                 48
  MALE                  3                161
[1] 2 2
[1] FALSE
D77V8, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 59 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CF-A3MF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CF-A3MG         TCGA-CF-A3MH         TCGA-CF-A3MI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CF-A47S         TCGA-CF-A47T         TCGA-CF-A47V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CF-A47W         TCGA-CF-A47X         TCGA-CF-A47Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A3IN         TCGA-DK-A3IV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DK-A3WX         TCGA-DK-A3X2         TCGA-DK-A6B2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DK-A6B5         TCGA-DK-A6B6         TCGA-E5-A2PC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E5-A4TZ         TCGA-E5-A4U1         TCGA-E7-A519 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-E7-A541         TCGA-E7-A7DV         TCGA-FT-A61P 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G2-A3IB         TCGA-G2-A3IE         TCGA-G2-A3VY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GC-A3BM         TCGA-GC-A3I6         TCGA-GC-A3OO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GC-A3RC         TCGA-GC-A3RD         TCGA-GC-A3YS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GC-A6I1         TCGA-GD-A3OS         TCGA-GD-A6C6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GV-A3JV         TCGA-GV-A3JW         TCGA-GV-A3JX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GV-A3QF         TCGA-GV-A3QH         TCGA-GV-A3QI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GV-A3QK         TCGA-GV-A40E         TCGA-GV-A40G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GV-A6ZA         TCGA-XF-A8HD         TCGA-XF-A8HE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-XF-A8HF         TCGA-XF-A8HG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V9, continuous
D77V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         1     4
  20Q LOSS WILD-TYPE    22                        10   166
D77V11, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                 22
  BLACK OR AFRICAN AMERICAN                1                 10
  WHITE                                    4                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    22  12
  21Q LOSS WILD-TYPE 129  45
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                34                174 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                12                 45 
$`21Q LOSS MUTATED`
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A47X 
       14.89         5.06         8.25         9.99         0.46         0.10 
TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A6B6 
       12.92         5.19         1.84         8.22        10.49        30.67 
TCGA-E5-A2PC TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43X TCGA-FD-A43Y 
       43.59         8.94        22.45         5.52         3.62        12.13 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FD-A6TD TCGA-G2-A2EF TCGA-G2-A2EJ 
        5.36         6.84        50.66         6.71        61.94        30.61 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-K4-A4AB 
        1.12         2.66         4.41         4.14        11.54         2.50 
TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-XF-A8HG 
        6.48         1.74         3.45        15.35 

$`21Q LOSS WILD-TYPE`
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-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06        14.96         8.35        17.16         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
        4.67        12.82         2.07        15.42        28.70        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-A47Y TCGA-CU-A0YO TCGA-CU-A0YR 
        0.07         0.10         0.07         0.10         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.46        16.31         9.34         2.53         2.14        31.40 
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-A3IS TCGA-DK-A3IT 
       87.32         2.20         3.98         7.82        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        48.53        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       32.28        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-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        1.22        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-A3SN 
       11.93        15.88        45.93        24.30        16.47        12.82 
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-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        14.93        13.38        37.15        11.01         6.87 
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-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-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.01        15.19         7.13         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        6.48         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12         0.85         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-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW 
       20.98         2.20         6.41         7.66        11.31         6.41 
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-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07         1.51         6.74        38.60         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-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       13.48        12.23        16.67        88.93        97.45        56.19 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             61.94             140.81 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             6.775              9.140 
[1] "0.1 - 61.9 (6.8)"  "0.1 - 140.8 (9.1)"
[1] "hr=" "1.7"
D78V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED          1       0        9        12       11
  21Q LOSS WILD-TYPE        0       2       59        60       56
D78V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                 9                 59
  STAGE III               12                 60
  STAGE IV                11                 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
  21Q LOSS MUTATED          9 14  7
  21Q LOSS WILD-TYPE       53 87 25
D78V4, multiclass
          clus
vv         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1+T2                9                 53
  T3                     14                 87
  T4                      7                 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
  21Q LOSS MUTATED    21   7   4   0
  21Q LOSS WILD-TYPE 109  15  34   7
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               21                109
  N1                7                 15
  N2                4                 34
  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   13  1 20
  21Q LOSS WILD-TYPE 93  4 82
D78V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               13                 93
  M1                1                  4
  MX               20                 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"
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     6  28
  21Q LOSS WILD-TYPE  44 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6   28
  21Q LOSS WILD-TYPE   44  136
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                6                 44
  MALE                 28                136
[1] 2 2
[1] FALSE
D78V8, continuous
D78V9, continuous
D78V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       2                         2    29
  21Q LOSS WILD-TYPE    20                         9   141
D78V11, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    2                 20
  BLACK OR AFRICAN AMERICAN                2                  9
  WHITE                                   29                141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   60 23
  22Q LOSS WILD-TYPE 91 34
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                83                125 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                23                 34 
$`22Q LOSS MUTATED`
TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        2.66        19.04         5.06        15.42        28.70         9.99 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
        8.98         1.94         0.10        12.92         5.46         5.19 
TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL 
       18.41         1.81        10.59         7.79       123.85         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 
        7.82         8.22        10.49        21.30         9.67        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A5KE 
       67.36        15.68        32.28        43.59        15.35         0.56 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 
        1.22        12.89        15.68         8.94         6.87        11.93 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       24.30        12.82         5.52        19.79         1.97        22.98 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       14.93        12.13         5.36         6.84        27.45         6.87 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 
        2.66         6.28         9.30         6.71         4.11        15.19 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3RC 
        4.08         6.48         7.04        20.12         0.85        15.91 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q 
        1.12         2.66         7.73         2.10         2.20         7.66 
TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-K4-A3WS 
       11.31         6.15        19.07        11.54         6.74         8.75 
TCGA-K4-A3WU TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 
        3.45         1.74         1.81         4.27         6.35         3.45 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        12.23        16.67        56.19        15.35 

$`22Q LOSS WILD-TYPE`
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-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-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-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
        4.67        12.82         2.07        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-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        0.10         4.90         7.20        16.31         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.53         2.14        31.40        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK 
      112.44        16.14        17.62        15.62        87.32         2.20 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       50.27        20.02         8.28        10.55       140.81        48.00 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 
       64.18        48.53        76.60        30.67        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-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
        0.82         4.01        12.43        15.88        45.93        22.45 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
       16.47        13.18        46.78        14.93        14.96         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 
       13.38        37.15        11.01         6.87         5.69        49.68 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        4.83         6.38        50.66         2.66         2.20         4.01 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        7.13         3.48         3.25        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       26.93        35.24        17.26         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P 
        4.50        14.07        17.75         3.12        20.98         6.41 
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-K4-A3WV TCGA-K4-A4AB 
        6.67         6.41         1.51        38.60         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A83P TCGA-XF-A8HD TCGA-XF-A8HE 
        6.48        10.52         6.38        88.93        97.45 

  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 
              8.75               8.35 
[1] "0.1 - 123.8 (8.8)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.2"
D79V2, continuous
                    vv
clus                 STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED          1       0       22        28       33
  22Q LOSS WILD-TYPE        0       2       46        44       34
D79V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE 0A                 1                  0
  STAGE I                  0                  2
  STAGE II                22                 46
  STAGE III               28                 44
  STAGE IV                33                 34
[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         20 40 15
  22Q LOSS WILD-TYPE       42 61 17
D79V4, multiclass
          clus
vv         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1+T2               20                 42
  T3                     40                 61
  T4                     15                 17
[1] 3 2
[1] 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   46 11 17  3
  22Q LOSS WILD-TYPE 84 11 21  4
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               46                 84
  N1               11                 11
  N2               17                 21
  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   31  2 50
  22Q LOSS WILD-TYPE 75  3 52
D79V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               31                 75
  M1                2                  3
  MX               50                 52
[1] 3 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    21  63
  22Q LOSS WILD-TYPE  29 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     21   63
  22Q LOSS WILD-TYPE   29  101
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               21                 29
  MALE                 63                101
[1] 2 2
[1] FALSE
D79V8, continuous
D79V9, continuous
D79V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       5                         5    69
  22Q LOSS WILD-TYPE    17                         6   101
D79V11, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    5                 17
  BLACK OR AFRICAN AMERICAN                5                  6
  WHITE                                   69                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    31   8
  XQ LOSS WILD-TYPE 120  49
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39               169 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                8                49 
$`XQ LOSS MUTATED`
TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47X 
       14.89         5.59         4.67        15.42         0.69         0.10 
TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IT 
        5.19         2.14         8.91        87.32        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-FD-A3B4 TCGA-FD-A3SN 
        9.67        32.28        43.59        24.66        15.68        12.82 
TCGA-FD-A3SS TCGA-FD-A5BY TCGA-FD-A62N TCGA-FJ-A3Z7 TCGA-G2-A2EL TCGA-G2-A3IB 
        1.97         6.84         2.66        15.19        26.93         7.04 
TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A3QI 
        2.66         2.20         6.41        11.31         6.15         4.14 
TCGA-GV-A40G TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
       19.07        38.60         4.67        10.52         1.74         1.81 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-XF-A8HF 
        3.45        12.23        56.19 

$`XQ LOSS WILD-TYPE`
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-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        3.65        12.82         2.07        28.70         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
        8.98         1.94        23.01         0.46         0.43         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-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        7.20         5.46        16.31         1.84         9.34         2.53 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       31.40        18.41        19.00       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-A3IU 
        2.20         3.98         7.82         8.22        10.49        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-A6B6 TCGA-E5-A4TZ 
       48.53        76.60        67.36        15.68        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       26.17         0.10         0.49         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B5 
        0.66         1.38         0.82         1.22        12.89         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-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        22.45        16.47         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-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        5.69        27.45         6.87        49.68         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.38        50.66         9.30         6.71         4.11         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.20         4.01         7.13         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES 
        6.48        61.94        30.61         5.69        35.24        17.26 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12         0.85         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-GU-A42Q TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ 
        3.12        20.98         7.66         4.41         6.41         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.63         7.79         6.67         6.41        11.54         1.51 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A6MB 
        6.74         8.75         3.45         2.50         6.48         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
        6.38         6.35        13.48        16.67        88.93        97.45 
TCGA-XF-A8HG 
       15.35 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.10              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            87.32            140.81 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             8.91              8.35 
[1] "0.1 - 87.3 (8.9)"  "0.1 - 140.8 (8.3)"
[1] "hr=" "1.4"
D80V2, continuous
                   vv
clus                STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED          0       0       17        10       12
  XQ LOSS WILD-TYPE        1       2       51        62       55
D80V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE 0A                0                 1
  STAGE I                 0                 2
  STAGE II               17                51
  STAGE III              10                62
  STAGE IV               12                55
[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         16 15  5
  XQ LOSS WILD-TYPE       46 86 27
D80V4, multiclass
          clus
vv         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1+T2              16                46
  T3                    15                86
  T4                     5                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
  XQ LOSS MUTATED    24   6   4   1
  XQ LOSS WILD-TYPE 106  16  34   6
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              24               106
  N1               6                16
  N2               4                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
  XQ LOSS MUTATED   18  0 23
  XQ LOSS WILD-TYPE 88  5 79
D80V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              18                88
  M1               0                 5
  MX              23                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"
D80V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     8  33
  XQ LOSS WILD-TYPE  42 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8   33
  XQ LOSS WILD-TYPE   42  131
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               8                42
  MALE                33               131
[1] 2 2
[1] FALSE
D80V8, continuous
D80V9, continuous
D80V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       5                         2    32
  XQ LOSS WILD-TYPE    17                         9   138
D80V11, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   5                17
  BLACK OR AFRICAN AMERICAN               2                 9
  WHITE                                  32               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"
