[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"        "-oTPRAD-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/PRAD-TP/11541653/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/11546321/transformed.cor.cli.txt"

nPatients in clinical file=368, in cluster file=492, common to both=363
[1]  65 363
[1] "AMP PEAK  1(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         25                         338 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         25                         338 
[1] "AMP PEAK  2(3Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                           49                           314 
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                           49                           314 
[1] "AMP PEAK  3(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                           57                           306 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                           57                           306 
[1] "AMP PEAK  4(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                           14                           349 
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                           14                           349 
[1] "AMP PEAK  5(4Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                           13                           350 
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                           13                           350 
[1] "AMP PEAK  6(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                           18                           345 
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                           18                           345 
[1] "AMP PEAK  7(7P14.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                           70                           293 
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                           70                           293 
[1] "AMP PEAK  8(7Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                           67                           296 
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                           67                           296 
[1] "AMP PEAK  9(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                            41                            322 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                            41                            322 
[1] "AMP PEAK 10(8Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                          103                           260 
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                          103                           260 
[1] "AMP PEAK 11(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            98                            265 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            98                            265 
[1] "AMP PEAK 12(9Q33.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                           38                           325 
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                           38                           325 
[1] "AMP PEAK 13(11Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                            25                            338 
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                            25                            338 
[1] "AMP PEAK 14(12Q23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                            21                            342 
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                            21                            342 
[1] "AMP PEAK 15(13Q12.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                             17                             346 
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                             17                             346 
[1] "AMP PEAK 16(14Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                            20                            343 
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                            20                            343 
[1] "AMP PEAK 17(15Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                            10                            353 
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                            10                            353 
[1] "AMP PEAK 18(16Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                            18                            345 
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                            18                            345 
[1] "AMP PEAK 19(17Q23.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                            13                            350 
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                            13                            350 
[1] "AMP PEAK 20(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                             10                             353 
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                             10                             353 
[1] "AMP PEAK 21(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                            26                            337 
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                            26                            337 
[1] "AMP PEAK 22(XP22.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                            17                            346 
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                            17                            346 
[1] "AMP PEAK 23(XP22.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                            16                            347 
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                            16                            347 
[1] "AMP PEAK 24(XP21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                           16                           347 
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                           16                           347 
[1] "AMP PEAK 25(XQ21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           13                           350 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           13                           350 
[1] "AMP PEAK 26(XQ21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                           11                           352 
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                           11                           352 
[1] "AMP PEAK 27(XQ25) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                         13                         350 
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                         13                         350 
[1] "AMP PEAK 28(XQ27.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                           14                           349 
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                           14                           349 
[1] "DEL PEAK  1(1P31.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                           43                           320 
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                           43                           320 
[1] "DEL PEAK  2(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           39                           324 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           39                           324 
[1] "DEL PEAK  3(1Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                           19                           344 
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                           19                           344 
[1] "DEL PEAK  4(1Q42.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                           32                           331 
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                           32                           331 
[1] "DEL PEAK  5(2P21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         33                         330 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         33                         330 
[1] "DEL PEAK  6(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           64                           299 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           64                           299 
[1] "DEL PEAK  7(2Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                           58                           305 
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                           58                           305 
[1] "DEL PEAK  8(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                         59                         304 
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                         59                         304 
[1] "DEL PEAK  9(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                         25                         338 
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                         25                         338 
[1] "DEL PEAK 10(4Q28.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                           37                           326 
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                           37                           326 
[1] "DEL PEAK 11(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                           62                           301 
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                           62                           301 
[1] "DEL PEAK 12(5Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                           64                           299 
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                           64                           299 
[1] "DEL PEAK 13(5Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                           76                           287 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                           76                           287 
[1] "DEL PEAK 14(6P25.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                           27                           336 
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                           27                           336 
[1] "DEL PEAK 15(6Q14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                          132                           231 
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                          132                           231 
[1] "DEL PEAK 16(7Q31.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                            24                            339 
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                            24                            339 
[1] "DEL PEAK 17(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                          153                           210 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                          153                           210 
[1] "DEL PEAK 18(8P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                          207                           156 
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                          207                           156 
[1] "DEL PEAK 19(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         32                         331 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         32                         331 
[1] "DEL PEAK 20(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            109                             254 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            109                             254 
[1] "DEL PEAK 21(11P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                            24                            339 
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                            24                            339 
[1] "DEL PEAK 22(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                            29                            334 
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                            29                            334 
[1] "DEL PEAK 23(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                            35                            328 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                            35                            328 
[1] "DEL PEAK 24(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            82                            281 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            82                            281 
[1] "DEL PEAK 25(12Q24.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                             31                             332 
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                             31                             332 
[1] "DEL PEAK 26(13Q14.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                            168                             195 
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                            168                             195 
[1] "DEL PEAK 27(13Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                           124                            239 
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                           124                            239 
[1] "DEL PEAK 28(15Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                            45                            318 
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                            45                            318 
[1] "DEL PEAK 29(16Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                           130                            233 
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                           130                            233 
[1] "DEL PEAK 30(16Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                           147                            216 
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                           147                            216 
[1] "DEL PEAK 31(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                           108                            255 
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                           108                            255 
[1] "DEL PEAK 32(17Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                             72                             291 
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                             72                             291 
[1] "DEL PEAK 33(18Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                             95                             268 
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                             95                             268 
[1] "DEL PEAK 34(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                         100                          263 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                         100                          263 
[1] "DEL PEAK 35(19Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                            33                            330 
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                            33                            330 
[1] "DEL PEAK 36(21Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                            37                            326 
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                            37                            326 
[1] "DEL PEAK 37(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                           111                            252 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                           111                            252 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "GLEASON_SCORE_COMBINED"                
[19] "GLEASON_SCORE_PRIMARY"                 
[20] "GLEASON_SCORE_SECONDARY"               
[21] "HIGHEST_GLEASON_SCORE"                 
[22] "GLEASON_SCORE"                         
[23] "PSA_RESULT_PREOP"                      
[24] "DAYS_TO_PREOP_PSA"                     
[25] "PSA_VALUE"                             
[26] "DAYS_TO_PSA"                           
[27] "RACE"                                  
[28] "ETHNICITY"                             
[29] "BATCHNUMBER"                           

Input Data has 29 rows and 363 columns.

[1] "Batch" "29"   
[1] "Last Follow UP"
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
         621         1332          671         1033          112          771 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
          91          212          671           31          395          425 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
          60          731           31          396         1065          943 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
          31           62           28         1339          365           31 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
         700           31          458          731           62          396 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
         486          821          304          974         1004           91 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
         882          826         1007          595          405          906 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
        1415         1365          800         1391          880          922 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
         827          727         1184         1464         1116         1476 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
        1172         1102         1832         1416         1454         1590 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
        1962         1578         2079         1310         1115         1179 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
        1209         1832         1273         1456          884          822 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
        1491         1860         2542          663          295          289 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
         285          510          233          533          175          842 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
         191            9          727         1167          787          781 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
         625          442          430          552          596          526 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
         114          701          606         1961         1946          821 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
          NA          314          162          129          532          299 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
          93          229          668          536          393          417 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
         560          278           91          230          864          469 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
         409          273          524          494           54         1266 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
        2657         2465         2068         2028         2110         1696 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
         554         2089         1515         1404         1542         1501 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
        1434         1415         1443         1378         1198         1363 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
         101         1222         1215         1156         1226          811 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
         958         1155         1393          765          830         1771 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
        1726         1608         1543         1164         1185          849 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
         942         1075          857          994           NA          643 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
         185          941          112          601           NA          162 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
          89           61           72          440          868           24 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
         870           60           51           72           89           52 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
          22           64           81           53           45           51 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
          63          748          792           60           34           98 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
         928           45          543          747           56          589 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
         682           95          726           66           69           59 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
         546          679           48          483           35          680 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
          23           54           61           67           49          167 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
          71          106           44           38          134         2391 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
        2684         2522           NA          614          374          662 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
         518          488          503          491          624          454 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
         523          183          405          528          279          279 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
         310          206          316          437          617          422 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
         178          323         2859         1712         1359         1879 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
        3524          913         1659         4604         2056         2753 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
        1498         3447         2040         1770          840         1063 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
         692           83          804           NA          158          209 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
         302          400          822          763          483          573 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
          97         1247         3487         1436         2620          362 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
         249          269          776          394          183          472 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
         481          917         1001          459          132         3253 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
         805         2576         2879           NA         2309         1690 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
        1853         2037          663         1486          655          542 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
         176         1131          846          119         1157         1461 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
         275           91          790          972          958          972 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
         868          930          889          824         1126         1206 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
         775         1611         1491         1173         1124         2183 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
        1890         1842          512         1384         1261         1373 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
          NA         1441         1395         1155          798         3247 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
        2170         1910          213          427         1259           NA 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
        1897          740         1518          862           50          150 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
          34          239          183 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=318,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE_COMBINED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'GLEASON_SCORE_PRIMARY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE_SECONDARY':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'HIGHEST_GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'PSA_RESULT_PREOP':	nDistinctValues=177,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'DAYS_TO_PREOP_PSA':	nDistinctValues=182,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 25:'PSA_VALUE':	nDistinctValues=81,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'DAYS_TO_PSA':	nDistinctValues=287,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 27:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 28:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'BATCH.NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "PATHOLOGY.T.STAGE"        
 [3] "PATHOLOGY.N.STAGE"         "HISTOLOGICAL.TYPE"        
 [5] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
 [7] "GLEASON_SCORE_COMBINED"    "GLEASON_SCORE_PRIMARY"    
 [9] "GLEASON_SCORE_SECONDARY"   "GLEASON_SCORE"            
[11] "PSA_RESULT_PREOP"          "PSA_VALUE"                
[13] "RACE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 363 columns, 1 survival variables, and 13 non-survival variables.
AGE, nv=35, binary=FALSE, numeric=TRUE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T2  T3  T4 
150 206   5 
[1] "table(vv)"
vv
 T2  T3  T4 
150 206   5 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T2  T3  T4 
150 206   5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
150 206   5 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=10, binary=FALSE, numeric=TRUE
GLEASON_SCORE_COMBINED, nv=6, binary=FALSE, numeric=TRUE
GLEASON_SCORE_PRIMARY, nv=5, binary=FALSE, numeric=TRUE
GLEASON_SCORE_SECONDARY, nv=4, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_RESULT_PREOP, nv=177, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=81, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q22) MUTATION ANALYSIS
D1V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  1(1Q22) MUTATED    25   0
  AMP PEAK  1(1Q22) WILD-TYPE 330   6
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         25                         336 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                          0                           6 
$`AMP PEAK  1(1Q22) MUTATED`
TCGA-CH-5766 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5525 TCGA-EJ-7784 TCGA-EJ-7788 
        1.02        52.27        64.50        36.66        25.68        14.14 
TCGA-EJ-A46G TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6499 
        3.06        15.42        13.45        47.44        45.30        50.73 
TCGA-HC-7080 TCGA-HC-7232 TCGA-HC-8265 TCGA-HI-7168 TCGA-J9-A52E TCGA-M7-A725 
        2.01         2.93        15.88        78.61        10.62        18.84 
TCGA-VN-A88K TCGA-VN-A88Q TCGA-VP-A875 TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-YL-A8HM 
       25.51        32.91        26.47        25.97        31.50        36.95 
TCGA-YL-A8SR 
        7.00 

$`AMP PEAK  1(1Q22) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
       23.01        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5521 TCGA-EJ-5522 
       36.23        60.23        46.55        47.80        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       43.07        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
        5.75        27.68         6.28         0.30        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       25.87        20.55        14.53        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       10.32         5.33         4.24        17.49         9.83         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        2.99         7.56        28.41         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6364 TCGA-G9-6365 
       50.70        49.35        47.15        46.52        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        52.87        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 
       30.94         3.68        19.76         5.33         2.93         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.37         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 
        2.27         1.94        17.95        22.32         1.58         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        5.85        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM 
       13.15        27.02        25.08        15.88         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R 
       12.95         6.02        15.52        15.81        30.15        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34       106.95        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
       48.03         9.04         2.99        31.96        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        38.56        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        41.39        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                       1.02                        0.30 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                      78.61                      151.36 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                      25.68                       23.90 
[1] "1.0 - 78.6 (25.7)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.7e+07"
D1V2, continuous
                             vv
clus                           T2  T3  T4
  AMP PEAK  1(1Q22) MUTATED     4  19   2
  AMP PEAK  1(1Q22) WILD-TYPE 146 187   3
D1V3, multiclass
    clus
vv   AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  T2                         4                         146
  T3                        19                         187
  T4                         2                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED    18   5
  AMP PEAK  1(1Q22) WILD-TYPE 245  39
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     18    5
  AMP PEAK  1(1Q22) WILD-TYPE  245   39
   clus
vv  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  0                        18                         245
  1                         5                          39
[1] 2 2
[1] FALSE
D1V5, binary
                             cls
clus                            0   1
  AMP PEAK  1(1Q22) MUTATED     3  22
  AMP PEAK  1(1Q22) WILD-TYPE  10 328
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED      3   22
  AMP PEAK  1(1Q22) WILD-TYPE   10  328
                                        clus
vv                                       AMP PEAK  1(1Q22) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           22
                                        clus
vv                                       AMP PEAK  1(1Q22) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            328
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  1(1Q22) MUTATED    16   8   0   0
  AMP PEAK  1(1Q22) WILD-TYPE 227  82   5  11
D1V6, multiclass
    clus
vv   AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  R0                        16                         227
  R1                         8                          82
  R2                         0                           5
  RX                         0                          11
[1] 4 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, continuous
D1V8, continuous
D1V9, continuous
D1V10, continuous
D1V11, continuous
D1V12, continuous
D1V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q22) MUTATED       0                         0    13
  AMP PEAK  1(1Q22) WILD-TYPE     2                         7   133
D1V14, multiclass
                           clus
vv                          AMP PEAK  1(1Q22) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            13
                           clus
vv                          AMP PEAK  1(1Q22) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             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(2) Variable = AMP PEAK  2(3Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(3Q21.3) MUTATED    47   2
  AMP PEAK  2(3Q21.3) WILD-TYPE 308   4
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                           49                           312 
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                            2                             4 
$`AMP PEAK  2(3Q21.3) MUTATED`
TCGA-CH-5751 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5514 TCGA-EJ-5518 
       35.01        13.02        26.99        33.01        36.23        52.27 
TCGA-EJ-5521 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7330 TCGA-EJ-7782 TCGA-EJ-8468 
       51.88        39.75        41.85         6.28        38.37        64.47 
TCGA-EJ-8469 TCGA-EJ-A65F TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI 
       63.98        18.41         2.99         7.56        15.42        13.45 
TCGA-G9-6338 TCGA-G9-6363 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-A9S0 TCGA-HC-7210 
       66.67        45.30        50.73        30.97        26.01        28.54 
TCGA-HC-7819 TCGA-HC-8216 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AP 
       17.85        22.42        15.88         0.76         1.78         2.33 
TCGA-HC-A6AS TCGA-J4-8200 TCGA-KK-A59Y TCGA-KK-A6E1 TCGA-KK-A8IB TCGA-KK-A8IF 
        1.45        12.30        44.68        54.54         2.73        26.43 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87H TCGA-XJ-A83G TCGA-XJ-A9DX 
       15.09       106.95        26.47        21.80        38.04        25.97 
TCGA-XK-AAIV TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WI 
       31.50        36.95        62.14        71.34        14.04        41.39 
TCGA-YL-A9WJ 
       60.99 

$`AMP PEAK  2(3Q21.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 
        1.02        15.06        24.03         2.04        15.98         9.99 
TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       32.02         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        48.53        38.53        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 
       64.50        68.35        43.07        36.66        38.76        60.23 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 
       17.52         5.75        27.68         0.30        23.90        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8470 TCGA-EJ-8474 
       17.29         3.75        23.05        19.92        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-FC-7708 
       21.96        17.62        12.92        13.71         9.14        28.41 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       81.04        67.99        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 
       25.15        27.29        58.22        56.75        52.87        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 
       38.96        27.91        35.34        28.18        32.68        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.01         2.37        14.47         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56         1.84        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 
        2.27         1.94        17.95        22.32         1.58         1.15 
TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ 
       22.36         2.01         2.20         1.61         5.49         3.48 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         4.41        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       20.19        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       61.78       115.86        30.02       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       22.75        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       27.02        25.08        15.88        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       32.91         4.34        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK 
        5.79        37.18        27.81         3.91        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
        2.99        31.96        31.96        28.54        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       27.09        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       38.56        71.77        60.56        16.83        45.50        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        47.38        45.86        37.97        26.24 
TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
      106.75        62.79         7.00        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                         0.76                          0.30 
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                       106.95                        151.36 
  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE 
                        28.54                         22.88 
[1] "0.8 - 107.0 (28.5)" "0.3 - 151.4 (22.9)"
[1] "hr=" "2.5"
D2V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  2(3Q21.3) MUTATED    11  35   3
  AMP PEAK  2(3Q21.3) WILD-TYPE 139 171   2
D2V3, multiclass
    clus
vv   AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE
  T2                          11                           139
  T3                          35                           171
  T4                           3                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                               cls
clus                              0   1
  AMP PEAK  2(3Q21.3) MUTATED    35  11
  AMP PEAK  2(3Q21.3) WILD-TYPE 228  33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(3Q21.3) MUTATED     35   11
  AMP PEAK  2(3Q21.3) WILD-TYPE  228   33
   clus
vv  AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE
  0                          35                           228
  1                          11                            33
[1] 2 2
[1] FALSE
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK  2(3Q21.3) MUTATED     3  46
  AMP PEAK  2(3Q21.3) WILD-TYPE  10 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(3Q21.3) MUTATED      3   46
  AMP PEAK  2(3Q21.3) WILD-TYPE   10  304
                                        clus
vv                                       AMP PEAK  2(3Q21.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             46
                                        clus
vv                                       AMP PEAK  2(3Q21.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              304
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(3Q21.3) MUTATED    26  14   2   4
  AMP PEAK  2(3Q21.3) WILD-TYPE 217  76   3   7
D2V6, multiclass
    clus
vv   AMP PEAK  2(3Q21.3) MUTATED AMP PEAK  2(3Q21.3) WILD-TYPE
  R0                          26                           217
  R1                          14                            76
  R2                           2                             3
  RX                           4                             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"
D2V7, continuous
D2V8, continuous
D2V9, continuous
D2V10, continuous
D2V11, continuous
D2V12, continuous
D2V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(3Q21.3) MUTATED       0                         1    16
  AMP PEAK  2(3Q21.3) WILD-TYPE     2                         6   130
D2V14, multiclass
                           clus
vv                          AMP PEAK  2(3Q21.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              16
                           clus
vv                          AMP PEAK  2(3Q21.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(3Q26.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(3Q26.2) MUTATED    55   2
  AMP PEAK  3(3Q26.2) WILD-TYPE 300   4
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                           57                           304 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                            2                             4 
$`AMP PEAK  3(3Q26.2) MUTATED`
TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5791 
       22.06        35.01         2.04        13.02        26.99        33.01 
TCGA-EJ-5497 TCGA-EJ-5505 TCGA-EJ-5510 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5521 
       13.32        30.31        36.69        36.23        52.27        51.88 
TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7330 TCGA-EJ-7782 TCGA-EJ-7792 
       39.75        41.85        29.06         6.28        38.37        17.29 
TCGA-EJ-8468 TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI 
       64.47         3.06         2.99         7.56        15.42        13.45 
TCGA-G9-6338 TCGA-G9-6363 TCGA-G9-6366 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-A9S0 
       66.67        45.30         3.32        50.73        30.97        26.01 
TCGA-G9-A9S7 TCGA-HC-7211 TCGA-HC-7819 TCGA-HC-8216 TCGA-HC-A4ZV TCGA-HC-A631 
       21.14         0.79        17.85        22.42         0.76         1.78 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-J4-8200 TCGA-J9-A52B TCGA-KK-A59Y TCGA-KK-A6E1 
        2.33         1.45        12.30        13.87        44.68        54.54 
TCGA-KK-A8IF TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A87H TCGA-XJ-A83G TCGA-XJ-A9DX 
       26.43        15.09       106.95        21.80        38.04        25.97 
TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SK TCGA-YL-A8SP 
       31.50        37.02        62.14        60.56        37.97        71.34 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       14.04        41.39        60.99 

$`AMP PEAK  3(3Q26.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5761 
       24.03         1.02        13.02        31.00         1.02         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 
       24.03         2.04        15.98         9.99        32.02         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5498 TCGA-EJ-5499 
       29.00        27.16        33.11        19.56        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5507 
       44.88        26.30        45.73        28.93        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       38.93        48.13        48.53        38.53        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       47.80        64.50        68.35        43.07        36.66        38.76 
TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        47.87        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 
       17.52         5.75        27.68         0.30        23.90        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
        3.75        23.05        19.92        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
        5.33         4.24        17.49         9.83         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-FC-7708 
       17.62        12.92        13.71        18.41         9.14        28.41 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       81.04        67.99        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       47.44        39.39        44.81        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        56.75        52.87        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       27.91        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 
        1.12         3.22        30.51         1.48        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6HX 
        2.01         2.20         1.61         5.49         3.48         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY 
        5.85        10.62        93.99        56.28        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       30.02       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
       67.07        58.19        27.62        34.95        22.75         2.73 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK 
        5.79        37.18        27.81         3.91        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
        2.99        31.96        31.96        28.54        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       27.09        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       36.95        71.77        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ 
       28.77        47.38        45.86        26.24       106.75        62.79 
TCGA-YL-A8SR TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
        7.00        62.37        24.33        49.91        28.34         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                         0.76                          0.30 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                       106.95                        151.36 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                        26.99                         23.46 
[1] "0.8 - 107.0 (27.0)" "0.3 - 151.4 (23.5)"
[1] "hr=" "2.4"
D3V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  3(3Q26.2) MUTATED    15  39   3
  AMP PEAK  3(3Q26.2) WILD-TYPE 135 167   2
D3V3, multiclass
    clus
vv   AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  T2                          15                           135
  T3                          39                           167
  T4                           3                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED    40  13
  AMP PEAK  3(3Q26.2) WILD-TYPE 223  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED     40   13
  AMP PEAK  3(3Q26.2) WILD-TYPE  223   31
   clus
vv  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  0                          40                           223
  1                          13                            31
[1] 2 2
[1] FALSE
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED     3  54
  AMP PEAK  3(3Q26.2) WILD-TYPE  10 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED      3   54
  AMP PEAK  3(3Q26.2) WILD-TYPE   10  296
                                        clus
vv                                       AMP PEAK  3(3Q26.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             54
                                        clus
vv                                       AMP PEAK  3(3Q26.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              296
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(3Q26.2) MUTATED    31  18   2   3
  AMP PEAK  3(3Q26.2) WILD-TYPE 212  72   3   8
D3V6, multiclass
    clus
vv   AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  R0                          31                           212
  R1                          18                            72
  R2                           2                             3
  RX                           3                             8
[1] 4 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, continuous
D3V8, continuous
D3V9, continuous
D3V10, continuous
D3V11, continuous
D3V12, continuous
D3V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q26.2) MUTATED       0                         1    24
  AMP PEAK  3(3Q26.2) WILD-TYPE     2                         6   122
D3V14, multiclass
                           clus
vv                          AMP PEAK  3(3Q26.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              24
                           clus
vv                          AMP PEAK  3(3Q26.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               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(4) Variable = AMP PEAK  4(4P16.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(4P16.3) MUTATED    13   0
  AMP PEAK  4(4P16.3) WILD-TYPE 342   6
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                           13                           348 
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                            0                             6 
$`AMP PEAK  4(4P16.3) MUTATED`
TCGA-CH-5751 TCGA-EJ-5521 TCGA-EJ-5542 TCGA-EJ-8469 TCGA-EJ-A46G TCGA-G9-6369 
       35.01        51.88        29.06        63.98         3.06        39.95 
TCGA-G9-6499 TCGA-HC-8265 TCGA-M7-A724 TCGA-VP-A875 TCGA-XJ-A9DX TCGA-YL-A8HO 
       50.73        15.88        15.88        26.47        25.97        71.77 
TCGA-YL-A8SR 
        7.00 

$`AMP PEAK  4(4P16.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       41.85        47.87        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       64.47        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        9.83         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
       18.41         9.14         2.99         7.56        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
        3.32        40.18        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       52.87        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      106.95        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        38.56        36.95        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        41.39        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                         3.06                          0.30 
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                        71.77                        151.36 
  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE 
                       29.060                        23.885 
[1] "3.1 - 71.8 (29.1)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D4V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  4(4P16.3) MUTATED     1  12   1
  AMP PEAK  4(4P16.3) WILD-TYPE 149 194   4
D4V3, multiclass
    clus
vv   AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE
  T2                           1                           149
  T3                          12                           194
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                               cls
clus                              0   1
  AMP PEAK  4(4P16.3) MUTATED    12   2
  AMP PEAK  4(4P16.3) WILD-TYPE 251  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4P16.3) MUTATED     12    2
  AMP PEAK  4(4P16.3) WILD-TYPE  251   42
   clus
vv  AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE
  0                          12                           251
  1                           2                            42
[1] 2 2
[1] FALSE
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(4P16.3) MUTATED     2  12
  AMP PEAK  4(4P16.3) WILD-TYPE  11 338
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4P16.3) MUTATED      2   12
  AMP PEAK  4(4P16.3) WILD-TYPE   11  338
                                        clus
vv                                       AMP PEAK  4(4P16.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             12
                                        clus
vv                                       AMP PEAK  4(4P16.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              338
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(4P16.3) MUTATED     7   6   0   1
  AMP PEAK  4(4P16.3) WILD-TYPE 236  84   5  10
D4V6, multiclass
    clus
vv   AMP PEAK  4(4P16.3) MUTATED AMP PEAK  4(4P16.3) WILD-TYPE
  R0                           7                           236
  R1                           6                            84
  R2                           0                             5
  RX                           1                            10
[1] 4 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, continuous
D4V8, continuous
D4V9, continuous
D4V10, continuous
D4V11, continuous
D4V12, continuous
D4V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(4P16.3) MUTATED       0                         0     5
  AMP PEAK  4(4P16.3) WILD-TYPE     2                         7   141
D4V14, multiclass
                           clus
vv                          AMP PEAK  4(4P16.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               5
                           clus
vv                          AMP PEAK  4(4P16.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               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(5) Variable = AMP PEAK  5(4Q13.3) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(4Q13.3) MUTATED    13   0
  AMP PEAK  5(4Q13.3) WILD-TYPE 342   6
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                           13                           348 
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                            0                             6 
$`AMP PEAK  5(4Q13.3) MUTATED`
TCGA-CH-5751 TCGA-EJ-5525 TCGA-EJ-5542 TCGA-KK-A6E1 TCGA-KK-A8IF TCGA-M7-A724 
       35.01        36.66        29.06        54.54        26.43        15.88 
TCGA-VN-A88N TCGA-VP-A875 TCGA-XJ-A9DX TCGA-XK-AAJT TCGA-YL-A8HK TCGA-YL-A8S8 
       15.52        26.47        25.97        37.02        49.02        62.14 
TCGA-YL-A9WI 
       41.39 

$`AMP PEAK  5(4Q13.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       51.88        68.35        43.07        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       41.85        47.87        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        52.87        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       61.78       115.86        30.02       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       22.75         2.73        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       13.15        27.02        25.08        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       25.51        12.95         6.02        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09         4.34       106.95        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV 
       38.04        48.03         9.04         2.99        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       31.96        28.54        30.58        29.23        27.09        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 
       25.48        52.96        38.56        36.95        71.77        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        14.04        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                        15.52                          0.30 
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                        62.14                        151.36 
  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE 
                        35.01                         23.03 
[1] "15.5 - 62.1 (35.0)" "0.3 - 151.4 (23.0)"
[1] "hr="     "2.6e+07"
D5V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  5(4Q13.3) MUTATED     2  10   1
  AMP PEAK  5(4Q13.3) WILD-TYPE 148 196   4
D5V3, multiclass
    clus
vv   AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE
  T2                           2                           148
  T3                          10                           196
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                               cls
clus                              0   1
  AMP PEAK  5(4Q13.3) MUTATED     9   4
  AMP PEAK  5(4Q13.3) WILD-TYPE 254  40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(4Q13.3) MUTATED      9    4
  AMP PEAK  5(4Q13.3) WILD-TYPE  254   40
   clus
vv  AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE
  0                           9                           254
  1                           4                            40
[1] 2 2
[1] FALSE
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK  5(4Q13.3) MUTATED     1  12
  AMP PEAK  5(4Q13.3) WILD-TYPE  12 338
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(4Q13.3) MUTATED      1   12
  AMP PEAK  5(4Q13.3) WILD-TYPE   12  338
                                        clus
vv                                       AMP PEAK  5(4Q13.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             12
                                        clus
vv                                       AMP PEAK  5(4Q13.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              338
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(4Q13.3) MUTATED     6   6   0   1
  AMP PEAK  5(4Q13.3) WILD-TYPE 237  84   5  10
D5V6, multiclass
    clus
vv   AMP PEAK  5(4Q13.3) MUTATED AMP PEAK  5(4Q13.3) WILD-TYPE
  R0                           6                           237
  R1                           6                            84
  R2                           0                             5
  RX                           1                            10
[1] 4 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, continuous
D5V8, continuous
D5V9, continuous
D5V10, continuous
D5V11, continuous
D5V12, continuous
D5V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q13.3) MUTATED       0                         0     3
  AMP PEAK  5(4Q13.3) WILD-TYPE     2                         7   143
D5V14, multiclass
                           clus
vv                          AMP PEAK  5(4Q13.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          AMP PEAK  5(4Q13.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               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(6) Variable = AMP PEAK  6(5Q35.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(5Q35.3) MUTATED    18   0
  AMP PEAK  6(5Q35.3) WILD-TYPE 337   6
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                           18                           343 
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                            0                             6 
$`AMP PEAK  6(5Q35.3) MUTATED`
TCGA-EJ-5495 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-7789 TCGA-EJ-A46G TCGA-HC-8265 
       33.11        52.27        51.88        18.15         3.06        15.88 
TCGA-HI-7168 TCGA-J9-A52E TCGA-KK-A59Z TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-VN-A88K 
       78.61        10.62        61.78        22.75         2.73        25.51 
TCGA-VP-A875 TCGA-VP-A87H TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SL TCGA-ZG-A8QZ 
       26.47        21.80        71.77        62.14        26.24         7.86 

$`AMP PEAK  6(5Q35.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       29.00        27.16        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5522 
       36.23        60.23        46.55        47.80        64.50        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        9.83         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
       18.41         9.14         2.99         7.56        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
        1.97         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
       22.32         1.58         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X 
       14.37        20.28        13.87         5.85        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       44.68       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       34.95        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 
       32.91        15.09         4.34       106.95        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       23.93        75.91        55.56        60.92        66.97        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.50        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       36.95        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        47.38        45.86        37.97       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A9ND 
        6.02 

  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                         2.73                          0.30 
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                        78.61                        151.36 
  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE 
                       25.875                        23.900 
[1] "2.7 - 78.6 (25.9)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.7e+07"
D6V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  6(5Q35.3) MUTATED     1  16   1
  AMP PEAK  6(5Q35.3) WILD-TYPE 149 190   4
D6V3, multiclass
    clus
vv   AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE
  T2                           1                           149
  T3                          16                           190
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                               cls
clus                              0   1
  AMP PEAK  6(5Q35.3) MUTATED    13   5
  AMP PEAK  6(5Q35.3) WILD-TYPE 250  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5Q35.3) MUTATED     13    5
  AMP PEAK  6(5Q35.3) WILD-TYPE  250   39
   clus
vv  AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE
  0                          13                           250
  1                           5                            39
[1] 2 2
[1] FALSE
D6V5, binary
                               cls
clus                              0   1
  AMP PEAK  6(5Q35.3) MUTATED     1  17
  AMP PEAK  6(5Q35.3) WILD-TYPE  12 333
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5Q35.3) MUTATED      1   17
  AMP PEAK  6(5Q35.3) WILD-TYPE   12  333
                                        clus
vv                                       AMP PEAK  6(5Q35.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             17
                                        clus
vv                                       AMP PEAK  6(5Q35.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              333
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(5Q35.3) MUTATED    11   6   1   0
  AMP PEAK  6(5Q35.3) WILD-TYPE 232  84   4  11
D6V6, multiclass
    clus
vv   AMP PEAK  6(5Q35.3) MUTATED AMP PEAK  6(5Q35.3) WILD-TYPE
  R0                          11                           232
  R1                           6                            84
  R2                           1                             4
  RX                           0                            11
[1] 4 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, continuous
D6V8, continuous
D6V9, continuous
D6V10, continuous
D6V11, continuous
D6V12, continuous
D6V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(5Q35.3) MUTATED       0                         1     4
  AMP PEAK  6(5Q35.3) WILD-TYPE     2                         6   142
D6V14, multiclass
                           clus
vv                          AMP PEAK  6(5Q35.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               4
                           clus
vv                          AMP PEAK  6(5Q35.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               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(7) Variable = AMP PEAK  7(7P14.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(7P14.3) MUTATED    69   1
  AMP PEAK  7(7P14.3) WILD-TYPE 286   5
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                           70                           291 
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                            1                             5 
$`AMP PEAK  7(7P14.3) MUTATED`
TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 
       35.01         2.04        44.02        24.03        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5509 TCGA-EJ-5542 
       26.99        33.01        27.16        33.11        48.13        29.06 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-EJ-7789 
       61.15         9.70         6.28        25.68        14.53        18.15 
TCGA-EJ-A46F TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6366 
        9.83         7.56        15.42        13.45        66.67         3.32 
TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7523 
       40.31        31.50        56.75        52.87        50.73        28.18 
TCGA-HC-7078 TCGA-HC-7213 TCGA-HC-7742 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 
        5.33         1.97         1.48         1.94        17.95        15.88 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AP TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-8198 
        0.76         1.78         2.33        78.61        43.69        20.19 
TCGA-J9-A52E TCGA-KK-A59Z TCGA-KK-A6E8 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A721 
       10.62        61.78        58.19         2.73        26.43        13.15 
TCGA-QU-A6IM TCGA-TP-A8TV TCGA-VN-A88P TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87B 
       41.00         8.19        30.15       106.95        26.47        75.91 
TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A9DX TCGA-XK-AAJ3 TCGA-YL-A8HM 
       21.80        17.82        37.18        25.97        28.54        36.95 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SQ TCGA-YL-A8SR 
       71.77        62.14        45.50        45.14        62.79         7.00 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A8QX 
       14.04        41.39        62.37         4.93 

$`AMP PEAK  7(7P14.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        0.92        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5769 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5496 
        2.04         9.99        32.02         2.99        29.00        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 
       28.93        30.31        27.19        23.90        38.93        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       38.76        39.75        60.23        41.85        47.87        27.02 
TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       49.02        83.57        21.80         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 
        7.66        17.52         5.75        27.68         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
       38.37        25.87        20.55        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H 
       10.32         5.33         4.24        17.49         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        2.99        28.41         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 
       41.62        87.35        81.04        67.99        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 
       40.18        39.95        38.01        26.66        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       30.97        35.34        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       30.94         3.68        19.76         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL 
       22.32         1.58         1.15        22.36         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61         5.49         3.48         1.45         1.25         4.41 
TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       88.24        82.92        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V 
       10.39        14.37        20.28        13.87         5.85        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       56.28        44.68       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ 
       67.59        90.51        49.25       113.33        67.07        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       34.95        22.75        20.65         5.19         6.87         9.93 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN 
       27.02        25.08        15.88        18.84         3.19       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       47.21        86.14        11.90         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
        6.02        15.52        15.81        32.91        15.09         4.34 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       84.69        94.65        23.93        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       48.85        21.53         5.79        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
       48.03         9.04         2.99        31.96        31.50        31.96 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC 
       52.96        49.02        38.56        60.56        16.83        41.46 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       71.34        60.99        24.33        49.91        28.34         1.64 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                         0.76                          0.30 
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                       106.95                        151.36 
  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE 
                        26.45                         23.05 
[1] "0.8 - 107.0 (26.4)" "0.3 - 151.4 (23.1)"
[1] "hr=" "1.4"
D7V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  7(7P14.3) MUTATED    21  48   1
  AMP PEAK  7(7P14.3) WILD-TYPE 129 158   4
D7V3, multiclass
    clus
vv   AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE
  T2                          21                           129
  T3                          48                           158
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                               cls
clus                              0   1
  AMP PEAK  7(7P14.3) MUTATED    54   8
  AMP PEAK  7(7P14.3) WILD-TYPE 209  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P14.3) MUTATED     54    8
  AMP PEAK  7(7P14.3) WILD-TYPE  209   36
   clus
vv  AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE
  0                          54                           209
  1                           8                            36
[1] 2 2
[1] FALSE
D7V5, binary
                               cls
clus                              0   1
  AMP PEAK  7(7P14.3) MUTATED     2  68
  AMP PEAK  7(7P14.3) WILD-TYPE  11 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P14.3) MUTATED      2   68
  AMP PEAK  7(7P14.3) WILD-TYPE   11  282
                                        clus
vv                                       AMP PEAK  7(7P14.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             68
                                        clus
vv                                       AMP PEAK  7(7P14.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              282
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(7P14.3) MUTATED    36  27   1   3
  AMP PEAK  7(7P14.3) WILD-TYPE 207  63   4   8
D7V6, multiclass
    clus
vv   AMP PEAK  7(7P14.3) MUTATED AMP PEAK  7(7P14.3) WILD-TYPE
  R0                          36                           207
  R1                          27                            63
  R2                           1                             4
  RX                           3                             8
[1] 4 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, continuous
D7V8, continuous
D7V9, continuous
D7V10, continuous
D7V11, continuous
D7V12, continuous
D7V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(7P14.3) MUTATED       0                         1    29
  AMP PEAK  7(7P14.3) WILD-TYPE     2                         6   117
D7V14, multiclass
                           clus
vv                          AMP PEAK  7(7P14.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              29
                           clus
vv                          AMP PEAK  7(7P14.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               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(8) Variable = AMP PEAK  8(7Q22.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(7Q22.1) MUTATED    66   1
  AMP PEAK  8(7Q22.1) WILD-TYPE 289   5
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                           67                           294 
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                            1                             5 
$`AMP PEAK  8(7Q22.1) MUTATED`
TCGA-CH-5751 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5791 
       35.01        24.03        13.02        15.98        26.99        33.01 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5509 TCGA-EJ-5525 TCGA-EJ-5542 TCGA-EJ-7125 
       27.16        33.11        48.13        36.66        29.06        61.15 
TCGA-EJ-7314 TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-A46F 
        9.70         6.28        25.68        14.53        18.15         9.83 
TCGA-EJ-A46G TCGA-EJ-A65M TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6366 TCGA-G9-6371 
        3.06         7.56        13.45        66.67         3.32        40.31 
TCGA-G9-6377 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7523 TCGA-HC-7742 
       31.50        56.75        52.87        50.73        28.18         1.48 
TCGA-HC-8216 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 
       22.42         1.94        17.95        15.88         0.76         1.78 
TCGA-HC-A6AP TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-8198 TCGA-J9-A52E TCGA-KK-A59Z 
        2.33        78.61        43.69        20.19        10.62        61.78 
TCGA-KK-A6E8 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A721 TCGA-QU-A6IM TCGA-TP-A8TV 
       58.19         2.73        26.43        13.15        41.00         8.19 
TCGA-VN-A88P TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-AA1N 
       30.15       106.95        26.47        75.91        21.80        17.82 
TCGA-X4-A8KQ TCGA-XK-AAJ3 TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SB 
       37.18        28.54        36.95        71.77        62.14        45.50 
TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK 
      106.75        62.79         7.00        14.04        41.39        62.37 
TCGA-ZG-A8QX 
        4.93 

$`AMP PEAK  8(7Q22.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 
        1.02        15.06         2.04         9.99        32.02         2.99 
TCGA-CH-5794 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       29.00        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       38.93        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       43.07        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 
       27.02        49.02        83.57        21.80         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 
       16.77         7.66        17.52         5.75        27.68         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7791 
       23.90        38.37        25.87        20.55        14.14        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H 
       26.99        10.32         5.33         4.24        17.49         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        2.99        28.41        15.42         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 
        1.78        41.62        87.35        81.04        67.99        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6373 TCGA-G9-6378 
       44.81        40.18        39.95        38.01        26.66        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7510 
       45.80        25.15        27.29        58.22        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        30.97        35.34        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
        1.97         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.10         2.66         1.74         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56         1.84        19.36         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F 
        2.17         2.27        22.32         1.58         1.15        22.36 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.01         2.20         1.61         5.49         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67K 
        1.25         4.41        88.24        82.92        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 
        5.85        93.99        56.28        44.68       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y 
       67.07        27.62        34.95        22.75        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        6.87         9.93        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I 
        3.19       114.64        47.21        86.14        11.90         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q 
       25.51        12.95         6.02        15.52        15.81        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C 
       15.09         4.34        84.69        94.65        23.93        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS 
       60.92        66.97        48.85        21.53         5.79        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.50        31.96        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WJ TCGA-YL-A9WL 
       45.86        37.97        26.24        71.34        60.99        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       49.91        28.34         1.64         1.12         7.86         6.02 

  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                         0.76                          0.30 
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                       106.95                        151.36 
  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE 
                        26.99                         23.03 
[1] "0.8 - 107.0 (27.0)" "0.3 - 151.4 (23.0)"
[1] "hr=" "1.4"
D8V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK  8(7Q22.1) MUTATED    22  44   1
  AMP PEAK  8(7Q22.1) WILD-TYPE 128 162   4
D8V3, multiclass
    clus
vv   AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE
  T2                          22                           128
  T3                          44                           162
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q22.1) MUTATED    52   6
  AMP PEAK  8(7Q22.1) WILD-TYPE 211  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q22.1) MUTATED     52    6
  AMP PEAK  8(7Q22.1) WILD-TYPE  211   38
   clus
vv  AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE
  0                          52                           211
  1                           6                            38
[1] 2 2
[1] FALSE
D8V5, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q22.1) MUTATED     2  65
  AMP PEAK  8(7Q22.1) WILD-TYPE  11 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q22.1) MUTATED      2   65
  AMP PEAK  8(7Q22.1) WILD-TYPE   11  285
                                        clus
vv                                       AMP PEAK  8(7Q22.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             65
                                        clus
vv                                       AMP PEAK  8(7Q22.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              285
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(7Q22.1) MUTATED    37  24   1   3
  AMP PEAK  8(7Q22.1) WILD-TYPE 206  66   4   8
D8V6, multiclass
    clus
vv   AMP PEAK  8(7Q22.1) MUTATED AMP PEAK  8(7Q22.1) WILD-TYPE
  R0                          37                           206
  R1                          24                            66
  R2                           1                             4
  RX                           3                             8
[1] 4 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, continuous
D8V8, continuous
D8V9, continuous
D8V10, continuous
D8V11, continuous
D8V12, continuous
D8V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7Q22.1) MUTATED       0                         1    25
  AMP PEAK  8(7Q22.1) WILD-TYPE     2                         6   121
D8V14, multiclass
                           clus
vv                          AMP PEAK  8(7Q22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              25
                           clus
vv                          AMP PEAK  8(7Q22.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(8P11.23) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(8P11.23) MUTATED    41   0
  AMP PEAK  9(8P11.23) WILD-TYPE 314   6
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                            41                            320 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                             0                              6 
$`AMP PEAK  9(8P11.23) MUTATED`
TCGA-CH-5751 TCGA-CH-5767 TCGA-CH-5788 TCGA-EJ-5509 TCGA-EJ-5514 TCGA-EJ-5526 
       35.01        15.06        26.99        48.13        36.23        38.76 
TCGA-EJ-7125 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI 
       61.15        23.90        25.68         7.56        15.42        13.45 
TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-6499 TCGA-HC-7078 TCGA-HC-7210 TCGA-HC-7213 
        3.32        26.66        50.73         5.33        28.54         1.97 
TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HI-7168 TCGA-J9-A52B TCGA-KK-A59V TCGA-KK-A59Z 
        1.15         0.76        78.61        13.87        93.99        61.78 
TCGA-KK-A6DY TCGA-KK-A8IB TCGA-M7-A725 TCGA-VN-A943 TCGA-VP-A87H TCGA-VP-AA1N 
      115.86         2.73        18.84         4.34        21.80        17.82 
TCGA-XJ-A83G TCGA-XJ-A9DX TCGA-XK-AAJT TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       38.04        25.97        37.02        36.95        71.77        62.14 
TCGA-YL-A8SK TCGA-YL-A8SQ TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A9ND 
       37.97        62.79        41.39        62.37         6.02 

$`AMP PEAK  9(8P11.23) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 
        1.02        24.03         2.04        13.02        15.98         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        48.53        38.53        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       49.02        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
        0.30        38.37        25.87        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7708 
       12.92        13.71        18.41         9.14         2.99        28.41 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 
       46.52        47.44        45.30        39.39        44.81        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       39.95        38.01        40.31        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 
       25.15        27.29        58.22        56.75        52.87        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 
        2.93         2.01         2.37        14.47         0.79        28.60 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56         1.84        19.36        22.42         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.58        15.88        22.36         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
        4.41        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 
        5.85        10.62        56.28        44.68        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF TCGA-KK-A8IL 
       58.19        27.62        34.95        22.75        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       15.88         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 
       15.52        15.81        30.15        32.91        15.09       106.95 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       26.47        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       60.92        66.97        48.85        21.53         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR 
       27.81         3.91        48.03         9.04         2.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.50        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S9 
       39.65        25.48        52.96        49.02        38.56        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH 
       45.86        26.24       106.75        71.34         7.00        14.04 
TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       60.99        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        1.12         7.86 

  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                          0.76                           0.30 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                        115.86                         151.36 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                         26.99                          23.03 
[1] "0.8 - 115.9 (27.0)" "0.3 - 151.4 (23.0)"
[1] "hr="     "8.7e+07"
D9V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK  9(8P11.23) MUTATED    11  29   1
  AMP PEAK  9(8P11.23) WILD-TYPE 139 177   4
D9V3, multiclass
    clus
vv   AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  T2                           11                            139
  T3                           29                            177
  T4                            1                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                                cls
clus                               0   1
  AMP PEAK  9(8P11.23) MUTATED    32   6
  AMP PEAK  9(8P11.23) WILD-TYPE 231  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED     32    6
  AMP PEAK  9(8P11.23) WILD-TYPE  231   38
   clus
vv  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  0                           32                            231
  1                            6                             38
[1] 2 2
[1] FALSE
D9V5, binary
                                cls
clus                               0   1
  AMP PEAK  9(8P11.23) MUTATED     1  40
  AMP PEAK  9(8P11.23) WILD-TYPE  12 310
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED      1   40
  AMP PEAK  9(8P11.23) WILD-TYPE   12  310
                                        clus
vv                                       AMP PEAK  9(8P11.23) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              40
                                        clus
vv                                       AMP PEAK  9(8P11.23) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               310
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  9(8P11.23) MUTATED    23  14   1   0
  AMP PEAK  9(8P11.23) WILD-TYPE 220  76   4  11
D9V6, multiclass
    clus
vv   AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  R0                           23                            220
  R1                           14                             76
  R2                            1                              4
  RX                            0                             11
[1] 4 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, continuous
D9V8, continuous
D9V9, continuous
D9V10, continuous
D9V11, continuous
D9V12, continuous
D9V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8P11.23) MUTATED       0                         0    17
  AMP PEAK  9(8P11.23) WILD-TYPE     2                         7   129
D9V14, multiclass
                           clus
vv                          AMP PEAK  9(8P11.23) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               17
                           clus
vv                          AMP PEAK  9(8P11.23) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                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(10) Variable = AMP PEAK 10(8Q22.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(8Q22.1) MUTATED   100   3
  AMP PEAK 10(8Q22.1) WILD-TYPE 255   3
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                          103                           258 
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                            3                             3 
$`AMP PEAK 10(8Q22.1) MUTATED`
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5753 
       22.06        33.96         3.68        22.06        35.01         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5767 TCGA-CH-5771 TCGA-EJ-5504 
        2.04         0.92        44.02        15.06        13.02        28.93 
TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5518 
       23.90        48.13        48.53        36.23        47.80        52.27 
TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5532 TCGA-EJ-7123 
       51.88        36.66        38.76        39.75        47.87        49.02 
TCGA-EJ-7125 TCGA-EJ-7312 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-8469 
       61.15        21.80        23.90        25.68        18.15        63.98 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A65F TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 
        9.83         3.06        18.41         2.99         7.56        15.42 
TCGA-FC-A4JI TCGA-G9-6361 TCGA-G9-6366 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6494 
       13.45        46.52         3.32        26.66        31.50        58.22 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S0 TCGA-G9-A9S7 
       50.73        38.27        38.96        30.97        26.01        21.14 
TCGA-HC-7078 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-8216 
        5.33        28.60         1.97         1.48         2.07        22.42 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO 
       15.88         1.15         0.76         2.01         2.20         5.49 
TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-A67M TCGA-J4-A83J TCGA-J9-A52B TCGA-J9-A52E 
       78.61        43.69        16.04        10.19        13.87        10.62 
TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E8 TCGA-KK-A7AZ 
       93.99        44.68        61.78       115.86        58.19        27.62 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IO 
        2.73        26.43        15.88        18.84         3.19        47.21 
TCGA-VN-A88M TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A87D TCGA-VP-A87H 
        6.02        30.15         4.34        26.47        60.92        21.80 
TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YL-A8HM 
       17.82        37.18        38.04        31.50        37.02        36.95 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SQ 
       71.77        62.14        60.56        37.97       106.75        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WY 
        7.00        14.04        41.39        60.99        62.37        28.34 
TCGA-ZG-A9ND 
        6.02 

$`AMP PEAK 10(8Q22.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 
       20.42        43.79        25.35         2.99         6.97         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       12.99        13.97         1.97        24.03         1.02        13.02 
TCGA-CH-5752 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 
       31.00        12.00         1.02        23.01         1.02        24.03 
TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
        2.04        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 
       29.79        46.52        44.88        26.30        45.73        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       27.19        38.93        36.69        38.53        60.23        46.55 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5542 
       64.50        68.35        43.07        60.23        41.85        29.06 
TCGA-EJ-7115 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       27.02        83.57         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 
       38.37        25.87        20.55        14.53        14.14        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 
       17.29         3.75        23.05        19.92        64.47        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46H TCGA-EJ-A46I 
       10.32         5.33         4.24        17.49         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-FC-7708 TCGA-FC-A5OB 
       17.62        12.92        13.71         9.14        28.41         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 
       49.81        46.16        50.70        49.35        47.15        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        39.39        44.81        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 
       40.31        37.97        45.80        25.15        27.29        56.75 
TCGA-G9-6498 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       52.87        27.91        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       30.94         3.68        19.76         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       14.47        28.54         0.79         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
        1.71         0.72         2.10         2.66         1.74         1.68 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 
        1.48        17.85        24.56         1.84        19.36         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AQ 
        1.58        22.36         1.78         1.61         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
        1.45         1.25         4.41        88.24        82.92        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       12.30        21.76        17.03        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C 
        9.17         6.77        10.39        14.37        20.28         5.85 
TCGA-KK-A59X TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       56.28        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IL 
       49.25       113.33        67.07        34.95        22.75        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
       41.00       114.64        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R 
       25.51        12.95        15.52        15.81        32.91        15.09 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      106.95        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR 
       66.97        48.85        21.53         5.79        27.81         3.91 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        25.97        31.96        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL 
       28.54        30.58        29.23        27.09        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       52.96        49.02        38.56        16.83        45.50        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SP 
       45.14        28.77        47.38        45.86        26.24        71.34 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       24.33        49.91         1.64         4.93         1.12         7.86 

  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                         0.76                          0.30 
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                       115.86                        151.36 
  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE 
                       26.660                        22.555 
[1] "0.8 - 115.9 (26.7)" "0.3 - 151.4 (22.6)"
[1] "hr=" "2.1"
D10V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 10(8Q22.1) MUTATED    26  74   3
  AMP PEAK 10(8Q22.1) WILD-TYPE 124 132   2
D10V3, multiclass
    clus
vv   AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE
  T2                          26                           124
  T3                          74                           132
  T4                           3                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                               cls
clus                              0   1
  AMP PEAK 10(8Q22.1) MUTATED    80  17
  AMP PEAK 10(8Q22.1) WILD-TYPE 183  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(8Q22.1) MUTATED     80   17
  AMP PEAK 10(8Q22.1) WILD-TYPE  183   27
   clus
vv  AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE
  0                          80                           183
  1                          17                            27
[1] 2 2
[1] FALSE
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(8Q22.1) MUTATED     2 101
  AMP PEAK 10(8Q22.1) WILD-TYPE  11 249
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(8Q22.1) MUTATED      2  101
  AMP PEAK 10(8Q22.1) WILD-TYPE   11  249
                                        clus
vv                                       AMP PEAK 10(8Q22.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            101
                                        clus
vv                                       AMP PEAK 10(8Q22.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              249
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(8Q22.1) MUTATED    59  35   1   4
  AMP PEAK 10(8Q22.1) WILD-TYPE 184  55   4   7
D10V6, multiclass
    clus
vv   AMP PEAK 10(8Q22.1) MUTATED AMP PEAK 10(8Q22.1) WILD-TYPE
  R0                          59                           184
  R1                          35                            55
  R2                           1                             4
  RX                           4                             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"
D10V7, continuous
D10V8, continuous
D10V9, continuous
D10V10, continuous
D10V11, continuous
D10V12, continuous
D10V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(8Q22.1) MUTATED       0                         2    37
  AMP PEAK 10(8Q22.1) WILD-TYPE     2                         5   109
D10V14, multiclass
                           clus
vv                          AMP PEAK 10(8Q22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              37
                           clus
vv                          AMP PEAK 10(8Q22.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               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(11) Variable = AMP PEAK 11(8Q24.21) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(8Q24.21) MUTATED    96   2
  AMP PEAK 11(8Q24.21) WILD-TYPE 259   4
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            98                            263 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                             2                              4 
$`AMP PEAK 11(8Q24.21) MUTATED`
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5753 
       22.06        33.96         3.68        22.06        35.01         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5767 TCGA-CH-5771 TCGA-EJ-5504 
        2.04         0.92        44.02        15.06        13.02        28.93 
TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5521 
       23.90        48.13        48.53        36.23        47.80        51.88 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5532 TCGA-EJ-7123 TCGA-EJ-7125 
       36.66        38.76        39.75        47.87        49.02        61.15 
TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-8469 TCGA-EJ-A46F TCGA-EJ-A46G 
       23.90        25.68        18.15        63.98         9.83         3.06 
TCGA-EJ-A65F TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6366 
       18.41         2.99         7.56        15.42        13.45         3.32 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       26.66        31.50        58.22        50.73        38.27        38.96 
TCGA-G9-7521 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7212 TCGA-HC-7213 
       30.97        26.01        21.14         5.33        28.60         1.97 
TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-8216 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.48         2.07        22.42         1.58        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HI-7168 TCGA-HI-7171 
        0.76         2.01         2.20         5.49        78.61        43.69 
TCGA-J4-A67M TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       16.04        10.62        93.99        44.68        61.78       115.86 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A724 TCGA-M7-A725 
       58.19        27.62         2.73        26.43        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IO TCGA-VN-A88M TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A875 
        3.19        47.21         6.02        30.15         4.34        26.47 
TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XJ-A9DX 
       60.92        21.80        17.82        37.18        38.04        25.97 
TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       31.50        37.02        36.95        71.77        62.14        60.56 
TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       37.97       106.75        62.79         7.00        14.04        41.39 
TCGA-YL-A9WK TCGA-ZG-A9ND 
       62.37         6.02 

$`AMP PEAK 11(8Q24.21) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 
       20.42        43.79        25.35         2.99         6.97         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       12.99        13.97         1.97        24.03         1.02        13.02 
TCGA-CH-5752 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 
       31.00        12.00         1.02        23.01         1.02        24.03 
TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
        2.04        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 
       29.79        46.52        44.88        26.30        45.73        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       27.19        38.93        36.69        38.53        60.23        46.55 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5530 TCGA-EJ-5531 
       52.27        64.50        68.35        43.07        60.23        41.85 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       29.06        27.02        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 
        6.28         0.30        38.37        25.87        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       14.14        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       64.47        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G 
        7.53        21.96        17.62        12.92        13.71         9.14 
TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.41         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6379 
       40.18        39.95        38.01        40.31        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7519 TCGA-G9-7522 
       25.15        27.29        56.75        52.87        27.91        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       28.18        32.68         6.08        30.94         3.68        19.76 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        2.66         1.74         1.68        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
        1.84        19.36         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6AN 
        1.94        17.95        22.32        22.36         1.78         1.61 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 
        2.33         3.48         1.45         1.25         4.41        88.24 
TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N 
       82.92        20.19        12.30        21.76        17.03        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59X TCGA-KK-A6E0 
       14.37        20.28        13.87         5.85        56.28        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       67.07        34.95        22.75        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-QU-A6IM TCGA-QU-A6IN 
        9.93        13.15        27.02        25.08        41.00       114.64 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A876 
       15.52        15.81        32.91        15.09       106.95        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87J 
       94.65        23.93        75.91        55.56        66.97        48.85 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK 
       21.53         5.79        27.81         3.91        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
        2.99        31.96        31.96        28.54        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       27.09        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
       45.86        26.24        71.34        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       28.34         1.64         4.93         1.12         7.86 

  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                          0.76                           0.30 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                        115.86                         151.36 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                         26.45                          22.75 
[1] "0.8 - 115.9 (26.4)" "0.3 - 151.4 (22.8)"
[1] "hr=" "1.2"
D11V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 11(8Q24.21) MUTATED    25  71   2
  AMP PEAK 11(8Q24.21) WILD-TYPE 125 135   3
D11V3, multiclass
    clus
vv   AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  T2                           25                            125
  T3                           71                            135
  T4                            2                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED    75  17
  AMP PEAK 11(8Q24.21) WILD-TYPE 188  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     75   17
  AMP PEAK 11(8Q24.21) WILD-TYPE  188   27
   clus
vv  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  0                           75                            188
  1                           17                             27
[1] 2 2
[1] FALSE
D11V5, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED     3  95
  AMP PEAK 11(8Q24.21) WILD-TYPE  10 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED      3   95
  AMP PEAK 11(8Q24.21) WILD-TYPE   10  255
                                        clus
vv                                       AMP PEAK 11(8Q24.21) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              95
                                        clus
vv                                       AMP PEAK 11(8Q24.21) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               255
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 11(8Q24.21) MUTATED    58  31   1   4
  AMP PEAK 11(8Q24.21) WILD-TYPE 185  59   4   7
D11V6, multiclass
    clus
vv   AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  R0                           58                            185
  R1                           31                             59
  R2                            1                              4
  RX                            4                              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"
D11V7, continuous
D11V8, continuous
D11V9, continuous
D11V10, continuous
D11V11, continuous
D11V12, continuous
D11V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(8Q24.21) MUTATED       0                         2    35
  AMP PEAK 11(8Q24.21) WILD-TYPE     2                         5   111
D11V14, multiclass
                           clus
vv                          AMP PEAK 11(8Q24.21) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               35
                           clus
vv                          AMP PEAK 11(8Q24.21) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(9Q33.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(9Q33.3) MUTATED    37   0
  AMP PEAK 12(9Q33.3) WILD-TYPE 318   6
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                           37                           324 
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                            0                             6 
$`AMP PEAK 12(9Q33.3) MUTATED`
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5771 TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5496 
       35.01         1.02        13.02        33.01        33.11        19.56 
TCGA-EJ-5526 TCGA-EJ-7789 TCGA-EJ-A46G TCGA-EJ-A65F TCGA-FC-A4JI TCGA-G9-6356 
       38.76        18.15         3.06        18.41        13.45        47.15 
TCGA-G9-6373 TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8266 
       26.66        30.97         1.97         1.84        22.42         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HI-7168 TCGA-KK-A59Z TCGA-VN-A88I 
       22.36         0.76         1.78        78.61        61.78         8.84 
TCGA-VN-A88K TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87D TCGA-VP-A87H TCGA-X4-A8KQ 
       25.51       106.95        26.47        60.92        21.80        37.18 
TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8SC TCGA-YL-A8SL TCGA-YL-A8SQ 
       25.97        31.50        71.77        41.46        26.24        62.79 
TCGA-YL-A9WK 
       62.37 

$`AMP PEAK 12(9Q33.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5754 
        1.97        24.03         1.02        13.02        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5497 TCGA-EJ-5498 
       32.02         2.99        29.00        27.16        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 
       64.50        51.88        68.35        43.07        36.66        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.53        14.14        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
        4.24        17.49         9.83         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       12.92        13.71         9.14         2.99         7.56        28.41 
TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       15.42         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 
       40.18        39.95        38.01        40.31        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.27        38.96        27.91        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       28.54         0.79        28.60         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 
        3.22        30.51         1.48        17.85        24.56        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.32         1.58        15.88         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY 
        5.85        10.62        93.99        56.28        44.68       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       15.09         4.34        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       55.56        66.97        48.85        21.53        17.82         5.79 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       36.95        62.14        60.56        16.83        45.50        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        47.38        45.86        37.97       106.75        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        14.04        41.39        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                         0.76                          0.30 
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                       106.95                        151.36 
  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE 
                       26.240                        23.885 
[1] "0.8 - 107.0 (26.2)" "0.3 - 151.4 (23.9)"
[1] "hr="     "8.1e+07"
D12V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 12(9Q33.3) MUTATED     5  32   1
  AMP PEAK 12(9Q33.3) WILD-TYPE 145 174   4
D12V3, multiclass
    clus
vv   AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE
  T2                           5                           145
  T3                          32                           174
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                               cls
clus                              0   1
  AMP PEAK 12(9Q33.3) MUTATED    24  12
  AMP PEAK 12(9Q33.3) WILD-TYPE 239  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9Q33.3) MUTATED     24   12
  AMP PEAK 12(9Q33.3) WILD-TYPE  239   32
   clus
vv  AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE
  0                          24                           239
  1                          12                            32
[1] 2 2
[1] FALSE
D12V5, binary
                               cls
clus                              0   1
  AMP PEAK 12(9Q33.3) MUTATED     4  34
  AMP PEAK 12(9Q33.3) WILD-TYPE   9 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9Q33.3) MUTATED      4   34
  AMP PEAK 12(9Q33.3) WILD-TYPE    9  316
                                        clus
vv                                       AMP PEAK 12(9Q33.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             34
                                        clus
vv                                       AMP PEAK 12(9Q33.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              316
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(9Q33.3) MUTATED    22  13   1   1
  AMP PEAK 12(9Q33.3) WILD-TYPE 221  77   4  10
D12V6, multiclass
    clus
vv   AMP PEAK 12(9Q33.3) MUTATED AMP PEAK 12(9Q33.3) WILD-TYPE
  R0                          22                           221
  R1                          13                            77
  R2                           1                             4
  RX                           1                            10
[1] 4 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, continuous
D12V8, continuous
D12V9, continuous
D12V10, continuous
D12V11, continuous
D12V12, continuous
D12V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(9Q33.3) MUTATED       0                         1    12
  AMP PEAK 12(9Q33.3) WILD-TYPE     2                         6   134
D12V14, multiclass
                           clus
vv                          AMP PEAK 12(9Q33.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              12
                           clus
vv                          AMP PEAK 12(9Q33.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(11Q13.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(11Q13.2) MUTATED    24   0
  AMP PEAK 13(11Q13.2) WILD-TYPE 331   6
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                            24                            337 
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                             0                              6 
$`AMP PEAK 13(11Q13.2) MUTATED`
TCGA-CH-5751 TCGA-CH-5788 TCGA-EJ-5495 TCGA-EJ-5511 TCGA-EJ-7784 TCGA-EJ-A46G 
       35.01        26.99        33.11        48.53        25.68         3.06 
TCGA-FC-A4JI TCGA-G9-7523 TCGA-HC-7745 TCGA-HC-8216 TCGA-HC-8265 TCGA-HI-7168 
       13.45        28.18         2.07        22.42        15.88        78.61 
TCGA-KK-A6E8 TCGA-KK-A8IF TCGA-VN-A88K TCGA-X4-A8KS TCGA-XJ-A9DX TCGA-YL-A8HM 
       58.19        26.43        25.51        27.81        25.97        36.95 
TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SK TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI 
       60.56        45.50        37.97        62.79        14.04        41.39 

$`AMP PEAK 13(11Q13.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        36.69        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
        5.75        27.68         6.28         0.30        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.87        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB 
        9.14         2.99         7.56        28.41        15.42         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.48         1.68        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       17.95        22.32         1.58         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 
        3.48         1.45         1.25         4.41        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       93.99        56.28        44.68        61.78       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL 
       67.07        27.62        34.95        22.75         2.73        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M 
       86.14        11.90         8.19         8.84        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
       17.82         5.79        37.18         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA 
       52.96        49.02        38.56        71.77        62.14        16.83 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL 
       41.46        45.14        28.77        47.38        45.86        26.24 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
      106.75        71.34         7.00        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                          2.07                           0.30 
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                         78.61                         151.36 
  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE 
                        27.995                         22.750 
[1] "2.1 - 78.6 (28.0)"  "0.3 - 151.4 (22.8)"
[1] "hr="     "7.6e+07"
D13V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 13(11Q13.2) MUTATED     3  21   1
  AMP PEAK 13(11Q13.2) WILD-TYPE 147 185   4
D13V3, multiclass
    clus
vv   AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE
  T2                            3                            147
  T3                           21                            185
  T4                            1                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.2) MUTATED    15   8
  AMP PEAK 13(11Q13.2) WILD-TYPE 248  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.2) MUTATED     15    8
  AMP PEAK 13(11Q13.2) WILD-TYPE  248   36
   clus
vv  AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE
  0                           15                            248
  1                            8                             36
[1] 2 2
[1] FALSE
D13V5, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q13.2) MUTATED     2  23
  AMP PEAK 13(11Q13.2) WILD-TYPE  11 327
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.2) MUTATED      2   23
  AMP PEAK 13(11Q13.2) WILD-TYPE   11  327
                                        clus
vv                                       AMP PEAK 13(11Q13.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              23
                                        clus
vv                                       AMP PEAK 13(11Q13.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               327
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(11Q13.2) MUTATED    14   9   0   2
  AMP PEAK 13(11Q13.2) WILD-TYPE 229  81   5   9
D13V6, multiclass
    clus
vv   AMP PEAK 13(11Q13.2) MUTATED AMP PEAK 13(11Q13.2) WILD-TYPE
  R0                           14                            229
  R1                            9                             81
  R2                            0                              5
  RX                            2                              9
[1] 4 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, continuous
D13V8, continuous
D13V9, continuous
D13V10, continuous
D13V11, continuous
D13V12, continuous
D13V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(11Q13.2) MUTATED       0                         1     6
  AMP PEAK 13(11Q13.2) WILD-TYPE     2                         6   140
D13V14, multiclass
                           clus
vv                          AMP PEAK 13(11Q13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                6
                           clus
vv                          AMP PEAK 13(11Q13.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                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(14) Variable = AMP PEAK 14(12Q23.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(12Q23.1) MUTATED    21   0
  AMP PEAK 14(12Q23.1) WILD-TYPE 334   6
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                            21                            340 
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                             0                              6 
$`AMP PEAK 14(12Q23.1) MUTATED`
TCGA-2A-A8W3 TCGA-CH-5761 TCGA-CH-5762 TCGA-EJ-5510 TCGA-EJ-5514 TCGA-EJ-5519 
       25.35         0.92        44.02        36.69        36.23        64.50 
TCGA-EJ-5526 TCGA-EJ-A65F TCGA-FC-A4JI TCGA-G9-7521 TCGA-HC-8264 TCGA-HC-8265 
       38.76        18.41        13.45        30.97         1.58        15.88 
TCGA-KK-A7AZ TCGA-VP-A87H TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-YL-A8S8 TCGA-YL-A8SO 
       27.62        21.80        25.97        31.50        62.14       106.75 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WY 
       62.79        14.04        28.34 

$`AMP PEAK 14(12Q23.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 
       20.42        43.79        22.06        33.96         3.68         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.13        48.53        38.53        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 
       52.27        51.88        68.35        43.07        36.66        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        17.62        12.92        13.71         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        7.56        28.41        15.42         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        52.87        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       38.96        27.91        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       21.14         6.08        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60         1.97         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
       17.95        22.32         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        1.45         1.25         4.41        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       93.99        56.28        44.68        61.78       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       67.07        58.19        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       15.09         4.34       106.95        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       23.93        75.91        55.56        60.92        66.97        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIW 
       38.04        48.03         9.04         2.99        31.96        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SR 
       47.38        45.86        37.97        26.24        71.34         7.00 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW 
       41.39        60.99        62.37        24.33        49.91         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                          0.92                           0.30 
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                        106.75                         151.36 
  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE 
                         28.34                          23.46 
[1] "0.9 - 106.8 (28.3)" "0.3 - 151.4 (23.5)"
[1] "hr="     "7.5e+07"
D14V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 14(12Q23.1) MUTATED     2  19   0
  AMP PEAK 14(12Q23.1) WILD-TYPE 148 187   5
D14V3, multiclass
    clus
vv   AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE
  T2                            2                            148
  T3                           19                            187
  T4                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q23.1) MUTATED    11   8
  AMP PEAK 14(12Q23.1) WILD-TYPE 252  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q23.1) MUTATED     11    8
  AMP PEAK 14(12Q23.1) WILD-TYPE  252   36
   clus
vv  AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE
  0                           11                            252
  1                            8                             36
[1] 2 2
[1] FALSE
D14V5, binary
                                cls
clus                               0   1
  AMP PEAK 14(12Q23.1) MUTATED     2  19
  AMP PEAK 14(12Q23.1) WILD-TYPE  11 331
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q23.1) MUTATED      2   19
  AMP PEAK 14(12Q23.1) WILD-TYPE   11  331
                                        clus
vv                                       AMP PEAK 14(12Q23.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              19
                                        clus
vv                                       AMP PEAK 14(12Q23.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               331
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(12Q23.1) MUTATED    10  10   1   0
  AMP PEAK 14(12Q23.1) WILD-TYPE 233  80   4  11
D14V6, multiclass
    clus
vv   AMP PEAK 14(12Q23.1) MUTATED AMP PEAK 14(12Q23.1) WILD-TYPE
  R0                           10                            233
  R1                           10                             80
  R2                            1                              4
  RX                            0                             11
[1] 4 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, continuous
D14V8, continuous
D14V9, continuous
D14V10, continuous
D14V11, continuous
D14V12, continuous
D14V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(12Q23.1) MUTATED       0                         0     6
  AMP PEAK 14(12Q23.1) WILD-TYPE     2                         7   140
D14V14, multiclass
                           clus
vv                          AMP PEAK 14(12Q23.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                6
                           clus
vv                          AMP PEAK 14(12Q23.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                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(15) Variable = AMP PEAK 15(13Q12.11) MUTATION ANALYSIS
D15V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 15(13Q12.11) MUTATED    16   0
  AMP PEAK 15(13Q12.11) WILD-TYPE 339   6
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                             16                             345 
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                              0                               6 
$`AMP PEAK 15(13Q12.11) MUTATED`
TCGA-CH-5751 TCGA-CH-5788 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-A46G TCGA-EJ-A65M 
       35.01        26.99        25.68        18.15         3.06         7.56 
TCGA-FC-A4JI TCGA-G9-6329 TCGA-HC-7209 TCGA-J9-A52B TCGA-J9-A52E TCGA-VP-A872 
       13.45        41.62        14.47        13.87        10.62       106.95 
TCGA-XJ-A9DX TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SF 
       25.97        71.77        60.56        45.14 

$`AMP PEAK 15(13Q12.11) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       23.90        38.37        25.87        20.55        14.53        14.14 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        9.83         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB 
       18.41         9.14         2.99        28.41        15.42         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       17.23        16.24         1.78        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7210 
       19.76         5.33         2.93         2.01         2.37        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        5.85        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 
       30.15        32.91        15.09         4.34        26.47        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       94.65        23.93        75.91        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        48.85        21.53        17.82         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        31.50        31.96        28.54        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       27.09        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       38.56        36.95        62.14        16.83        45.50        41.46 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                           3.06                            0.30 
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                         106.95                          151.36 
  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE 
                         25.825                          23.900 
[1] "3.1 - 107.0 (25.8)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D15V2, continuous
                                 vv
clus                               T2  T3  T4
  AMP PEAK 15(13Q12.11) MUTATED     4  12   1
  AMP PEAK 15(13Q12.11) WILD-TYPE 146 194   4
D15V3, multiclass
    clus
vv   AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE
  T2                             4                             146
  T3                            12                             194
  T4                             1                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                                 cls
clus                                0   1
  AMP PEAK 15(13Q12.11) MUTATED    12   3
  AMP PEAK 15(13Q12.11) WILD-TYPE 251  41
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(13Q12.11) MUTATED     12    3
  AMP PEAK 15(13Q12.11) WILD-TYPE  251   41
   clus
vv  AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE
  0                            12                             251
  1                             3                              41
[1] 2 2
[1] FALSE
D15V5, binary
                                 cls
clus                                0   1
  AMP PEAK 15(13Q12.11) MUTATED     3  14
  AMP PEAK 15(13Q12.11) WILD-TYPE  10 336
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(13Q12.11) MUTATED      3   14
  AMP PEAK 15(13Q12.11) WILD-TYPE   10  336
                                        clus
vv                                       AMP PEAK 15(13Q12.11) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               14
                                        clus
vv                                       AMP PEAK 15(13Q12.11) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                336
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 15(13Q12.11) MUTATED     9   7   0   0
  AMP PEAK 15(13Q12.11) WILD-TYPE 234  83   5  11
D15V6, multiclass
    clus
vv   AMP PEAK 15(13Q12.11) MUTATED AMP PEAK 15(13Q12.11) WILD-TYPE
  R0                             9                             234
  R1                             7                              83
  R2                             0                               5
  RX                             0                              11
[1] 4 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, continuous
D15V8, continuous
D15V9, continuous
D15V10, continuous
D15V11, continuous
D15V12, continuous
D15V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(13Q12.11) MUTATED       0                         1     5
  AMP PEAK 15(13Q12.11) WILD-TYPE     2                         6   141
D15V14, multiclass
                           clus
vv                          AMP PEAK 15(13Q12.11) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                 5
                           clus
vv                          AMP PEAK 15(13Q12.11) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               6
  WHITE                                                 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(16) Variable = AMP PEAK 16(14Q21.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(14Q21.1) MUTATED    19   1
  AMP PEAK 16(14Q21.1) WILD-TYPE 336   5
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                            20                            341 
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                             1                              5 
$`AMP PEAK 16(14Q21.1) MUTATED`
TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5772 TCGA-EJ-5495 TCGA-EJ-5514 TCGA-EJ-7331 
       31.00         0.92        15.98        33.11        36.23         0.30 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-FC-A4JI TCGA-G9-6366 TCGA-G9-A9S0 TCGA-HC-8261 
        3.06         2.99        13.45         3.32        26.01        17.95 
TCGA-HC-8265 TCGA-HC-A631 TCGA-KK-A59Z TCGA-VP-A872 TCGA-XJ-A9DX TCGA-XK-AAIV 
       15.88         1.78        61.78       106.95        25.97        31.50 
TCGA-XK-AAJ3 TCGA-YL-A8SK 
       28.54        37.97 

$`AMP PEAK 16(14Q21.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        35.01         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 
       32.02        33.01         2.99        29.00        27.16        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        48.53        38.53        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       27.02        49.02        61.15        83.57        21.80         9.70 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
        9.50         9.37        16.77         7.66        17.52         5.75 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
       27.68         6.28        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       10.32         5.33         4.24        17.49         9.83         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        7.56        28.41        15.42         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       39.39        44.81        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        52.87        50.73        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 
       27.91        30.97        35.34        28.18        32.68        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
        1.97         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8262 
        3.12        23.87         2.17         2.27         1.94        22.32 
TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL 
        1.58         1.15        22.36         0.76         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       44.68       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       26.47        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
        9.04         2.99        31.96        31.96        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       27.09        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       38.56        36.95        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       45.50        41.46        45.14        28.77        47.38        45.86 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       26.24       106.75        71.34        62.79         7.00        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       41.39        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                          0.30                           0.72 
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                        106.95                         151.36 
  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE 
                         21.96                          23.93 
[1] "0.3 - 107.0 (22.0)" "0.7 - 151.4 (23.9)"
[1] "hr=" "4"  
D16V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 16(14Q21.1) MUTATED     5  15   0
  AMP PEAK 16(14Q21.1) WILD-TYPE 145 191   5
D16V3, multiclass
    clus
vv   AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE
  T2                            5                            145
  T3                           15                            191
  T4                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                                cls
clus                               0   1
  AMP PEAK 16(14Q21.1) MUTATED    12   5
  AMP PEAK 16(14Q21.1) WILD-TYPE 251  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(14Q21.1) MUTATED     12    5
  AMP PEAK 16(14Q21.1) WILD-TYPE  251   39
   clus
vv  AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE
  0                           12                            251
  1                            5                             39
[1] 2 2
[1] FALSE
D16V5, binary
                                cls
clus                               0   1
  AMP PEAK 16(14Q21.1) MUTATED     3  17
  AMP PEAK 16(14Q21.1) WILD-TYPE  10 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(14Q21.1) MUTATED      3   17
  AMP PEAK 16(14Q21.1) WILD-TYPE   10  333
                                        clus
vv                                       AMP PEAK 16(14Q21.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              17
                                        clus
vv                                       AMP PEAK 16(14Q21.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               333
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(14Q21.1) MUTATED    13   7   0   0
  AMP PEAK 16(14Q21.1) WILD-TYPE 230  83   5  11
D16V6, multiclass
    clus
vv   AMP PEAK 16(14Q21.1) MUTATED AMP PEAK 16(14Q21.1) WILD-TYPE
  R0                           13                            230
  R1                            7                             83
  R2                            0                              5
  RX                            0                             11
[1] 4 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, continuous
D16V8, continuous
D16V9, continuous
D16V10, continuous
D16V11, continuous
D16V12, continuous
D16V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(14Q21.1) MUTATED       0                         0     7
  AMP PEAK 16(14Q21.1) WILD-TYPE     2                         7   139
D16V14, multiclass
                           clus
vv                          AMP PEAK 16(14Q21.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                7
                           clus
vv                          AMP PEAK 16(14Q21.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                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(17) Variable = AMP PEAK 17(15Q11.2) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(15Q11.2) MUTATED     8   1
  AMP PEAK 17(15Q11.2) WILD-TYPE 347   5
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                             9                            352 
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                             1                              5 
$`AMP PEAK 17(15Q11.2) MUTATED`
TCGA-EJ-5514 TCGA-EJ-7328 TCGA-G9-7525 TCGA-HC-A6AO TCGA-XJ-A9DX TCGA-XK-AAIV 
       36.23        27.68        32.68         5.49        25.97        31.50 
TCGA-YL-A8SK TCGA-YL-A9WH TCGA-YL-A9WJ 
       37.97        14.04        60.99 

$`AMP PEAK 17(15Q11.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       38.53        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 
       16.77         7.66        17.52         5.75         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        5.85        10.62        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       26.47        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        9.04         2.99        31.96        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        38.56        36.95        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        26.24       106.75        71.34        62.79         7.00 
TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       41.39        62.37        24.33        49.91        28.34         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                          5.49                           0.30 
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                         60.99                         151.36 
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                        31.500                         23.885 
[1] "5.5 - 61.0 (31.5)"  "0.3 - 151.4 (23.9)"
[1] "hr=" "6.4"
D17V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 17(15Q11.2) MUTATED     3   7   0
  AMP PEAK 17(15Q11.2) WILD-TYPE 147 199   5
D17V3, multiclass
    clus
vv   AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE
  T2                            3                            147
  T3                            7                            199
  T4                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q11.2) MUTATED     4   5
  AMP PEAK 17(15Q11.2) WILD-TYPE 259  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q11.2) MUTATED      4    5
  AMP PEAK 17(15Q11.2) WILD-TYPE  259   39
   clus
vv  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE
  0                            4                            259
  1                            5                             39
[1] 2 2
[1] FALSE
D17V5, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q11.2) MUTATED     1   9
  AMP PEAK 17(15Q11.2) WILD-TYPE  12 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q11.2) MUTATED      1    9
  AMP PEAK 17(15Q11.2) WILD-TYPE   12  341
                                        clus
vv                                       AMP PEAK 17(15Q11.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               9
                                        clus
vv                                       AMP PEAK 17(15Q11.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               341
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(15Q11.2) MUTATED     5   5   0   0
  AMP PEAK 17(15Q11.2) WILD-TYPE 238  85   5  11
D17V6, multiclass
    clus
vv   AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE
  R0                            5                            238
  R1                            5                             85
  R2                            0                              5
  RX                            0                             11
[1] 4 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, continuous
D17V8, continuous
D17V9, continuous
D17V10, continuous
D17V11, continuous
D17V12, continuous
D17V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(15Q11.2) MUTATED       0                         0     2
  AMP PEAK 17(15Q11.2) WILD-TYPE     2                         7   144
D17V14, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 17(15Q11.2) MUTATED"
clus
  AMP PEAK 17(15Q11.2) MUTATED AMP PEAK 17(15Q11.2) WILD-TYPE 
                             2                            153 
                    TCGA-CH-5737                     TCGA-CH-5738 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5739                     TCGA-CH-5740 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5741                     TCGA-CH-5743 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5744                     TCGA-CH-5746 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5748                     TCGA-CH-5750 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5751                     TCGA-CH-5752 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5753                     TCGA-CH-5754 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5761                     TCGA-CH-5762 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5763                     TCGA-CH-5764 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5765                     TCGA-CH-5766 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5767                     TCGA-CH-5768 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5769                     TCGA-CH-5771 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5772                     TCGA-CH-5788 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5789                     TCGA-CH-5790 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5791                     TCGA-CH-5792 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-CH-5794                     TCGA-EJ-5494 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5495                     TCGA-EJ-5496 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5497                     TCGA-EJ-5498 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5499                     TCGA-EJ-5501 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5503                     TCGA-EJ-5504 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5505                     TCGA-EJ-5506 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5507                     TCGA-EJ-5508 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5509                     TCGA-EJ-5510 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5511                     TCGA-EJ-5512 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5515                     TCGA-EJ-5516 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5517                     TCGA-EJ-5518 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5519                     TCGA-EJ-5521 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5522                     TCGA-EJ-5524 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5525                     TCGA-EJ-5526 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5527                     TCGA-EJ-5530 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5531                     TCGA-EJ-5532 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-5542                     TCGA-EJ-7115 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7123                     TCGA-EJ-7125 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7314                     TCGA-EJ-7315 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7317                     TCGA-EJ-7321 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7327                     TCGA-EJ-7330 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7331                     TCGA-EJ-7781 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7782                     TCGA-EJ-7783 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7784                     TCGA-EJ-7785 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7786                     TCGA-EJ-7788 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7789                     TCGA-EJ-7791 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7792                     TCGA-EJ-7793 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-EJ-7794                     TCGA-EJ-7797 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-FC-7708                     TCGA-FC-7961 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6329                     TCGA-G9-6332 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6333                     TCGA-G9-6336 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6338                     TCGA-G9-6342 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6343                     TCGA-G9-6348 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6351                     TCGA-G9-6353 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6356                     TCGA-G9-6361 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6362                     TCGA-G9-6363 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6364                     TCGA-G9-6365 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6366                     TCGA-G9-6367 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6369                     TCGA-G9-6370 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6371                     TCGA-G9-6373 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6377                     TCGA-G9-6378 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6384                     TCGA-G9-6385 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6494                     TCGA-G9-6496 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-G9-6499                     TCGA-H9-7775 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7075                     TCGA-HC-7077 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7078                     TCGA-HC-7079 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7080                     TCGA-HC-7081 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7209                     TCGA-HC-7210 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7211                     TCGA-HC-7212 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7213                     TCGA-HC-7230 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7231                     TCGA-HC-7232 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7233                     TCGA-HC-7736 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7737                     TCGA-HC-7738 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7740                     TCGA-HC-7742 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7744                     TCGA-HC-7745 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7747                     TCGA-HC-7748 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7749                     TCGA-HC-7750 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7752                     TCGA-HC-7818 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7819                     TCGA-HC-7820 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HC-7821                     TCGA-HI-7168 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HI-7169                     TCGA-HI-7170 
"AMP PEAK 17(15Q11.2) WILD-TYPE" "AMP PEAK 17(15Q11.2) WILD-TYPE" 
                    TCGA-HI-7171 
"AMP PEAK 17(15Q11.2) WILD-TYPE" 

Clustering(18) Variable = AMP PEAK 18(16Q11.2) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(16Q11.2) MUTATED    18   0
  AMP PEAK 18(16Q11.2) WILD-TYPE 337   6
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                            18                            343 
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                             0                              6 
$`AMP PEAK 18(16Q11.2) MUTATED`
TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-7328 TCGA-EJ-7783 TCGA-EJ-8469 
       22.06        35.01         0.92        27.68        25.87        63.98 
TCGA-FC-A4JI TCGA-HC-7210 TCGA-HC-7232 TCGA-HC-7742 TCGA-HC-A4ZV TCGA-HI-7168 
       13.45        28.54         2.93         1.48         0.76        78.61 
TCGA-KK-A8IF TCGA-QU-A6IL TCGA-VP-A87K TCGA-XJ-A9DX TCGA-YL-A8S9 TCGA-YL-A9WH 
       26.43         3.19        21.53        25.97        60.56        14.04 

$`AMP PEAK 18(16Q11.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        31.00         1.02         2.04 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       17.52         5.75         6.28         0.30        23.90        38.37 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 
       17.29         3.75        23.05        19.92        64.47        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB 
        9.14         2.99         7.56        28.41        15.42         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       14.47         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
        1.71         0.72         2.10         2.66         1.74         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 
        3.48         1.45         1.25         4.41        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       93.99        56.28        44.68        61.78       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
       67.07        58.19        27.62        34.95        22.75         2.73 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08        15.88        18.84        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
        4.34       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
       48.03         9.04         2.99        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       62.14        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       62.79         7.00        41.39        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                          0.76                           0.30 
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                         78.61                         151.36 
  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE 
                        23.965                         23.930 
[1] "0.8 - 78.6 (24.0)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D18V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 18(16Q11.2) MUTATED     2  15   1
  AMP PEAK 18(16Q11.2) WILD-TYPE 148 191   4
D18V3, multiclass
    clus
vv   AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE
  T2                            2                            148
  T3                           15                            191
  T4                            1                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                                cls
clus                               0   1
  AMP PEAK 18(16Q11.2) MUTATED    13   3
  AMP PEAK 18(16Q11.2) WILD-TYPE 250  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16Q11.2) MUTATED     13    3
  AMP PEAK 18(16Q11.2) WILD-TYPE  250   41
   clus
vv  AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE
  0                           13                            250
  1                            3                             41
[1] 2 2
[1] FALSE
D18V5, binary
                                cls
clus                               0   1
  AMP PEAK 18(16Q11.2) MUTATED     2  16
  AMP PEAK 18(16Q11.2) WILD-TYPE  11 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16Q11.2) MUTATED      2   16
  AMP PEAK 18(16Q11.2) WILD-TYPE   11  334
                                        clus
vv                                       AMP PEAK 18(16Q11.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              16
                                        clus
vv                                       AMP PEAK 18(16Q11.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               334
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(16Q11.2) MUTATED    11   6   0   1
  AMP PEAK 18(16Q11.2) WILD-TYPE 232  84   5  10
D18V6, multiclass
    clus
vv   AMP PEAK 18(16Q11.2) MUTATED AMP PEAK 18(16Q11.2) WILD-TYPE
  R0                           11                            232
  R1                            6                             84
  R2                            0                              5
  RX                            1                             10
[1] 4 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, continuous
D18V8, continuous
D18V9, continuous
D18V10, continuous
D18V11, continuous
D18V12, continuous
D18V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(16Q11.2) MUTATED       0                         0     9
  AMP PEAK 18(16Q11.2) WILD-TYPE     2                         7   137
D18V14, multiclass
                           clus
vv                          AMP PEAK 18(16Q11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                9
                           clus
vv                          AMP PEAK 18(16Q11.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                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(19) Variable = AMP PEAK 19(17Q23.2) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(17Q23.2) MUTATED    13   0
  AMP PEAK 19(17Q23.2) WILD-TYPE 342   6
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                            13                            348 
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                             0                              6 
$`AMP PEAK 19(17Q23.2) MUTATED`
TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5527 TCGA-EJ-7781 TCGA-EJ-A46G TCGA-EJ-A65F 
       23.90        36.23        39.75        23.90         3.06        18.41 
TCGA-HC-7745 TCGA-HC-8216 TCGA-HI-7168 TCGA-J4-A67L TCGA-TP-A8TT TCGA-XK-AAIV 
        2.07        22.42        78.61        17.03        11.90        31.50 
TCGA-YL-A9WH 
       14.04 

$`AMP PEAK 19(17Q23.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       27.19        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        43.07        36.66        38.76        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       17.52         5.75        27.68         6.28         0.30        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        9.83         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 
        2.66         1.74         1.48         1.68        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56         1.84        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
        4.41        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       21.76        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        5.85        10.62        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TV 
        3.19        41.00       114.64        47.21        86.14         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       30.15        32.91        15.09         4.34       106.95        26.47 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        25.97        31.96        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        38.56        36.95        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        41.39        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                          2.07                           0.30 
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                         78.61                         151.36 
  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE 
                         22.42                          24.18 
[1] "2.1 - 78.6 (22.4)"  "0.3 - 151.4 (24.2)"
[1] "hr="     "9300000"
D19V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 19(17Q23.2) MUTATED     2  11   0
  AMP PEAK 19(17Q23.2) WILD-TYPE 148 195   5
D19V3, multiclass
    clus
vv   AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE
  T2                            2                            148
  T3                           11                            195
  T4                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q23.2) MUTATED    10   3
  AMP PEAK 19(17Q23.2) WILD-TYPE 253  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q23.2) MUTATED     10    3
  AMP PEAK 19(17Q23.2) WILD-TYPE  253   41
   clus
vv  AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE
  0                           10                            253
  1                            3                             41
[1] 2 2
[1] FALSE
D19V5, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q23.2) MUTATED     2  11
  AMP PEAK 19(17Q23.2) WILD-TYPE  11 339
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q23.2) MUTATED      2   11
  AMP PEAK 19(17Q23.2) WILD-TYPE   11  339
                                        clus
vv                                       AMP PEAK 19(17Q23.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              11
                                        clus
vv                                       AMP PEAK 19(17Q23.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               339
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(17Q23.2) MUTATED    11   2   0   0
  AMP PEAK 19(17Q23.2) WILD-TYPE 232  88   5  11
D19V6, multiclass
    clus
vv   AMP PEAK 19(17Q23.2) MUTATED AMP PEAK 19(17Q23.2) WILD-TYPE
  R0                           11                            232
  R1                            2                             88
  R2                            0                              5
  RX                            0                             11
[1] 4 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, continuous
D19V8, continuous
D19V9, continuous
D19V10, continuous
D19V11, continuous
D19V12, continuous
D19V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(17Q23.2) MUTATED       0                         0     6
  AMP PEAK 19(17Q23.2) WILD-TYPE     2                         7   140
D19V14, multiclass
                           clus
vv                          AMP PEAK 19(17Q23.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                6
                           clus
vv                          AMP PEAK 19(17Q23.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                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(20) Variable = AMP PEAK 20(19Q13.43) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(19Q13.43) MUTATED    10   0
  AMP PEAK 20(19Q13.43) WILD-TYPE 345   6
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                             10                             351 
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                              0                               6 
$`AMP PEAK 20(19Q13.43) MUTATED`
TCGA-EJ-5518 TCGA-EJ-A46G TCGA-HC-7078 TCGA-HC-7213 TCGA-HI-7168 TCGA-VP-A875 
       52.27         3.06         5.33         1.97        78.61        26.47 
TCGA-VP-A87D TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8SB 
       60.92        31.50        71.77        45.50 

$`AMP PEAK 20(19Q13.43) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 
       38.53        36.23        60.23        46.55        47.80        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
        5.33         4.24        17.49         9.83         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       19.76         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
        0.79        28.60         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 
        2.33         3.48         1.45         1.25         4.41        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        21.76        17.03 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       16.04        16.54        16.14        20.52        14.93        17.19 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        13.32        17.36         9.17         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C 
        6.77        10.39        14.37        20.28        13.87         5.85 
TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       10.62        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 
       30.15        32.91        15.09         4.34       106.95        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H 
       94.65        23.93        75.91        55.56        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       48.85        21.53        17.82         5.79        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF 
       36.95        62.14        60.56        16.83        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                           1.97                            0.30 
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                          78.61                          151.36 
  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE 
                           38.5                            23.9 
[1] "2.0 - 78.6 (38.5)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D20V2, continuous
                                 vv
clus                               T2  T3  T4
  AMP PEAK 20(19Q13.43) MUTATED     0   9   1
  AMP PEAK 20(19Q13.43) WILD-TYPE 150 197   4
D20V3, multiclass
    clus
vv   AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE
  T2                             0                             150
  T3                             9                             197
  T4                             1                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                                 cls
clus                                0   1
  AMP PEAK 20(19Q13.43) MUTATED     8   2
  AMP PEAK 20(19Q13.43) WILD-TYPE 255  42
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.43) MUTATED      8    2
  AMP PEAK 20(19Q13.43) WILD-TYPE  255   42
   clus
vv  AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE
  0                             8                             255
  1                             2                              42
[1] 2 2
[1] FALSE
D20V5, binary
                                 cls
clus                                0   1
  AMP PEAK 20(19Q13.43) MUTATED     1   9
  AMP PEAK 20(19Q13.43) WILD-TYPE  12 341
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.43) MUTATED      1    9
  AMP PEAK 20(19Q13.43) WILD-TYPE   12  341
                                        clus
vv                                       AMP PEAK 20(19Q13.43) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                9
                                        clus
vv                                       AMP PEAK 20(19Q13.43) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                341
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(19Q13.43) MUTATED     6   4   0   0
  AMP PEAK 20(19Q13.43) WILD-TYPE 237  86   5  11
D20V6, multiclass
    clus
vv   AMP PEAK 20(19Q13.43) MUTATED AMP PEAK 20(19Q13.43) WILD-TYPE
  R0                             6                             237
  R1                             4                              86
  R2                             0                               5
  RX                             0                              11
[1] 4 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, continuous
D20V8, continuous
D20V9, continuous
D20V10, continuous
D20V11, continuous
D20V12, continuous
D20V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(19Q13.43) MUTATED       0                         0     4
  AMP PEAK 20(19Q13.43) WILD-TYPE     2                         7   142
D20V14, multiclass
                           clus
vv                          AMP PEAK 20(19Q13.43) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 4
                           clus
vv                          AMP PEAK 20(19Q13.43) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               7
  WHITE                                                 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(21) Variable = AMP PEAK 21(20Q13.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(20Q13.2) MUTATED    25   0
  AMP PEAK 21(20Q13.2) WILD-TYPE 330   6
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                            25                            336 
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                             0                              6 
$`AMP PEAK 21(20Q13.2) MUTATED`
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5772 TCGA-EJ-5518 TCGA-EJ-5532 TCGA-EJ-7314 
        0.92        44.02        15.98        52.27        47.87         9.70 
TCGA-EJ-7315 TCGA-EJ-A65M TCGA-G9-6494 TCGA-G9-6499 TCGA-HC-8265 TCGA-HI-7168 
        9.50         7.56        58.22        50.73        15.88        78.61 
TCGA-J9-A52E TCGA-KK-A6E8 TCGA-KK-A8IF TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87D 
       10.62        58.19        26.43       106.95        26.47        60.92 
TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A9WH TCGA-YL-A9WI 
       25.97        31.50        36.95        62.14        14.04        41.39 
TCGA-ZG-A8QY 
        1.12 

$`AMP PEAK 21(20Q13.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        1.02         2.04        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       46.55        47.80        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5542 
       36.66        38.76        39.75        60.23        41.85        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7317 
       27.02        49.02        61.15        83.57        21.80         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        2.99        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       25.15        27.29        56.75        52.87        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       21.14         6.08        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60         1.97         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       17.95        22.32         1.58         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 
        3.48         1.45         1.25         4.41        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V 
       10.39        14.37        20.28        13.87         5.85        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y 
       27.62        34.95        22.75         2.73        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E 
       84.69        94.65        23.93        75.91        55.56        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        48.85        21.53        17.82         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       71.77        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       71.34        62.79         7.00        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       49.91        28.34         1.64         4.93         7.86         6.02 

  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                          0.92                           0.30 
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                        106.95                         151.36 
  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE 
                         31.50                          23.46 
[1] "0.9 - 107.0 (31.5)" "0.3 - 151.4 (23.5)"
[1] "hr="     "7.7e+07"
D21V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 21(20Q13.2) MUTATED     2  22   2
  AMP PEAK 21(20Q13.2) WILD-TYPE 148 184   3
D21V3, multiclass
    clus
vv   AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE
  T2                            2                            148
  T3                           22                            184
  T4                            2                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                                cls
clus                               0   1
  AMP PEAK 21(20Q13.2) MUTATED    20   6
  AMP PEAK 21(20Q13.2) WILD-TYPE 243  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20Q13.2) MUTATED     20    6
  AMP PEAK 21(20Q13.2) WILD-TYPE  243   38
   clus
vv  AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE
  0                           20                            243
  1                            6                             38
[1] 2 2
[1] FALSE
D21V5, binary
                                cls
clus                               0   1
  AMP PEAK 21(20Q13.2) MUTATED     2  24
  AMP PEAK 21(20Q13.2) WILD-TYPE  11 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20Q13.2) MUTATED      2   24
  AMP PEAK 21(20Q13.2) WILD-TYPE   11  326
                                        clus
vv                                       AMP PEAK 21(20Q13.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              24
                                        clus
vv                                       AMP PEAK 21(20Q13.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               326
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(20Q13.2) MUTATED    13  10   0   2
  AMP PEAK 21(20Q13.2) WILD-TYPE 230  80   5   9
D21V6, multiclass
    clus
vv   AMP PEAK 21(20Q13.2) MUTATED AMP PEAK 21(20Q13.2) WILD-TYPE
  R0                           13                            230
  R1                           10                             80
  R2                            0                              5
  RX                            2                              9
[1] 4 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, continuous
D21V8, continuous
D21V9, continuous
D21V10, continuous
D21V11, continuous
D21V12, continuous
D21V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(20Q13.2) MUTATED       0                         0    10
  AMP PEAK 21(20Q13.2) WILD-TYPE     2                         7   136
D21V14, multiclass
                           clus
vv                          AMP PEAK 21(20Q13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               10
                           clus
vv                          AMP PEAK 21(20Q13.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                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(22) Variable = AMP PEAK 22(XP22.11) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(XP22.11) MUTATED    17   0
  AMP PEAK 22(XP22.11) WILD-TYPE 338   6
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                            17                            344 
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                             0                              6 
$`AMP PEAK 22(XP22.11) MUTATED`
TCGA-EJ-7789 TCGA-EJ-A46G TCGA-EJ-A65D TCGA-HC-7742 TCGA-HC-7747 TCGA-HC-7818 
       18.15         3.06        12.92         1.48        24.59         1.48 
TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-A4ZV TCGA-KK-A6E8 TCGA-TP-A8TT TCGA-VN-A943 
        1.84        22.42         0.76        58.19        11.90         4.34 
TCGA-VP-A87H TCGA-XK-AAJA TCGA-YL-A8S8 TCGA-YL-A8SC TCGA-YL-A8SK 
       21.80        30.58        62.14        41.46        37.97 

$`AMP PEAK 22(XP22.11) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        14.53        14.14        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
        5.33         4.24        17.49         9.83         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       17.62        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        52.87        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
        1.71         0.72         2.10         2.66         1.74         1.68 
TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
        2.07        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       17.85        24.56        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.15        22.36         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 
       90.51        49.25       113.33        67.07        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TV 
        3.19        41.00       114.64        47.21        86.14         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       30.15        32.91        15.09       106.95        26.47        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       94.65        23.93        75.91        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       48.85        21.53        17.82         5.79        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.50        31.96        28.54        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       36.95        71.77        60.56        16.83        45.50        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        47.38        45.86        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                          0.76                           0.30 
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                         62.14                         151.36 
  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE 
                         18.15                          24.18 
[1] "0.8 - 62.1 (18.1)"  "0.3 - 151.4 (24.2)"
[1] "hr="     "2.5e+07"
D22V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 22(XP22.11) MUTATED     4  13   0
  AMP PEAK 22(XP22.11) WILD-TYPE 146 193   5
D22V3, multiclass
    clus
vv   AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE
  T2                            4                            146
  T3                           13                            193
  T4                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                                cls
clus                               0   1
  AMP PEAK 22(XP22.11) MUTATED    15   2
  AMP PEAK 22(XP22.11) WILD-TYPE 248  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(XP22.11) MUTATED     15    2
  AMP PEAK 22(XP22.11) WILD-TYPE  248   42
   clus
vv  AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE
  0                           15                            248
  1                            2                             42
[1] 2 2
[1] FALSE
D22V5, binary
                                cls
clus                               0   1
  AMP PEAK 22(XP22.11) MUTATED     2  15
  AMP PEAK 22(XP22.11) WILD-TYPE  11 335
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(XP22.11) MUTATED      2   15
  AMP PEAK 22(XP22.11) WILD-TYPE   11  335
                                        clus
vv                                       AMP PEAK 22(XP22.11) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              15
                                        clus
vv                                       AMP PEAK 22(XP22.11) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               335
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(XP22.11) MUTATED     9   4   1   1
  AMP PEAK 22(XP22.11) WILD-TYPE 234  86   4  10
D22V6, multiclass
    clus
vv   AMP PEAK 22(XP22.11) MUTATED AMP PEAK 22(XP22.11) WILD-TYPE
  R0                            9                            234
  R1                            4                             86
  R2                            1                              4
  RX                            1                             10
[1] 4 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, continuous
D22V8, continuous
D22V9, continuous
D22V10, continuous
D22V11, continuous
D22V12, continuous
D22V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(XP22.11) MUTATED       0                         1     4
  AMP PEAK 22(XP22.11) WILD-TYPE     2                         6   142
D22V14, multiclass
                           clus
vv                          AMP PEAK 22(XP22.11) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                4
                           clus
vv                          AMP PEAK 22(XP22.11) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                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(23) Variable = AMP PEAK 23(XP22.11) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(XP22.11) MUTATED    16   0
  AMP PEAK 23(XP22.11) WILD-TYPE 339   6
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                            16                            345 
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                             0                              6 
$`AMP PEAK 23(XP22.11) MUTATED`
TCGA-EJ-5502 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-7789 TCGA-EJ-A46G TCGA-EJ-A65D 
       26.30        46.55        47.80        18.15         3.06        12.92 
TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-A4ZV TCGA-KK-A6E8 TCGA-VN-A943 TCGA-VP-A87H 
        1.84        22.42         0.76        58.19         4.34        21.80 
TCGA-XK-AAJA TCGA-YL-A8S8 TCGA-YL-A8SC TCGA-YL-A8SK 
       30.58        62.14        41.46        37.97 

$`AMP PEAK 23(XP22.11) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       46.52        44.88        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       36.23        60.23        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F 
        9.83         7.53        21.96        17.62        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       17.85        24.56        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.15        22.36         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 
       90.51        49.25       113.33        67.07        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        30.15        32.91        15.09       106.95        26.47 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        48.85        21.53        17.82         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP 
       25.97        31.96        31.50        31.96        28.54        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       27.09        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       38.56        36.95        71.77        60.56        16.83        45.50 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        47.38        45.86        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                          0.76                           0.30 
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                         62.14                         151.36 
  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE 
                         24.36                          23.93 
[1] "0.8 - 62.1 (24.4)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D23V2, continuous
                                vv
clus                              T2  T3  T4
  AMP PEAK 23(XP22.11) MUTATED     4  12   0
  AMP PEAK 23(XP22.11) WILD-TYPE 146 194   5
D23V3, multiclass
    clus
vv   AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE
  T2                            4                            146
  T3                           12                            194
  T4                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                                cls
clus                               0   1
  AMP PEAK 23(XP22.11) MUTATED    14   2
  AMP PEAK 23(XP22.11) WILD-TYPE 249  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(XP22.11) MUTATED     14    2
  AMP PEAK 23(XP22.11) WILD-TYPE  249   42
   clus
vv  AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE
  0                           14                            249
  1                            2                             42
[1] 2 2
[1] FALSE
D23V5, binary
                                cls
clus                               0   1
  AMP PEAK 23(XP22.11) MUTATED     2  14
  AMP PEAK 23(XP22.11) WILD-TYPE  11 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(XP22.11) MUTATED      2   14
  AMP PEAK 23(XP22.11) WILD-TYPE   11  336
                                        clus
vv                                       AMP PEAK 23(XP22.11) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              14
                                        clus
vv                                       AMP PEAK 23(XP22.11) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               336
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(XP22.11) MUTATED     9   4   1   1
  AMP PEAK 23(XP22.11) WILD-TYPE 234  86   4  10
D23V6, multiclass
    clus
vv   AMP PEAK 23(XP22.11) MUTATED AMP PEAK 23(XP22.11) WILD-TYPE
  R0                            9                            234
  R1                            4                             86
  R2                            1                              4
  RX                            1                             10
[1] 4 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, continuous
D23V8, continuous
D23V9, continuous
D23V10, continuous
D23V11, continuous
D23V12, continuous
D23V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(XP22.11) MUTATED       0                         1     3
  AMP PEAK 23(XP22.11) WILD-TYPE     2                         6   143
D23V14, multiclass
                           clus
vv                          AMP PEAK 23(XP22.11) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                3
                           clus
vv                          AMP PEAK 23(XP22.11) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                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(24) Variable = AMP PEAK 24(XP21.1) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 24(XP21.1) MUTATED    16   0
  AMP PEAK 24(XP21.1) WILD-TYPE 339   6
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                           16                           345 
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                            0                             6 
$`AMP PEAK 24(XP21.1) MUTATED`
TCGA-EJ-5495 TCGA-EJ-5499 TCGA-EJ-5530 TCGA-EJ-7789 TCGA-EJ-A46G TCGA-EJ-A65D 
       33.11        46.52        60.23        18.15         3.06        12.92 
TCGA-HC-8216 TCGA-HC-A4ZV TCGA-KK-A6E8 TCGA-VN-A943 TCGA-VP-A87H TCGA-XJ-A9DX 
       22.42         0.76        58.19         4.34        21.80        25.97 
TCGA-XK-AAJA TCGA-YL-A8S8 TCGA-YL-A8SC TCGA-YL-A8SK 
       30.58        62.14        41.46        37.97 

$`AMP PEAK 24(XP21.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5501 
       29.00        27.16        19.56        13.32        29.79        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 
       68.35        43.07        36.66        38.76        39.75        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F 
        9.83         7.53        21.96        17.62        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56         1.84        19.36         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
       15.88         1.15        22.36         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ 
       67.59        90.51        49.25       113.33        67.07        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 
       15.52        15.81        30.15        32.91        15.09       106.95 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       26.47        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       60.92        66.97        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP 
        2.99        31.96        31.50        31.96        28.54        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       27.09        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       38.56        36.95        71.77        60.56        16.83        45.50 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        47.38        45.86        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                         0.76                          0.30 
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                        62.14                        151.36 
  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE 
                       28.275                        23.900 
[1] "0.8 - 62.1 (28.3)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D24V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 24(XP21.1) MUTATED     3  13   0
  AMP PEAK 24(XP21.1) WILD-TYPE 147 193   5
D24V3, multiclass
    clus
vv   AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE
  T2                           3                           147
  T3                          13                           193
  T4                           0                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                               cls
clus                              0   1
  AMP PEAK 24(XP21.1) MUTATED    13   3
  AMP PEAK 24(XP21.1) WILD-TYPE 250  41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP21.1) MUTATED     13    3
  AMP PEAK 24(XP21.1) WILD-TYPE  250   41
   clus
vv  AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE
  0                          13                           250
  1                           3                            41
[1] 2 2
[1] FALSE
D24V5, binary
                               cls
clus                              0   1
  AMP PEAK 24(XP21.1) MUTATED     3  13
  AMP PEAK 24(XP21.1) WILD-TYPE  10 337
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP21.1) MUTATED      3   13
  AMP PEAK 24(XP21.1) WILD-TYPE   10  337
                                        clus
vv                                       AMP PEAK 24(XP21.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             13
                                        clus
vv                                       AMP PEAK 24(XP21.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              337
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 24(XP21.1) MUTATED     9   5   1   1
  AMP PEAK 24(XP21.1) WILD-TYPE 234  85   4  10
D24V6, multiclass
    clus
vv   AMP PEAK 24(XP21.1) MUTATED AMP PEAK 24(XP21.1) WILD-TYPE
  R0                           9                           234
  R1                           5                            85
  R2                           1                             4
  RX                           1                            10
[1] 4 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, continuous
D24V8, continuous
D24V9, continuous
D24V10, continuous
D24V11, continuous
D24V12, continuous
D24V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(XP21.1) MUTATED       1                         1     2
  AMP PEAK 24(XP21.1) WILD-TYPE     1                         6   144
D24V14, multiclass
                           clus
vv                          AMP PEAK 24(XP21.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               2
                           clus
vv                          AMP PEAK 24(XP21.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               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(25) Variable = AMP PEAK 25(XQ21.1) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 25(XQ21.1) MUTATED    13   0
  AMP PEAK 25(XQ21.1) WILD-TYPE 342   6
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           13                           348 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                            0                             6 
$`AMP PEAK 25(XQ21.1) MUTATED`
TCGA-EJ-5505 TCGA-EJ-5507 TCGA-EJ-5521 TCGA-EJ-5530 TCGA-EJ-5542 TCGA-EJ-7789 
       30.31        23.90        51.88        60.23        29.06        18.15 
TCGA-G9-6499 TCGA-KK-A6E8 TCGA-VN-A943 TCGA-VP-A87H TCGA-YL-A8S8 TCGA-YL-A8SC 
       50.73        58.19         4.34        21.80        62.14        41.46 
TCGA-YL-A9WI 
       41.39 

$`AMP PEAK 25(XQ21.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5506 
       46.52        44.88        26.30        45.73        28.93        27.19 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 
       60.23        46.55        47.80        52.27        64.50        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-5532 
       43.07        36.66        38.76        39.75        41.85        47.87 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       27.02        49.02        61.15        83.57        21.80         9.70 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
        9.50         9.37        16.77         7.66        17.52         5.75 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28         0.30        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
       25.68        20.55        14.53        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       52.87        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         4.41        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       14.37        20.28        13.87         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        25.97        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        45.50        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        14.04        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                         4.34                          0.30 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                        62.14                        151.36 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                        41.39                         23.46 
[1] "4.3 - 62.1 (41.4)"  "0.3 - 151.4 (23.5)"
[1] "hr="     "2.6e+07"
D25V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 25(XQ21.1) MUTATED     4   9   0
  AMP PEAK 25(XQ21.1) WILD-TYPE 146 197   5
D25V3, multiclass
    clus
vv   AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE
  T2                           4                           146
  T3                           9                           197
  T4                           0                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                               cls
clus                              0   1
  AMP PEAK 25(XQ21.1) MUTATED    11   2
  AMP PEAK 25(XQ21.1) WILD-TYPE 252  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ21.1) MUTATED     11    2
  AMP PEAK 25(XQ21.1) WILD-TYPE  252   42
   clus
vv  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE
  0                          11                           252
  1                           2                            42
[1] 2 2
[1] FALSE
D25V5, binary
                               cls
clus                              0   1
  AMP PEAK 25(XQ21.1) MUTATED     0  13
  AMP PEAK 25(XQ21.1) WILD-TYPE  13 337
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ21.1) MUTATED      0   13
  AMP PEAK 25(XQ21.1) WILD-TYPE   13  337
                                        clus
vv                                       AMP PEAK 25(XQ21.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             13
                                        clus
vv                                       AMP PEAK 25(XQ21.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              337
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 25(XQ21.1) MUTATED     9   2   1   1
  AMP PEAK 25(XQ21.1) WILD-TYPE 234  88   4  10
D25V6, multiclass
    clus
vv   AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE
  R0                           9                           234
  R1                           2                            88
  R2                           1                             4
  RX                           1                            10
[1] 4 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, continuous
D25V8, continuous
D25V9, continuous
D25V10, continuous
D25V11, continuous
D25V12, continuous
D25V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(XQ21.1) MUTATED       0                         1     6
  AMP PEAK 25(XQ21.1) WILD-TYPE     2                         6   140
D25V14, multiclass
                           clus
vv                          AMP PEAK 25(XQ21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               6
                           clus
vv                          AMP PEAK 25(XQ21.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               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(26) Variable = AMP PEAK 26(XQ21.1) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 26(XQ21.1) MUTATED    11   0
  AMP PEAK 26(XQ21.1) WILD-TYPE 344   6
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                           11                           350 
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                            0                             6 
$`AMP PEAK 26(XQ21.1) MUTATED`
TCGA-EJ-5519 TCGA-EJ-5531 TCGA-EJ-7789 TCGA-G9-6499 TCGA-HC-7737 TCGA-KK-A6E8 
       64.50        41.85        18.15        50.73         2.10        58.19 
TCGA-VN-A943 TCGA-VP-A87H TCGA-YL-A8S8 TCGA-YL-A8SC TCGA-YL-A9WI 
        4.34        21.80        62.14        41.46        41.39 

$`AMP PEAK 26(XQ21.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       60.23        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       14.14        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        56.75        52.87        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       21.14         6.08        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60         1.97         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        0.72         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 
        3.48         1.45         1.25         4.41        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        21.76        17.03 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       16.04        16.54        16.14        20.52        14.93        17.19 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        13.32        17.36         9.17         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C 
        6.77        10.39        14.37        20.28        13.87         5.85 
TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       10.62        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
      113.33        67.07        27.62        34.95        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       27.02        25.08        15.88        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       32.91        15.09       106.95        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       23.93        75.91        55.56        60.92        66.97        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.50        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       36.95        71.77        60.56        16.83        45.50        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79         7.00        14.04        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                          2.1                           0.3 
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                        64.50                        151.36 
  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE 
                        41.46                         23.90 
[1] "2.1 - 64.5 (41.5)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D26V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 26(XQ21.1) MUTATED     3   8   0
  AMP PEAK 26(XQ21.1) WILD-TYPE 147 198   5
D26V3, multiclass
    clus
vv   AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE
  T2                           3                           147
  T3                           8                           198
  T4                           0                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                               cls
clus                              0   1
  AMP PEAK 26(XQ21.1) MUTATED     8   3
  AMP PEAK 26(XQ21.1) WILD-TYPE 255  41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 26(XQ21.1) MUTATED      8    3
  AMP PEAK 26(XQ21.1) WILD-TYPE  255   41
   clus
vv  AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE
  0                           8                           255
  1                           3                            41
[1] 2 2
[1] FALSE
D26V5, binary
                               cls
clus                              0   1
  AMP PEAK 26(XQ21.1) MUTATED     0  11
  AMP PEAK 26(XQ21.1) WILD-TYPE  13 339
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 26(XQ21.1) MUTATED      0   11
  AMP PEAK 26(XQ21.1) WILD-TYPE   13  339
                                        clus
vv                                       AMP PEAK 26(XQ21.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             11
                                        clus
vv                                       AMP PEAK 26(XQ21.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              339
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 26(XQ21.1) MUTATED     7   2   1   1
  AMP PEAK 26(XQ21.1) WILD-TYPE 236  88   4  10
D26V6, multiclass
    clus
vv   AMP PEAK 26(XQ21.1) MUTATED AMP PEAK 26(XQ21.1) WILD-TYPE
  R0                           7                           236
  R1                           2                            88
  R2                           1                             4
  RX                           1                            10
[1] 4 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, continuous
D26V8, continuous
D26V9, continuous
D26V10, continuous
D26V11, continuous
D26V12, continuous
D26V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(XQ21.1) MUTATED       0                         2     3
  AMP PEAK 26(XQ21.1) WILD-TYPE     2                         5   143
D26V14, multiclass
                           clus
vv                          AMP PEAK 26(XQ21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                               3
                           clus
vv                          AMP PEAK 26(XQ21.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               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(27) Variable = AMP PEAK 27(XQ25) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 27(XQ25) MUTATED    13   0
  AMP PEAK 27(XQ25) WILD-TYPE 342   6
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                         13                         348 
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                          0                           6 
$`AMP PEAK 27(XQ25) MUTATED`
TCGA-EJ-5499 TCGA-EJ-5505 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-7789 TCGA-G9-6499 
       46.52        30.31        68.35        38.76        18.15        50.73 
TCGA-KK-A6E8 TCGA-VN-A943 TCGA-VP-A87H TCGA-XK-AAJA TCGA-YL-A8S8 TCGA-YL-A8SC 
       58.19         4.34        21.80        30.58        62.14        41.46 
TCGA-YL-A9WI 
       41.39 

$`AMP PEAK 27(XQ25) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5507 
       44.88        26.30        45.73        28.93        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       43.07        36.66        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
        5.75        27.68         6.28         0.30        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 
       25.87        25.68        20.55        14.53        14.14        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        3.06         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
       18.41         9.14         2.99         7.56        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        52.87        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56         1.84        19.36        22.42         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        1.45         1.25         4.41        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       93.99        56.28        44.68        61.78       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       67.07        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       75.91        55.56        60.92        66.97        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       31.96        28.54        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        45.50        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        14.04        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                       4.34                        0.30 
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                      68.35                      151.36 
  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE 
                      41.39                       23.46 
[1] "4.3 - 68.3 (41.4)"  "0.3 - 151.4 (23.5)"
[1] "hr="     "2.7e+07"
D27V2, continuous
                             vv
clus                           T2  T3  T4
  AMP PEAK 27(XQ25) MUTATED     4   9   0
  AMP PEAK 27(XQ25) WILD-TYPE 146 197   5
D27V3, multiclass
    clus
vv   AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE
  T2                         4                         146
  T3                         9                         197
  T4                         0                           5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ25) MUTATED    11   2
  AMP PEAK 27(XQ25) WILD-TYPE 252  42
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ25) MUTATED     11    2
  AMP PEAK 27(XQ25) WILD-TYPE  252   42
   clus
vv  AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE
  0                        11                         252
  1                         2                          42
[1] 2 2
[1] FALSE
D27V5, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ25) MUTATED     0  13
  AMP PEAK 27(XQ25) WILD-TYPE  13 337
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ25) MUTATED      0   13
  AMP PEAK 27(XQ25) WILD-TYPE   13  337
                                        clus
vv                                       AMP PEAK 27(XQ25) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           13
                                        clus
vv                                       AMP PEAK 27(XQ25) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            337
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 27(XQ25) MUTATED     9   2   1   1
  AMP PEAK 27(XQ25) WILD-TYPE 234  88   4  10
D27V6, multiclass
    clus
vv   AMP PEAK 27(XQ25) MUTATED AMP PEAK 27(XQ25) WILD-TYPE
  R0                         9                         234
  R1                         2                          88
  R2                         1                           4
  RX                         1                          10
[1] 4 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, continuous
D27V8, continuous
D27V9, continuous
D27V10, continuous
D27V11, continuous
D27V12, continuous
D27V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(XQ25) MUTATED       1                         1     4
  AMP PEAK 27(XQ25) WILD-TYPE     1                         6   142
D27V14, multiclass
                           clus
vv                          AMP PEAK 27(XQ25) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                             4
                           clus
vv                          AMP PEAK 27(XQ25) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             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(28) Variable = AMP PEAK 28(XQ27.1) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 28(XQ27.1) MUTATED    14   0
  AMP PEAK 28(XQ27.1) WILD-TYPE 341   6
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                           14                           347 
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                            0                             6 
$`AMP PEAK 28(XQ27.1) MUTATED`
TCGA-EJ-7331 TCGA-EJ-7783 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-G9-6499 
        0.30        25.87        18.15        17.29        23.05        50.73 
TCGA-H9-7775 TCGA-HC-7744 TCGA-HC-7749 TCGA-KK-A6E8 TCGA-VN-A943 TCGA-VP-A87H 
        6.08         1.68         1.97        58.19         4.34        21.80 
TCGA-YL-A8S8 TCGA-YL-A9WI 
       62.14        41.39 

$`AMP PEAK 28(XQ27.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        6.28        23.90        38.37        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       14.14        19.59         3.75        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        3.06         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
       18.41         9.14         2.99         7.56        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        52.87        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-A6BX 
       35.34        28.18        32.68        26.01        21.14        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 
        1.74         1.48         2.07        24.59        26.04         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 
       90.51        49.25       113.33        67.07        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        30.15        32.91        15.09       106.95        26.47 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        48.85        21.53        17.82         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       25.97        31.96        31.50        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        38.56        36.95        71.77        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       45.50        41.46        45.14        28.77        47.38        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       37.97        26.24       106.75        71.34        62.79         7.00 
TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       14.04        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                         0.30                          0.72 
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                        62.14                        151.36 
  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE 
                       19.975                        24.030 
[1] "0.3 - 62.1 (20.0)"  "0.7 - 151.4 (24.0)"
[1] "hr="     "2.5e+07"
D28V2, continuous
                               vv
clus                             T2  T3  T4
  AMP PEAK 28(XQ27.1) MUTATED     6   8   0
  AMP PEAK 28(XQ27.1) WILD-TYPE 144 198   5
D28V3, multiclass
    clus
vv   AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE
  T2                           6                           144
  T3                           8                           198
  T4                           0                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                               cls
clus                              0   1
  AMP PEAK 28(XQ27.1) MUTATED    12   1
  AMP PEAK 28(XQ27.1) WILD-TYPE 251  43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 28(XQ27.1) MUTATED     12    1
  AMP PEAK 28(XQ27.1) WILD-TYPE  251   43
   clus
vv  AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE
  0                          12                           251
  1                           1                            43
[1] 2 2
[1] FALSE
D28V5, binary
                               cls
clus                              0   1
  AMP PEAK 28(XQ27.1) MUTATED     0  14
  AMP PEAK 28(XQ27.1) WILD-TYPE  13 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 28(XQ27.1) MUTATED      0   14
  AMP PEAK 28(XQ27.1) WILD-TYPE   13  336
                                        clus
vv                                       AMP PEAK 28(XQ27.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             14
                                        clus
vv                                       AMP PEAK 28(XQ27.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              336
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 28(XQ27.1) MUTATED     9   2   1   1
  AMP PEAK 28(XQ27.1) WILD-TYPE 234  88   4  10
D28V6, multiclass
    clus
vv   AMP PEAK 28(XQ27.1) MUTATED AMP PEAK 28(XQ27.1) WILD-TYPE
  R0                           9                           234
  R1                           2                            88
  R2                           1                             4
  RX                           1                            10
[1] 4 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, continuous
D28V8, continuous
D28V9, continuous
D28V10, continuous
D28V11, continuous
D28V12, continuous
D28V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(XQ27.1) MUTATED       0                         1     8
  AMP PEAK 28(XQ27.1) WILD-TYPE     2                         6   138
D28V14, multiclass
                           clus
vv                          AMP PEAK 28(XQ27.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               8
                           clus
vv                          AMP PEAK 28(XQ27.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               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"

Clustering(29) Variable = DEL PEAK  1(1P31.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  1(1P31.3) MUTATED    41   1
  DEL PEAK  1(1P31.3) WILD-TYPE 314   5
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                           42                           319 
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                            1                             5 
$`DEL PEAK  1(1P31.3) MUTATED`
TCGA-CH-5740 TCGA-CH-5753 TCGA-CH-5769 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5499 
        1.02         1.02         2.04        33.01        29.00        46.52 
TCGA-EJ-5504 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-FC-7961 TCGA-G9-6332 TCGA-G9-6342 
       28.93        25.68        14.14        15.42        87.35        55.76 
TCGA-G9-6351 TCGA-G9-6361 TCGA-G9-6379 TCGA-G9-6499 TCGA-G9-7525 TCGA-HC-7078 
       46.16        46.52        45.80        50.73        32.68         5.33 
TCGA-HC-7081 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 
        2.37         1.97         2.37        22.36         0.76         2.01 
TCGA-HI-7168 TCGA-HI-7171 TCGA-J9-A52E TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 
       78.61        43.69        10.62        61.78        30.02        54.54 
TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-M7-A725 TCGA-QU-A6IL TCGA-VN-A88L TCGA-VP-A875 
       90.51       113.33        18.84         3.19        12.95        26.47 
TCGA-VP-AA1N TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WL 
       17.82        45.86        26.24        62.79        14.04        24.33 

$`DEL PEAK  1(1P31.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97        22.06        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 
       24.03         1.02        13.02        35.01        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
       32.02         2.99        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 
       29.79        44.88        26.30        45.73        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30        23.90        38.37        25.87        20.55        14.53 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        13.45         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6343 
       41.62        81.04        67.99        66.67        69.37        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 
       68.68        49.81        50.70        49.35        47.15        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 
       38.01        40.31        26.66        31.50        37.97        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        56.75        52.87        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        30.97        35.34        28.18        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 
        6.08        30.94         3.68        19.76         2.93         2.01 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7232 
       14.47        28.54         0.79        28.60         1.68         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        1.78         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
        1.45         1.25         4.41        88.24        82.92        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       20.28        13.87         5.85        93.99        56.28        44.68 
TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 
      115.86       151.36        67.59        49.25        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
       15.88        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.19         8.84        25.51         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 
       30.15        32.91        15.09         4.34       106.95        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       94.65        23.93        75.91        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        48.85        21.53         5.79        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        31.50        31.96        28.54        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       27.09        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       38.56        36.95        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       45.50        41.46        45.14        28.77        47.38        37.97 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
      106.75        71.34         7.00        41.39        60.99        62.37 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                         0.76                          0.30 
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                       113.33                        151.36 
  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE 
                       26.355                        23.870 
[1] "0.8 - 113.3 (26.4)" "0.3 - 151.4 (23.9)"
[1] "hr=" "1.2"
D29V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  1(1P31.3) MUTATED    11  32   0
  DEL PEAK  1(1P31.3) WILD-TYPE 139 174   5
D29V3, multiclass
    clus
vv   DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE
  T2                          11                           139
  T3                          32                           174
  T4                           0                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, binary
                               cls
clus                              0   1
  DEL PEAK  1(1P31.3) MUTATED    33   6
  DEL PEAK  1(1P31.3) WILD-TYPE 230  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P31.3) MUTATED     33    6
  DEL PEAK  1(1P31.3) WILD-TYPE  230   38
   clus
vv  DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE
  0                          33                           230
  1                           6                            38
[1] 2 2
[1] FALSE
D29V5, binary
                               cls
clus                              0   1
  DEL PEAK  1(1P31.3) MUTATED     0  43
  DEL PEAK  1(1P31.3) WILD-TYPE  13 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P31.3) MUTATED      0   43
  DEL PEAK  1(1P31.3) WILD-TYPE   13  307
                                        clus
vv                                       DEL PEAK  1(1P31.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             43
                                        clus
vv                                       DEL PEAK  1(1P31.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              307
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  1(1P31.3) MUTATED    26  14   1   1
  DEL PEAK  1(1P31.3) WILD-TYPE 217  76   4  10
D29V6, multiclass
    clus
vv   DEL PEAK  1(1P31.3) MUTATED DEL PEAK  1(1P31.3) WILD-TYPE
  R0                          26                           217
  R1                          14                            76
  R2                           1                             4
  RX                           1                            10
[1] 4 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, continuous
D29V8, continuous
D29V9, continuous
D29V10, continuous
D29V11, continuous
D29V12, continuous
D29V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P31.3) MUTATED       1                         0    20
  DEL PEAK  1(1P31.3) WILD-TYPE     1                         7   126
D29V14, multiclass
                           clus
vv                          DEL PEAK  1(1P31.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              20
                           clus
vv                          DEL PEAK  1(1P31.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               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(30) Variable = DEL PEAK  2(1P22.1) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P22.1) MUTATED    38   0
  DEL PEAK  2(1P22.1) WILD-TYPE 317   6
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           38                           323 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                            0                             6 
$`DEL PEAK  2(1P22.1) MUTATED`
TCGA-CH-5753 TCGA-CH-5754 TCGA-EJ-7312 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-EJ-8470 
        1.02         2.04        21.80        25.68        14.14        26.99 
TCGA-FC-7961 TCGA-G9-6332 TCGA-G9-6338 TCGA-G9-6351 TCGA-G9-6369 TCGA-HC-7078 
       15.42        87.35        66.67        46.16        39.95         5.33 
TCGA-HC-7213 TCGA-HC-7736 TCGA-HC-7745 TCGA-HC-8257 TCGA-HC-A6HY TCGA-J4-A67N 
        1.97         0.72         2.07        23.87         4.41        16.54 
TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E6 TCGA-KK-A8IB TCGA-M7-A725 TCGA-VN-A88L 
       61.78        30.02       113.33         2.73        18.84        12.95 
TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-AA1N TCGA-XJ-A83G TCGA-XK-AAJT TCGA-YL-A8HM 
       26.47        94.65        17.82        38.04        37.02        36.95 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WL 
       45.86        26.24        62.79         7.00        14.04        24.33 
TCGA-ZG-A8QY TCGA-ZG-A9ND 
        1.12         6.02 

$`DEL PEAK  2(1P22.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7791 
       38.37        25.87        20.55        14.53        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB 
        9.14         2.99         7.56        28.41        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 
       17.23        16.24         1.78        41.62        81.04        67.99 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6353 
       69.37        55.76        18.21        68.68        49.81        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       44.81         3.32        40.18        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 
        6.08        30.94         3.68        19.76         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.37        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.37         2.93         1.71         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.48         1.68        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        22.42         3.12         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HI-7168 TCGA-HI-7169 
        2.33         3.48         1.45         1.25        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        21.76        17.03 
TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.04        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 
       93.99        56.28        44.68       115.86        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       67.59        90.51        49.25        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       34.95        22.75        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL 
        9.93        13.15        27.02        25.08        15.88         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        25.51         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A879 
       32.91        15.09         4.34       106.95        84.69        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI 
       21.53         5.79        37.18        27.81         3.91        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        25.97        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL 
       28.54        30.58        29.23        27.09        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        38.56        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       37.97       106.75        71.34        41.39        60.99        62.37 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         7.86 

  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                         0.72                          0.30 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       113.33                        151.36 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       22.835                        24.030 
[1] "0.7 - 113.3 (22.8)" "0.3 - 151.4 (24.0)"
[1] "hr="   "8e+07"
D30V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  2(1P22.1) MUTATED     9  30   0
  DEL PEAK  2(1P22.1) WILD-TYPE 141 176   5
D30V3, multiclass
    clus
vv   DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  T2                           9                           141
  T3                          30                           176
  T4                           0                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED    30   7
  DEL PEAK  2(1P22.1) WILD-TYPE 233  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     30    7
  DEL PEAK  2(1P22.1) WILD-TYPE  233   37
   clus
vv  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  0                          30                           233
  1                           7                            37
[1] 2 2
[1] FALSE
D30V5, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P22.1) MUTATED     0  39
  DEL PEAK  2(1P22.1) WILD-TYPE  13 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED      0   39
  DEL PEAK  2(1P22.1) WILD-TYPE   13  311
                                        clus
vv                                       DEL PEAK  2(1P22.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             39
                                        clus
vv                                       DEL PEAK  2(1P22.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              311
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P22.1) MUTATED    23  11   0   1
  DEL PEAK  2(1P22.1) WILD-TYPE 220  79   5  10
D30V6, multiclass
    clus
vv   DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  R0                          23                           220
  R1                          11                            79
  R2                           0                             5
  RX                           1                            10
[1] 4 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, continuous
D30V8, continuous
D30V9, continuous
D30V10, continuous
D30V11, continuous
D30V12, continuous
D30V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P22.1) MUTATED       0                         0    13
  DEL PEAK  2(1P22.1) WILD-TYPE     2                         7   133
D30V14, multiclass
                           clus
vv                          DEL PEAK  2(1P22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              13
                           clus
vv                          DEL PEAK  2(1P22.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               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(31) Variable = DEL PEAK  3(1Q23.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1Q23.1) MUTATED    18   1
  DEL PEAK  3(1Q23.1) WILD-TYPE 337   5
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                           19                           342 
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                            1                             5 
$`DEL PEAK  3(1Q23.1) MUTATED`
TCGA-EJ-5525 TCGA-EJ-7115 TCGA-EJ-7315 TCGA-FC-7961 TCGA-HC-7075 TCGA-HC-7080 
       36.66        27.02         9.50        15.42        19.76         2.01 
TCGA-HC-7209 TCGA-HC-7744 TCGA-HC-7752 TCGA-HC-8257 TCGA-J4-A67M TCGA-KK-A59X 
       14.47         1.68         3.22        23.87        16.04        56.28 
TCGA-KK-A6E0 TCGA-VN-A943 TCGA-VP-A87B TCGA-XK-AAJA TCGA-XK-AAJP TCGA-YL-A8S8 
       30.02         4.34        75.91        30.58        29.23        62.14 
TCGA-YL-A8SH 
       28.77 

$`DEL PEAK  3(1Q23.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 
       64.50        51.88        68.35        43.07        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7125 
       60.23        41.85        47.87        29.06        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        21.80         9.70         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        13.45         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        52.87        50.73        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7078 TCGA-HC-7079 
       21.14         6.08        30.94         3.68         5.33         2.93 
TCGA-HC-7081 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
        2.37        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.74         1.48         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        1.12        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36        22.42         3.12         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       17.03        16.54        16.14        20.52        14.93        17.19 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        13.32        17.36         9.17         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C 
        6.77        10.39        14.37        20.28        13.87         5.85 
TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 
       10.62        93.99        44.68        61.78       115.86        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       58.19        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       31.96        28.54        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 
       52.96        49.02        38.56        36.95        71.77        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ 
       16.83        45.50        41.46        45.14        47.38        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       37.97        26.24       106.75        71.34        62.79         7.00 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        41.39        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                         1.68                          0.30 
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                        75.91                        151.36 
  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE 
                        23.87                         23.98 
[1] "1.7 - 75.9 (23.9)"  "0.3 - 151.4 (24.0)"
[1] "hr=" "3.8"
D31V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  3(1Q23.1) MUTATED     7  12   0
  DEL PEAK  3(1Q23.1) WILD-TYPE 143 194   5
D31V3, multiclass
    clus
vv   DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE
  T2                           7                           143
  T3                          12                           194
  T4                           0                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                               cls
clus                              0   1
  DEL PEAK  3(1Q23.1) MUTATED    16   2
  DEL PEAK  3(1Q23.1) WILD-TYPE 247  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1Q23.1) MUTATED     16    2
  DEL PEAK  3(1Q23.1) WILD-TYPE  247   42
   clus
vv  DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE
  0                          16                           247
  1                           2                            42
[1] 2 2
[1] FALSE
D31V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(1Q23.1) MUTATED     0  19
  DEL PEAK  3(1Q23.1) WILD-TYPE  13 331
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1Q23.1) MUTATED      0   19
  DEL PEAK  3(1Q23.1) WILD-TYPE   13  331
                                        clus
vv                                       DEL PEAK  3(1Q23.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             19
                                        clus
vv                                       DEL PEAK  3(1Q23.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              331
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1Q23.1) MUTATED    14   4   0   0
  DEL PEAK  3(1Q23.1) WILD-TYPE 229  86   5  11
D31V6, multiclass
    clus
vv   DEL PEAK  3(1Q23.1) MUTATED DEL PEAK  3(1Q23.1) WILD-TYPE
  R0                          14                           229
  R1                           4                            86
  R2                           0                             5
  RX                           0                            11
[1] 4 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, continuous
D31V8, continuous
D31V9, continuous
D31V10, continuous
D31V11, continuous
D31V12, continuous
D31V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q23.1) MUTATED       0                         0     9
  DEL PEAK  3(1Q23.1) WILD-TYPE     2                         7   137
D31V14, multiclass
                           clus
vv                          DEL PEAK  3(1Q23.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               9
                           clus
vv                          DEL PEAK  3(1Q23.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               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(32) Variable = DEL PEAK  4(1Q42.3) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(1Q42.3) MUTATED    28   4
  DEL PEAK  4(1Q42.3) WILD-TYPE 327   2
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                           32                           329 
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                            4                             2 
$`DEL PEAK  4(1Q42.3) MUTATED`
TCGA-CH-5737 TCGA-CH-5740 TCGA-CH-5764 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5519 
        2.99         1.02         1.02        36.23        52.27        64.50 
TCGA-EJ-7123 TCGA-EJ-7330 TCGA-EJ-8470 TCGA-G9-6364 TCGA-G9-6379 TCGA-G9-A9S0 
       49.02         6.28        26.99        39.39        45.80        26.01 
TCGA-HC-7210 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A631 
       28.54         0.72         2.10         1.58        22.36         1.78 
TCGA-HI-7171 TCGA-J4-A67S TCGA-KK-A6E5 TCGA-KK-A8IL TCGA-M7-A724 TCGA-QU-A6IO 
       43.69        17.19        49.25        20.65        15.88        47.21 
TCGA-VP-A878 TCGA-WW-A8ZI TCGA-XK-AAJR TCGA-YL-A8SH TCGA-YL-A8SK TCGA-YL-A8SQ 
       94.65         5.79        27.09        28.77        37.97        62.79 
TCGA-YL-A8SR TCGA-ZG-A8QY 
        7.00         1.12 

$`DEL PEAK  4(1Q42.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
        6.97        22.06        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        0.92        44.02        12.00        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        36.69        48.53        38.53        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       47.80        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 
       16.77         7.66        17.52         5.75        27.68         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       19.92        64.47        63.98        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       26.66        31.50        37.97        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 
       30.97        35.34        28.18        32.68        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
        2.37        14.47         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        2.37         2.93         1.71         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV 
        1.94        17.95        22.32        15.88         1.15         0.76 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        1.45         1.25         4.41        78.61        88.24        82.92 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       16.14        20.52        14.93         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       67.59        90.51       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A71Y TCGA-M7-A71Z 
       34.95        22.75         2.73        26.43         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 TCGA-QU-A6IL 
        9.93        13.15        27.02        25.08        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
       41.00       114.64        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       32.91        15.09         4.34       106.95        26.47        84.69 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        75.91        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       48.85        21.53        17.82        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJT 
       31.50        31.96        28.54        30.58        29.23        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       39.65        25.48        52.96        49.02        38.56        36.95 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        45.50        41.46 
TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       45.14        47.38        45.86        26.24       106.75        71.34 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        41.39        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         7.86         6.02 

  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                         0.72                          0.30 
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                        94.65                        151.36 
  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE 
                         26.5                          23.9 
[1] "0.7 - 94.7 (26.5)"  "0.3 - 151.4 (23.9)"
[1] "hr=" "19" 
D32V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  4(1Q42.3) MUTATED    13  18   1
  DEL PEAK  4(1Q42.3) WILD-TYPE 137 188   4
D32V3, multiclass
    clus
vv   DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE
  T2                          13                           137
  T3                          18                           188
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                               cls
clus                              0   1
  DEL PEAK  4(1Q42.3) MUTATED    23   9
  DEL PEAK  4(1Q42.3) WILD-TYPE 240  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1Q42.3) MUTATED     23    9
  DEL PEAK  4(1Q42.3) WILD-TYPE  240   35
   clus
vv  DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE
  0                          23                           240
  1                           9                            35
[1] 2 2
[1] FALSE
D32V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(1Q42.3) MUTATED     0  32
  DEL PEAK  4(1Q42.3) WILD-TYPE  13 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1Q42.3) MUTATED      0   32
  DEL PEAK  4(1Q42.3) WILD-TYPE   13  318
                                        clus
vv                                       DEL PEAK  4(1Q42.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             32
                                        clus
vv                                       DEL PEAK  4(1Q42.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              318
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(1Q42.3) MUTATED    14  15   0   1
  DEL PEAK  4(1Q42.3) WILD-TYPE 229  75   5  10
D32V6, multiclass
    clus
vv   DEL PEAK  4(1Q42.3) MUTATED DEL PEAK  4(1Q42.3) WILD-TYPE
  R0                          14                           229
  R1                          15                            75
  R2                           0                             5
  RX                           1                            10
[1] 4 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, continuous
D32V8, continuous
D32V9, continuous
D32V10, continuous
D32V11, continuous
D32V12, continuous
D32V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(1Q42.3) MUTATED       0                         1    12
  DEL PEAK  4(1Q42.3) WILD-TYPE     2                         6   134
D32V14, multiclass
                           clus
vv                          DEL PEAK  4(1Q42.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              12
                           clus
vv                          DEL PEAK  4(1Q42.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK  5(2P21) MUTATION ANALYSIS
D33V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  5(2P21) MUTATED    33   0
  DEL PEAK  5(2P21) WILD-TYPE 322   6
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         33                         328 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                          0                           6 
$`DEL PEAK  5(2P21) MUTATED`
TCGA-CH-5751 TCGA-CH-5753 TCGA-EJ-5504 TCGA-EJ-5524 TCGA-EJ-5542 TCGA-EJ-7312 
       35.01         1.02        28.93        43.07        29.06        21.80 
TCGA-EJ-A46F TCGA-FC-7961 TCGA-G9-7525 TCGA-HC-7213 TCGA-HC-7747 TCGA-HC-7749 
        9.83        15.42        32.68         1.97        24.59         1.97 
TCGA-HC-7819 TCGA-HC-8257 TCGA-HC-A48F TCGA-J4-A67M TCGA-KK-A59V TCGA-KK-A59X 
       17.85        23.87        22.36        16.04        93.99        56.28 
TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7AZ TCGA-TP-A8TV TCGA-VP-A875 TCGA-VP-A87D 
       90.51       113.33        27.62         8.19        26.47        60.92 
TCGA-XK-AAJT TCGA-YL-A8HO TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SJ TCGA-YL-A9WK 
       37.02        71.77        16.83        41.46        45.86        62.37 
TCGA-YL-A9WL TCGA-ZG-A8QY TCGA-ZG-A9ND 
       24.33         1.12         6.02 

$`DEL PEAK  5(2P21) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5754 
        1.97        24.03         1.02        13.02        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       26.30        45.73        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       27.02        49.02        61.15        83.57         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H 
       10.32         5.33         4.24        17.49         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        2.99         7.56        28.41        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
        0.79        28.60         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
        2.07        26.04         1.12         3.22        30.51         1.48 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 
       24.56         1.84        19.36        22.42         3.12         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.15         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       21.76        17.03        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
        5.85        10.62        44.68        61.78       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 
       54.54       151.36        67.59        49.25        67.07        58.19 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       11.90         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E 
       84.69        94.65        23.93        75.91        55.56        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        48.85        21.53        17.82         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       25.97        31.96        31.50        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       29.23        27.09        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SF 
       38.56        36.95        62.14        60.56        45.50        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        47.38        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WX 
       62.79         7.00        14.04        41.39        60.99        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ 
       28.34         1.64         4.93         7.86 

  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                       1.02                        0.30 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                     113.33                      151.36 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                     26.470                      23.475 
[1] "1.0 - 113.3 (26.5)" "0.3 - 151.4 (23.5)"
[1] "hr="     "7.9e+07"
D33V2, continuous
                             vv
clus                           T2  T3  T4
  DEL PEAK  5(2P21) MUTATED     6  26   1
  DEL PEAK  5(2P21) WILD-TYPE 144 180   4
D33V3, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  T2                         6                         144
  T3                        26                         180
  T4                         1                           4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED    24   9
  DEL PEAK  5(2P21) WILD-TYPE 239  35
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED     24    9
  DEL PEAK  5(2P21) WILD-TYPE  239   35
   clus
vv  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  0                        24                         239
  1                         9                          35
[1] 2 2
[1] FALSE
D33V5, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED     0  33
  DEL PEAK  5(2P21) WILD-TYPE  13 317
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED      0   33
  DEL PEAK  5(2P21) WILD-TYPE   13  317
                                        clus
vv                                       DEL PEAK  5(2P21) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           33
                                        clus
vv                                       DEL PEAK  5(2P21) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            317
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  5(2P21) MUTATED    18  11   1   1
  DEL PEAK  5(2P21) WILD-TYPE 225  79   4  10
D33V6, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  R0                        18                         225
  R1                        11                          79
  R2                         1                           4
  RX                         1                          10
[1] 4 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, continuous
D33V8, continuous
D33V9, continuous
D33V10, continuous
D33V11, continuous
D33V12, continuous
D33V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2P21) MUTATED       0                         0    10
  DEL PEAK  5(2P21) WILD-TYPE     2                         7   136
D33V14, multiclass
                           clus
vv                          DEL PEAK  5(2P21) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            10
                           clus
vv                          DEL PEAK  5(2P21) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             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(34) Variable = DEL PEAK  6(2Q22.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q22.1) MUTATED    63   1
  DEL PEAK  6(2Q22.1) WILD-TYPE 292   5
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           64                           297 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                            1                             5 
$`DEL PEAK  6(2Q22.1) MUTATED`
TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5767 TCGA-CH-5788 TCGA-EJ-5504 TCGA-EJ-5518 
       33.96         3.68        15.06        26.99        28.93        52.27 
TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7330 TCGA-EJ-7782 TCGA-EJ-7784 
       49.02        83.57         9.50         6.28        38.37        25.68 
TCGA-EJ-7789 TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6369 TCGA-G9-6499 
       18.15         7.56        15.42        13.45        39.95        50.73 
TCGA-G9-7510 TCGA-G9-7525 TCGA-HC-7080 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7736 
       38.96        32.68         2.01         1.97         2.37         0.72 
TCGA-HC-7744 TCGA-HC-7749 TCGA-HC-8257 TCGA-HC-8266 TCGA-HC-A632 TCGA-HC-A6AP 
        1.68         1.97        23.87         1.15         2.01         2.33 
TCGA-HI-7171 TCGA-J4-A83J TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E4 TCGA-KK-A6E5 
       43.69        10.19        61.78        30.02        90.51        49.25 
TCGA-KK-A6E8 TCGA-KK-A8IF TCGA-M7-A724 TCGA-QU-A6IM TCGA-TP-A8TV TCGA-VN-A88R 
       58.19        26.43        15.88        41.00         8.19        15.09 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-AA1N TCGA-XA-A8JR 
      106.95        26.47        94.65        75.91        17.82         3.91 
TCGA-XJ-A83G TCGA-XK-AAJP TCGA-XK-AAJT TCGA-Y6-A8TL TCGA-YL-A8HM TCGA-YL-A8HO 
       38.04        29.23        37.02        25.48        36.95        71.77 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WY 
       45.86        26.24       106.75        41.39        62.37        28.34 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

$`DEL PEAK  6(2Q22.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 
       20.42        43.79        22.06        25.35         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 
       24.03         2.04        13.02        15.98         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7125 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       61.15        21.80         9.70         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 
       17.52         5.75        27.68         0.30        23.90        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        14.53        14.14        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        2.99        28.41         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       44.81         3.32        40.18        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       56.75        52.87        38.27        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       28.18        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       19.76         5.33         2.93         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 
        0.79        28.60         1.68         2.93         1.71         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        2.66         1.74         1.48         2.07        24.59        26.04 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 
        1.84        19.36        22.42         3.12         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F 
        1.94        17.95        22.32         1.58        15.88        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ 
        0.76         1.78         2.20         1.61         5.49         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        1.45         1.25         4.41        78.61        88.24        82.92 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       17.36         9.17         9.17         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E6 
       44.68       115.86        54.54       151.36        67.59       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL 
       67.07        27.62        34.95        22.75         2.73        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
       18.84         3.19       114.64        47.21        86.14        11.90 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87C 
       30.15        32.91         4.34        84.69        23.93        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       60.92        66.97        21.80        48.85        21.53         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       37.18        27.81        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJR 
       31.96        31.50        31.96        28.54        30.58        27.09 
TCGA-XK-AAJU TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 
       39.65        52.96        49.02        38.56        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SK TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ 
       37.97        71.34        62.79         7.00        14.04        60.99 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW 
       24.33        49.91         1.64 

  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                         0.72                          0.30 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                       106.95                        151.36 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                        26.45                         23.01 
[1] "0.7 - 107.0 (26.4)" "0.3 - 151.4 (23.0)"
[1] "hr=" "1.3"
D34V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  6(2Q22.1) MUTATED    23  40   1
  DEL PEAK  6(2Q22.1) WILD-TYPE 127 166   4
D34V3, multiclass
    clus
vv   DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  T2                          23                           127
  T3                          40                           166
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q22.1) MUTATED    51   9
  DEL PEAK  6(2Q22.1) WILD-TYPE 212  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED     51    9
  DEL PEAK  6(2Q22.1) WILD-TYPE  212   35
   clus
vv  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  0                          51                           212
  1                           9                            35
[1] 2 2
[1] FALSE
D34V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q22.1) MUTATED     1  63
  DEL PEAK  6(2Q22.1) WILD-TYPE  12 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED      1   63
  DEL PEAK  6(2Q22.1) WILD-TYPE   12  287
                                        clus
vv                                       DEL PEAK  6(2Q22.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             63
                                        clus
vv                                       DEL PEAK  6(2Q22.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              287
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q22.1) MUTATED    37  19   1   3
  DEL PEAK  6(2Q22.1) WILD-TYPE 206  71   4   8
D34V6, multiclass
    clus
vv   DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  R0                          37                           206
  R1                          19                            71
  R2                           1                             4
  RX                           3                             8
[1] 4 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, continuous
D34V8, continuous
D34V9, continuous
D34V10, continuous
D34V11, continuous
D34V12, continuous
D34V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(2Q22.1) MUTATED       0                         2    18
  DEL PEAK  6(2Q22.1) WILD-TYPE     2                         5   128
D34V14, multiclass
                           clus
vv                          DEL PEAK  6(2Q22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              18
                           clus
vv                          DEL PEAK  6(2Q22.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               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(35) Variable = DEL PEAK  7(2Q22.3) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(2Q22.3) MUTATED    57   1
  DEL PEAK  7(2Q22.3) WILD-TYPE 298   5
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                           58                           303 
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                            1                             5 
$`DEL PEAK  7(2Q22.3) MUTATED`
TCGA-CH-5748 TCGA-CH-5767 TCGA-CH-5788 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5514 
        1.02        15.06        26.99        23.90        48.13        36.23 
TCGA-EJ-5518 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-7789 
       52.27        49.02        21.80         6.28        25.68        18.15 
TCGA-EJ-8470 TCGA-EJ-A65M TCGA-G9-6333 TCGA-G9-6496 TCGA-G9-6499 TCGA-HC-7078 
       26.99         7.56        81.04        56.75        50.73         5.33 
TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7744 TCGA-HC-7749 
        2.01        28.54         1.97         2.37         1.68         1.97 
TCGA-HC-8257 TCGA-HC-8261 TCGA-HC-8266 TCGA-HC-A632 TCGA-HC-A6AP TCGA-HI-7171 
       23.87        17.95         1.15         2.01         2.33        43.69 
TCGA-KK-A6E0 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-QU-A6IM TCGA-TP-A8TV 
       30.02        90.51        49.25        58.19        41.00         8.19 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A87B TCGA-XA-A8JR 
        4.34       106.95        26.47        94.65        75.91         3.91 
TCGA-XJ-A83G TCGA-XK-AAIV TCGA-XK-AAJP TCGA-XK-AAJT TCGA-Y6-A8TL TCGA-YL-A8HM 
       38.04        31.50        29.23        37.02        25.48        36.95 
TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WK 
       71.77        45.86        26.24       106.75         7.00        62.37 
TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         4.93         7.86         6.02 

$`DEL PEAK  7(2Q22.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 
        1.02        24.03         2.04        13.02        15.98         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 
       45.73        28.93        30.31        27.19        38.93        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 
       48.53        38.53        60.23        46.55        47.80        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 
       60.23        41.85        47.87        29.06        27.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       17.52         5.75        27.68         0.30        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
       25.87        20.55        14.53        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8474 
        3.75        23.05        19.92        64.47        63.98        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        2.99        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6336 TCGA-G9-6338 
       16.24         1.78        41.62        87.35        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       27.29        58.22        52.87        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7081 
        6.08        30.94         3.68        19.76         2.93         2.37 
TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 
       14.47         0.79        28.60         1.68         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 
        0.72         2.10         2.66         1.74         1.48         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        26.04         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56         1.84        19.36        22.42         3.12 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.17         2.27         1.94        22.32         1.58        15.88 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         0.76         1.78         2.20         1.61         5.49 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 
        3.48         1.45         1.25         4.41        78.61        88.24 
TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       82.92        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 
       93.99        56.28        44.68        61.78       115.86        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 
      151.36        67.59       113.33        67.07        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I 
        3.19       114.64        47.21        86.14        11.90         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D 
       32.91        15.09        84.69        23.93        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       37.18        27.81        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJU 
       31.96        31.96        28.54        30.58        27.09        39.65 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       52.96        49.02        38.56        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       45.50        41.46        45.14        28.77        47.38        37.97 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL 
       71.34        62.79        14.04        41.39        60.99        24.33 
TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QY 
       49.91         1.64         1.12 

  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                         1.02                          0.30 
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                       106.95                        151.36 
  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE 
                        26.73                         22.75 
[1] "1.0 - 107.0 (26.7)" "0.3 - 151.4 (22.8)"
[1] "hr=" "1.2"
D35V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK  7(2Q22.3) MUTATED    23  34   1
  DEL PEAK  7(2Q22.3) WILD-TYPE 127 172   4
D35V3, multiclass
    clus
vv   DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE
  T2                          23                           127
  T3                          34                           172
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q22.3) MUTATED    46   8
  DEL PEAK  7(2Q22.3) WILD-TYPE 217  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.3) MUTATED     46    8
  DEL PEAK  7(2Q22.3) WILD-TYPE  217   36
   clus
vv  DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE
  0                          46                           217
  1                           8                            36
[1] 2 2
[1] FALSE
D35V5, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q22.3) MUTATED     1  57
  DEL PEAK  7(2Q22.3) WILD-TYPE  12 293
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q22.3) MUTATED      1   57
  DEL PEAK  7(2Q22.3) WILD-TYPE   12  293
                                        clus
vv                                       DEL PEAK  7(2Q22.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             57
                                        clus
vv                                       DEL PEAK  7(2Q22.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              293
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(2Q22.3) MUTATED    36  16   1   2
  DEL PEAK  7(2Q22.3) WILD-TYPE 207  74   4   9
D35V6, multiclass
    clus
vv   DEL PEAK  7(2Q22.3) MUTATED DEL PEAK  7(2Q22.3) WILD-TYPE
  R0                          36                           207
  R1                          16                            74
  R2                           1                             4
  RX                           2                             9
[1] 4 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, continuous
D35V8, continuous
D35V9, continuous
D35V10, continuous
D35V11, continuous
D35V12, continuous
D35V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(2Q22.3) MUTATED       0                         1    21
  DEL PEAK  7(2Q22.3) WILD-TYPE     2                         6   125
D35V14, multiclass
                           clus
vv                          DEL PEAK  7(2Q22.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              21
                           clus
vv                          DEL PEAK  7(2Q22.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK  8(3P13) MUTATION ANALYSIS
D36V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  8(3P13) MUTATED    58   0
  DEL PEAK  8(3P13) WILD-TYPE 297   6
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                         58                         303 
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                          0                           6 
$`DEL PEAK  8(3P13) MUTATED`
TCGA-2A-A8VV TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5752 
       22.06         6.97        22.06        12.99        24.03        31.00 
TCGA-CH-5753 TCGA-CH-5764 TCGA-EJ-5497 TCGA-EJ-5501 TCGA-EJ-5505 TCGA-EJ-5510 
        1.02         1.02        13.32        44.88        30.31        36.69 
TCGA-EJ-5517 TCGA-EJ-5542 TCGA-EJ-7327 TCGA-EJ-7788 TCGA-EJ-7797 TCGA-EJ-8469 
       47.80        29.06         5.75        14.14        19.92        63.98 
TCGA-EJ-A65D TCGA-G9-6332 TCGA-G9-6354 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       12.92        87.35        49.35        47.44        45.30        39.39 
TCGA-G9-6384 TCGA-G9-7523 TCGA-G9-A9S7 TCGA-H9-A6BY TCGA-HC-7747 TCGA-HC-7749 
       25.15        28.18        21.14         3.68        24.59         1.97 
TCGA-HC-8213 TCGA-HC-8259 TCGA-HC-A6AL TCGA-HC-A6HY TCGA-J4-A67S TCGA-J4-A6M7 
       19.36         2.27         2.20         4.41        17.19         9.17 
TCGA-J4-A83M TCGA-KK-A59Y TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E6 TCGA-KK-A7AZ 
       14.37        44.68        54.54       151.36       113.33        27.62 
TCGA-KK-A7B1 TCGA-M7-A71Z TCGA-M7-A725 TCGA-QU-A6IM TCGA-VN-A88L TCGA-VN-A88M 
       34.95         6.87        18.84        41.00        12.95         6.02 
TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87K TCGA-YL-A8HK 
       32.91         4.34        26.47        84.69        21.53        49.02 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WL 
       26.24        71.34        62.79        24.33 

$`DEL PEAK  8(3P13) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5737 
       20.42        43.79        33.96         3.68        25.35         2.99 
TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.02        13.97         1.97         1.02        13.02        35.01 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 
        2.04         0.92        44.02        12.00        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5502 TCGA-EJ-5503 
       33.11        19.56        29.79        46.52        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 
       28.93        27.19        23.90        38.93        48.13        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5519 
       38.53        36.23        60.23        46.55        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       60.23        41.85        47.87        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
        7.66        17.52        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 
       38.37        25.87        25.68        20.55        14.53        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-8470 
       19.59        17.29         3.75        23.05        64.47        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
        7.53        21.96        17.62        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 
       17.23        16.24         1.78        41.62        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6365 TCGA-G9-6366 
       46.16        50.70        47.15        46.52        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       37.97        45.80        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX TCGA-HC-7075 TCGA-HC-7078 
       32.68        26.01         6.08        30.94        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60         1.97         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
        2.07        26.04         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56         1.84        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.17         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN 
        1.15        22.36         0.76         1.78         2.01         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HI-7168 
        5.49         2.33         3.48         1.45         1.25        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
        6.02        13.32        17.36         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       10.39        20.28        13.87         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E3 TCGA-KK-A6E4 
       56.28        61.78       115.86        30.02        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       49.25        67.07        58.19        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       20.65         5.19         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
       15.88         3.19       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.19         8.84        25.51        15.52        15.81        30.15 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       15.09       106.95        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-AA1N TCGA-WW-A8ZI 
       60.92        66.97        21.80        48.85        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        38.56        36.95        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       45.86        37.97       106.75         7.00        14.04        41.39 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       60.99        62.37        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                       1.02                        0.30 
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                     151.36                      115.86 
  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE 
                      24.46                       23.90 
[1] "1.0 - 151.4 (24.5)" "0.3 - 115.9 (23.9)"
[1] "hr="     "8.9e+07"
D36V2, continuous
                             vv
clus                           T2  T3  T4
  DEL PEAK  8(3P13) MUTATED    23  35   1
  DEL PEAK  8(3P13) WILD-TYPE 127 171   4
D36V3, multiclass
    clus
vv   DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE
  T2                        23                         127
  T3                        35                         171
  T4                         1                           4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                             cls
clus                            0   1
  DEL PEAK  8(3P13) MUTATED    46   5
  DEL PEAK  8(3P13) WILD-TYPE 217  39
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3P13) MUTATED     46    5
  DEL PEAK  8(3P13) WILD-TYPE  217   39
   clus
vv  DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE
  0                        46                         217
  1                         5                          39
[1] 2 2
[1] FALSE
D36V5, binary
                             cls
clus                            0   1
  DEL PEAK  8(3P13) MUTATED     3  56
  DEL PEAK  8(3P13) WILD-TYPE  10 294
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3P13) MUTATED      3   56
  DEL PEAK  8(3P13) WILD-TYPE   10  294
                                        clus
vv                                       DEL PEAK  8(3P13) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           56
                                        clus
vv                                       DEL PEAK  8(3P13) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            294
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  8(3P13) MUTATED    43  11   0   4
  DEL PEAK  8(3P13) WILD-TYPE 200  79   5   7
D36V6, multiclass
    clus
vv   DEL PEAK  8(3P13) MUTATED DEL PEAK  8(3P13) WILD-TYPE
  R0                        43                         200
  R1                        11                          79
  R2                         0                           5
  RX                         4                           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"
D36V7, continuous
D36V8, continuous
D36V9, continuous
D36V10, continuous
D36V11, continuous
D36V12, continuous
D36V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P13) MUTATED       0                         1    23
  DEL PEAK  8(3P13) WILD-TYPE     2                         6   123
D36V14, multiclass
                           clus
vv                          DEL PEAK  8(3P13) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            23
                           clus
vv                          DEL PEAK  8(3P13) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK  9(3Q29) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  9(3Q29) MUTATED    25   0
  DEL PEAK  9(3Q29) WILD-TYPE 330   6
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                         25                         336 
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                          0                           6 
$`DEL PEAK  9(3Q29) MUTATED`
TCGA-2A-A8VL TCGA-CH-5768 TCGA-EJ-5497 TCGA-EJ-5542 TCGA-EJ-7792 TCGA-EJ-A46G 
       20.42        24.03        13.32        29.06        17.29         3.06 
TCGA-EJ-A65F TCGA-EJ-A65M TCGA-G9-6332 TCGA-G9-6361 TCGA-G9-7523 TCGA-G9-7525 
       18.41         7.56        87.35        46.52        28.18        32.68 
TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8257 TCGA-J4-8200 TCGA-KK-A59Y TCGA-KK-A6E6 
       17.85         1.84        23.87        12.30        44.68       113.33 
TCGA-VN-A88R TCGA-VP-A876 TCGA-YL-A8HK TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SQ 
       15.09        84.69        49.02        37.97        26.24        62.79 
TCGA-ZG-A8QZ 
        7.86 

$`DEL PEAK  9(3Q29) WILD-TYPE`
TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5737 
       43.79        22.06        33.96         3.68        25.35         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
        1.02        15.06         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       33.11        19.56        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       47.87        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
        5.75        27.68         6.28         0.30        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       19.59         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G 
        7.53        21.96        17.62        12.92        13.71         9.14 
TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        2.99        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       16.24         1.78        41.62        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       50.70        49.35        47.15        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        52.87        50.73        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       27.91        30.97        35.34        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 
       24.56        19.36        22.42         3.12         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67K 
       78.61        88.24        82.92        43.69        20.19        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY 
        5.85        10.62        93.99        56.28        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
       67.07        58.19        27.62        34.95        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       27.02        25.08        15.88        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A879 
       32.91         4.34       106.95        26.47        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.50        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM 
       37.02        39.65        25.48        52.96        38.56        36.95 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        45.50        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SP 
       45.14        28.77        47.38        45.86       106.75        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        7.00        14.04        41.39        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9ND 
       49.91        28.34         1.64         4.93         1.12         6.02 

  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                       1.84                        0.30 
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                     113.33                      151.36 
  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE 
                     24.030                      23.915 
[1] "1.8 - 113.3 (24.0)" "0.3 - 151.4 (23.9)"
[1] "hr="     "7.5e+07"
D37V2, continuous
                             vv
clus                           T2  T3  T4
  DEL PEAK  9(3Q29) MUTATED     9  16   0
  DEL PEAK  9(3Q29) WILD-TYPE 141 190   5
D37V3, multiclass
    clus
vv   DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE
  T2                         9                         141
  T3                        16                         190
  T4                         0                           5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                             cls
clus                            0   1
  DEL PEAK  9(3Q29) MUTATED    19   6
  DEL PEAK  9(3Q29) WILD-TYPE 244  38
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(3Q29) MUTATED     19    6
  DEL PEAK  9(3Q29) WILD-TYPE  244   38
   clus
vv  DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE
  0                        19                         244
  1                         6                          38
[1] 2 2
[1] FALSE
D37V5, binary
                             cls
clus                            0   1
  DEL PEAK  9(3Q29) MUTATED     2  23
  DEL PEAK  9(3Q29) WILD-TYPE  11 327
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(3Q29) MUTATED      2   23
  DEL PEAK  9(3Q29) WILD-TYPE   11  327
                                        clus
vv                                       DEL PEAK  9(3Q29) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           23
                                        clus
vv                                       DEL PEAK  9(3Q29) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            327
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  9(3Q29) MUTATED    14   7   1   1
  DEL PEAK  9(3Q29) WILD-TYPE 229  83   4  10
D37V6, multiclass
    clus
vv   DEL PEAK  9(3Q29) MUTATED DEL PEAK  9(3Q29) WILD-TYPE
  R0                        14                         229
  R1                         7                          83
  R2                         1                           4
  RX                         1                          10
[1] 4 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, continuous
D37V8, continuous
D37V9, continuous
D37V10, continuous
D37V11, continuous
D37V12, continuous
D37V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3Q29) MUTATED       0                         0     8
  DEL PEAK  9(3Q29) WILD-TYPE     2                         7   138
D37V14, multiclass
                           clus
vv                          DEL PEAK  9(3Q29) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                             8
                           clus
vv                          DEL PEAK  9(3Q29) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             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"

Clustering(38) Variable = DEL PEAK 10(4Q28.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q28.2) MUTATED    37   0
  DEL PEAK 10(4Q28.2) WILD-TYPE 318   6
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                           37                           324 
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                            0                             6 
$`DEL PEAK 10(4Q28.2) MUTATED`
TCGA-CH-5751 TCGA-CH-5788 TCGA-EJ-5509 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-7123 
       35.01        26.99        48.13        52.27        51.88        49.02 
TCGA-EJ-7312 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7789 TCGA-EJ-A65B 
       21.80         6.28         0.30        38.37        18.15        17.62 
TCGA-FC-7961 TCGA-G9-6361 TCGA-G9-6499 TCGA-HC-7080 TCGA-HC-7738 TCGA-HC-A48F 
       15.42        46.52        50.73         2.01         2.66        22.36 
TCGA-HC-A6AO TCGA-J9-A52B TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E8 TCGA-KK-A8IB 
        5.49        13.87        61.78        30.02        58.19         2.73 
TCGA-M7-A721 TCGA-M7-A722 TCGA-VN-A88P TCGA-VP-A87K TCGA-VP-AA1N TCGA-XJ-A83G 
       13.15        27.02        30.15        21.53        17.82        38.04 
TCGA-XK-AAIR TCGA-XK-AAJA TCGA-XK-AAJT TCGA-YL-A8HM TCGA-YL-A8SL TCGA-YL-A9WH 
       31.96        30.58        37.02        36.95        26.24        14.04 
TCGA-YL-A9WL 
       24.33 

$`DEL PEAK 10(4Q28.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       38.93        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       46.55        47.80        64.50        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       27.02        61.15        83.57         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7781 
       16.77         7.66        17.52         5.75        27.68        23.90 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 
       25.87        25.68        20.55        14.53        14.14        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        3.06         7.53        21.96        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB 
        9.14         2.99         7.56        28.41        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 
       49.81        46.16        50.70        49.35        47.15        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 
       25.15        27.29        58.22        56.75        52.87        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        5.33         2.93         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60         1.97         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        0.72         2.10         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 
       22.32         1.58        15.88         1.15         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.01         2.20         1.61         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         4.41        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       14.37        20.28         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       44.68       115.86        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       49.25       113.33        67.07        27.62        34.95        22.75 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A723 
       26.43        20.65         5.19         6.87         9.93        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
        6.02        15.52        15.81        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-WW-A8ZI 
       55.56        60.92        66.97        21.80        48.85         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.18        27.81         3.91        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR 
       25.97        31.50        31.96        28.54        29.23        27.09 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       39.65        25.48        52.96        49.02        38.56        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        47.38        45.86        37.97       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX 
       62.79         7.00        41.39        60.99        62.37        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                         0.30                          0.72 
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                        61.78                        151.36 
  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE 
                       26.990                        23.885 
[1] "0.3 - 61.8 (27.0)"  "0.7 - 151.4 (23.9)"
[1] "hr="     "7.9e+07"
D38V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 10(4Q28.2) MUTATED    13  22   2
  DEL PEAK 10(4Q28.2) WILD-TYPE 137 184   3
D38V3, multiclass
    clus
vv   DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE
  T2                          13                           137
  T3                          22                           184
  T4                           2                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q28.2) MUTATED    29   5
  DEL PEAK 10(4Q28.2) WILD-TYPE 234  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q28.2) MUTATED     29    5
  DEL PEAK 10(4Q28.2) WILD-TYPE  234   39
   clus
vv  DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE
  0                          29                           234
  1                           5                            39
[1] 2 2
[1] FALSE
D38V5, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q28.2) MUTATED     2  35
  DEL PEAK 10(4Q28.2) WILD-TYPE  11 315
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q28.2) MUTATED      2   35
  DEL PEAK 10(4Q28.2) WILD-TYPE   11  315
                                        clus
vv                                       DEL PEAK 10(4Q28.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             35
                                        clus
vv                                       DEL PEAK 10(4Q28.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              315
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q28.2) MUTATED    22  12   0   1
  DEL PEAK 10(4Q28.2) WILD-TYPE 221  78   5  10
D38V6, multiclass
    clus
vv   DEL PEAK 10(4Q28.2) MUTATED DEL PEAK 10(4Q28.2) WILD-TYPE
  R0                          22                           221
  R1                          12                            78
  R2                           0                             5
  RX                           1                            10
[1] 4 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, continuous
D38V8, continuous
D38V9, continuous
D38V10, continuous
D38V11, continuous
D38V12, continuous
D38V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4Q28.2) MUTATED       0                         2    13
  DEL PEAK 10(4Q28.2) WILD-TYPE     2                         5   133
D38V14, multiclass
                           clus
vv                          DEL PEAK 10(4Q28.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              13
                           clus
vv                          DEL PEAK 10(4Q28.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               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(39) Variable = DEL PEAK 11(5Q11.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(5Q11.2) MUTATED    59   1
  DEL PEAK 11(5Q11.2) WILD-TYPE 296   5
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                           60                           301 
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                            1                             5 
$`DEL PEAK 11(5Q11.2) MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5792 
       35.01         0.92        23.01         1.02        24.03         2.99 
TCGA-EJ-5501 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5519 TCGA-EJ-5525 TCGA-EJ-5526 
       44.88        23.90        48.13        64.50        36.66        38.76 
TCGA-EJ-7115 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7789 TCGA-EJ-8468 TCGA-EJ-8474 
       27.02        21.80        17.52        18.15        64.47        10.32 
TCGA-EJ-A65M TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 
        7.56        13.45        66.67        50.73        38.96        30.97 
TCGA-H9-7775 TCGA-HC-7078 TCGA-HC-7821 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F 
        6.08         5.33         1.84         1.58         1.15        22.36 
TCGA-HI-7168 TCGA-J4-A83J TCGA-J9-A52B TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
       78.61        10.19        13.87        56.28        44.68        61.78 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-QU-A6IN TCGA-TP-A8TV 
       30.02        54.54         2.73        26.43       114.64         8.19 
TCGA-VN-A88K TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A878 TCGA-VP-A87D TCGA-VP-A87H 
       25.51        15.09       106.95        94.65        60.92        21.80 
TCGA-VP-AA1N TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJT TCGA-YL-A8HM TCGA-YL-A8S8 
       17.82        28.54        29.23        37.02        36.95        62.14 
TCGA-YL-A8SA TCGA-YL-A8SH TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WL TCGA-ZG-A9ND 
       16.83        28.77       106.75         7.00        24.33         6.02 

$`DEL PEAK 11(5Q11.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5767 TCGA-CH-5769 
        2.04        44.02        12.00         1.02        15.06         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       46.52        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       38.93        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       46.55        47.80        52.27        51.88        68.35        43.07 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7123 
       39.75        60.23        41.85        47.87        29.06        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       61.15        83.57         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
        7.66         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 
       19.59        17.29         3.75        23.05        19.92        63.98 
TCGA-EJ-8470 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       26.99         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V 
        9.14         2.99        28.41        15.42         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7519 
       27.29        58.22        56.75        52.87        38.27        27.91 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-A6BX 
       35.34        28.18        32.68        26.01        21.14        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
        3.68        19.76         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 
        1.94        17.95        22.32        15.88         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       17.36         9.17         9.17         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A6DY TCGA-KK-A6E2 
       20.28         5.85        10.62        93.99       115.86       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       27.62        34.95        22.75        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I 
        3.19        41.00        47.21        86.14        11.90         8.84 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
        4.34        26.47        84.69        23.93        75.91        55.56 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       66.97        48.85        21.53         5.79        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJU 
       31.96        31.50        31.96        30.58        27.09        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S9 
       25.48        52.96        49.02        38.56        71.77        60.56 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       45.50        41.46        45.14        47.38        45.86        37.97 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       26.24        71.34        62.79        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       62.37        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ 
        7.86 

  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                         0.92                          0.30 
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                       114.64                        151.36 
  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE 
                        25.97                         23.05 
[1] "0.9 - 114.6 (26.0)" "0.3 - 151.4 (23.1)"
[1] "hr=" "1.3"
D39V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 11(5Q11.2) MUTATED    11  50   1
  DEL PEAK 11(5Q11.2) WILD-TYPE 139 156   4
D39V3, multiclass
    clus
vv   DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE
  T2                          11                           139
  T3                          50                           156
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q11.2) MUTATED    43  15
  DEL PEAK 11(5Q11.2) WILD-TYPE 220  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q11.2) MUTATED     43   15
  DEL PEAK 11(5Q11.2) WILD-TYPE  220   29
   clus
vv  DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE
  0                          43                           220
  1                          15                            29
[1] 2 2
[1] FALSE
D39V5, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q11.2) MUTATED     1  61
  DEL PEAK 11(5Q11.2) WILD-TYPE  12 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q11.2) MUTATED      1   61
  DEL PEAK 11(5Q11.2) WILD-TYPE   12  289
                                        clus
vv                                       DEL PEAK 11(5Q11.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             61
                                        clus
vv                                       DEL PEAK 11(5Q11.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              289
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(5Q11.2) MUTATED    38  18   1   2
  DEL PEAK 11(5Q11.2) WILD-TYPE 205  72   4   9
D39V6, multiclass
    clus
vv   DEL PEAK 11(5Q11.2) MUTATED DEL PEAK 11(5Q11.2) WILD-TYPE
  R0                          38                           205
  R1                          18                            72
  R2                           1                             4
  RX                           2                             9
[1] 4 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, continuous
D39V8, continuous
D39V9, continuous
D39V10, continuous
D39V11, continuous
D39V12, continuous
D39V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(5Q11.2) MUTATED       0                         2    19
  DEL PEAK 11(5Q11.2) WILD-TYPE     2                         5   127
D39V14, multiclass
                           clus
vv                          DEL PEAK 11(5Q11.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              19
                           clus
vv                          DEL PEAK 11(5Q11.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               127
[1] 3 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 = DEL PEAK 12(5Q13.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q13.2) MUTATED    62   1
  DEL PEAK 12(5Q13.2) WILD-TYPE 293   5
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                           63                           298 
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                            1                             5 
$`DEL PEAK 12(5Q13.2) MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5792 
       35.01         0.92        23.01         1.02        24.03         2.99 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5516 TCGA-EJ-5519 
       46.52        44.88        23.90        48.13        46.55        64.50 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-7115 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7789 
       43.07        38.76        27.02        21.80        17.52        18.15 
TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6499 TCGA-G9-7510 
        7.56        15.42        13.45        66.67        50.73        38.96 
TCGA-G9-7521 TCGA-HC-7211 TCGA-HC-8216 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 
       30.97         0.79        22.42         1.15        22.36         2.01 
TCGA-HI-7168 TCGA-J4-A83J TCGA-J9-A52B TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 
       78.61        10.19        13.87        56.28        61.78        30.02 
TCGA-KK-A6E1 TCGA-KK-A7B1 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-TP-A8TV TCGA-VN-A88K 
       54.54        34.95         2.73        26.43         8.19        25.51 
TCGA-VN-A88N TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-AA1N 
       15.52        15.09       106.95        60.92        21.80        17.82 
TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XK-AAJP TCGA-XK-AAJT TCGA-YL-A8HM TCGA-YL-A8S8 
       37.18        38.04        29.23        37.02        36.95        62.14 
TCGA-YL-A8SA TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WL 
       16.83        28.77        45.86       106.75         7.00        24.33 
TCGA-YL-A9WY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         7.86         6.02 

$`DEL PEAK 12(5Q13.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5767 TCGA-CH-5769 
        2.04        44.02        12.00         1.02        15.06         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       26.30        45.73        28.93        30.31        27.19        38.93 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5517 
       36.69        48.53        38.53        36.23        60.23        47.80 
TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 
       52.27        51.88        68.35        36.66        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       41.85        47.87        29.06        49.02        61.15        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
        9.70         9.50         9.37        16.77         7.66         5.75 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28         0.30        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
       25.68        20.55        14.53        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        9.14         2.99        28.41         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 
        1.78        41.62        87.35        81.04        67.99        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7519 TCGA-G9-7522 
       58.22        56.75        52.87        38.27        27.91        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
        1.84        19.36         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV 
        1.94        17.95        22.32         1.58        15.88         0.76 
TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        1.78         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       17.36         9.17         9.17         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6DY 
       20.28         5.85        10.62        93.99        44.68       115.86 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       58.19        27.62        22.75        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
        8.84        12.95         6.02        15.81        30.15        32.91 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS 
       55.56        66.97        48.85        21.53         5.79        27.81 
TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
        3.91        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJU 
       31.50        31.96        28.54        30.58        27.09        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S9 
       25.48        52.96        49.02        38.56        71.77        60.56 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL 
       45.50        41.46        45.14        47.38        37.97        26.24 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79        14.04        41.39        60.99        62.37 
TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       49.91         1.64         4.93         1.12 

  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                         0.79                          0.30 
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                       106.95                        151.36 
  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE 
                        26.43                         22.90 
[1] "0.8 - 107.0 (26.4)" "0.3 - 151.4 (22.9)"
[1] "hr=" "1.2"
D40V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 12(5Q13.2) MUTATED     9  54   1
  DEL PEAK 12(5Q13.2) WILD-TYPE 141 152   4
D40V3, multiclass
    clus
vv   DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE
  T2                           9                           141
  T3                          54                           152
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q13.2) MUTATED    49  13
  DEL PEAK 12(5Q13.2) WILD-TYPE 214  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q13.2) MUTATED     49   13
  DEL PEAK 12(5Q13.2) WILD-TYPE  214   31
   clus
vv  DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE
  0                          49                           214
  1                          13                            31
[1] 2 2
[1] FALSE
D40V5, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q13.2) MUTATED     1  63
  DEL PEAK 12(5Q13.2) WILD-TYPE  12 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q13.2) MUTATED      1   63
  DEL PEAK 12(5Q13.2) WILD-TYPE   12  287
                                        clus
vv                                       DEL PEAK 12(5Q13.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             63
                                        clus
vv                                       DEL PEAK 12(5Q13.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              287
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q13.2) MUTATED    40  18   1   2
  DEL PEAK 12(5Q13.2) WILD-TYPE 203  72   4   9
D40V6, multiclass
    clus
vv   DEL PEAK 12(5Q13.2) MUTATED DEL PEAK 12(5Q13.2) WILD-TYPE
  R0                          40                           203
  R1                          18                            72
  R2                           1                             4
  RX                           2                             9
[1] 4 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, continuous
D40V8, continuous
D40V9, continuous
D40V10, continuous
D40V11, continuous
D40V12, continuous
D40V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(5Q13.2) MUTATED       1                         1    19
  DEL PEAK 12(5Q13.2) WILD-TYPE     1                         6   127
D40V14, multiclass
                           clus
vv                          DEL PEAK 12(5Q13.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              19
                           clus
vv                          DEL PEAK 12(5Q13.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               127
[1] 3 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 = DEL PEAK 13(5Q21.1) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q21.1) MUTATED    74   1
  DEL PEAK 13(5Q21.1) WILD-TYPE 281   5
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                           75                           286 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                            1                             5 
$`DEL PEAK 13(5Q21.1) MUTATED`
TCGA-2A-A8VX TCGA-CH-5737 TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5766 TCGA-CH-5788 
       33.96         2.99        35.01         0.92         1.02        26.99 
TCGA-CH-5792 TCGA-EJ-5501 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5507 TCGA-EJ-5509 
        2.99        44.88        28.93        30.31        23.90        48.13 
TCGA-EJ-5521 TCGA-EJ-5531 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7325 
       51.88        41.85        49.02        21.80         9.50        17.52 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-8468 
        6.28         0.30        38.37        25.68        18.15        64.47 
TCGA-EJ-8470 TCGA-EJ-A65E TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 
       26.99        13.71         7.56        15.42        13.45        66.67 
TCGA-G9-6369 TCGA-G9-6496 TCGA-G9-6499 TCGA-HC-7080 TCGA-HC-8216 TCGA-HC-8261 
       39.95        56.75        50.73         2.01        22.42        17.95 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A6AP TCGA-HI-7168 TCGA-J9-A52B TCGA-KK-A59X 
        1.15        22.36         2.33        78.61        13.87        56.28 
TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A721 
       61.78        30.02        54.54         2.73        26.43        13.15 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88R TCGA-VN-A943 
       41.00       114.64        11.90         8.19        15.09         4.34 
TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-AA1N TCGA-XJ-A83G TCGA-XK-AAIR TCGA-XK-AAJ3 
       94.65        75.91        17.82        38.04        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-Y6-A8TL TCGA-YL-A8HM 
       30.58        29.23        27.09        37.02        25.48        36.95 
TCGA-YL-A8SA TCGA-YL-A8SH TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WL 
       16.83        28.77       106.75         7.00        41.39        24.33 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9ND 
        4.93         1.12         6.02 

$`DEL PEAK 13(5Q21.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5738 
       20.42        43.79        22.06         3.68        25.35         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 
        1.02        13.02        31.00         1.02         2.04        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       12.00         1.02        23.01        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 
       13.02        15.98         9.99        32.02        33.01        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 
       26.30        45.73        27.19        38.93        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       64.50        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        47.87        29.06        27.02        61.15        83.57 
TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
        9.70         9.37        16.77         7.66         5.75        27.68 
TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 
       23.90        25.87        20.55        14.53        14.14        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8474 
       17.29         3.75        23.05        19.92        63.98        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        17.62        12.92        18.41         9.14         2.99 
TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.41         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       87.35        81.04        67.99        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       40.18        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6498 TCGA-G9-7509 
       45.80        25.15        27.29        58.22        52.87        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        5.33         2.93         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60         1.97         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8262 
        3.12        23.87         2.17         2.27         1.94        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.58        15.88         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61         5.49         3.48         1.45         1.25         4.41 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C 
       10.19         6.77        10.39        14.37        20.28         5.85 
TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E3 
       10.62        93.99        44.68       115.86       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       34.95        22.75        20.65         5.19         6.87         9.93 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IO 
       27.02        25.08        15.88        18.84         3.19        47.21 
TCGA-QU-A6IP TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       86.14         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       15.81        30.15        32.91       106.95        26.47        84.69 
TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       23.93        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI 
       21.53         5.79        37.18        27.81         3.91        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJU 
        9.04         2.99        25.97        31.50        31.96        39.65 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        38.56        71.77        62.14        60.56 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       45.50        41.46        45.14        47.38        45.86        37.97 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK 
       26.24        71.34        62.79        14.04        60.99        62.37 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QZ 
       49.91        28.34         1.64         7.86 

  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                         0.30                          0.72 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                       114.64                        151.36 
  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE 
                        26.43                         23.03 
[1] "0.3 - 114.6 (26.4)" "0.7 - 151.4 (23.0)"
[1] "hr=" "1.4"
D41V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 13(5Q21.1) MUTATED    26  49   1
  DEL PEAK 13(5Q21.1) WILD-TYPE 124 157   4
D41V3, multiclass
    clus
vv   DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  T2                          26                           124
  T3                          49                           157
  T4                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.1) MUTATED    60  11
  DEL PEAK 13(5Q21.1) WILD-TYPE 203  33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.1) MUTATED     60   11
  DEL PEAK 13(5Q21.1) WILD-TYPE  203   33
   clus
vv  DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  0                          60                           203
  1                          11                            33
[1] 2 2
[1] FALSE
D41V5, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.1) MUTATED     1  75
  DEL PEAK 13(5Q21.1) WILD-TYPE  12 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.1) MUTATED      1   75
  DEL PEAK 13(5Q21.1) WILD-TYPE   12  275
                                        clus
vv                                       DEL PEAK 13(5Q21.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             75
                                        clus
vv                                       DEL PEAK 13(5Q21.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              275
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q21.1) MUTATED    53  16   0   3
  DEL PEAK 13(5Q21.1) WILD-TYPE 190  74   5   8
D41V6, multiclass
    clus
vv   DEL PEAK 13(5Q21.1) MUTATED DEL PEAK 13(5Q21.1) WILD-TYPE
  R0                          53                           190
  R1                          16                            74
  R2                           0                             5
  RX                           3                             8
[1] 4 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, continuous
D41V8, continuous
D41V9, continuous
D41V10, continuous
D41V11, continuous
D41V12, continuous
D41V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(5Q21.1) MUTATED       0                         2    25
  DEL PEAK 13(5Q21.1) WILD-TYPE     2                         5   121
D41V14, multiclass
                           clus
vv                          DEL PEAK 13(5Q21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              25
                           clus
vv                          DEL PEAK 13(5Q21.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = DEL PEAK 14(6P25.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(6P25.1) MUTATED    27   0
  DEL PEAK 14(6P25.1) WILD-TYPE 328   6
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                           27                           334 
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                            0                             6 
$`DEL PEAK 14(6P25.1) MUTATED`
TCGA-CH-5740 TCGA-CH-5754 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5504 TCGA-EJ-5507 
        1.02         2.04        29.79        46.52        28.93        23.90 
TCGA-EJ-5524 TCGA-EJ-7123 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-FC-7708 
       43.07        49.02        38.37        25.68        14.53        28.41 
TCGA-HC-7213 TCGA-HC-7821 TCGA-HC-8257 TCGA-HC-A48F TCGA-HC-A632 TCGA-J9-A52B 
        1.97         1.84        23.87        22.36         2.01        13.87 
TCGA-VP-A87C TCGA-VP-AA1N TCGA-YL-A8HO TCGA-YL-A8SF TCGA-YL-A8SL TCGA-YL-A8SQ 
       55.56        17.82        71.77        45.14        26.24        62.79 
TCGA-YL-A9WH TCGA-YL-A9WL TCGA-ZG-A8QW 
       14.04        24.33         1.64 

$`DEL PEAK 14(6P25.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97        22.06        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       33.11        19.56        13.32        44.88        26.30        45.73 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       30.31        27.19        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       64.50        51.88        68.35        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 
       60.23        41.85        47.87        29.06        27.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       23.90        25.87        20.55        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        3.06         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI 
       18.41         9.14         2.99         7.56        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.37        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8258 TCGA-HC-8259 
       24.56        19.36        22.42         3.12         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        0.76         1.78         2.20         1.61         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 
        3.48         1.45         1.25         4.41        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        21.76        17.03 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       16.04        16.54        16.14        20.52        14.93        17.19 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        13.32        17.36         9.17         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E 
        6.77        10.39        14.37        20.28         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       93.99        56.28        44.68        61.78       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
       67.07        58.19        27.62        34.95        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       27.02        25.08        15.88        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       32.91        15.09         4.34       106.95        26.47        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       94.65        23.93        75.91        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       48.85        21.53         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.50        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       36.95        62.14        60.56        16.83        45.50        41.46 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        47.38        45.86        37.97       106.75        71.34 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY 
        7.00        41.39        60.99        62.37        49.91        28.34 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                         1.02                          0.30 
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                        71.77                        151.36 
  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE 
                       24.330                        23.915 
[1] "1.0 - 71.8 (24.3)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "7.4e+07"
D42V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 14(6P25.1) MUTATED     8  19   0
  DEL PEAK 14(6P25.1) WILD-TYPE 142 187   5
D42V3, multiclass
    clus
vv   DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE
  T2                           8                           142
  T3                          19                           187
  T4                           0                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, binary
                               cls
clus                              0   1
  DEL PEAK 14(6P25.1) MUTATED    18   9
  DEL PEAK 14(6P25.1) WILD-TYPE 245  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(6P25.1) MUTATED     18    9
  DEL PEAK 14(6P25.1) WILD-TYPE  245   35
   clus
vv  DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE
  0                          18                           245
  1                           9                            35
[1] 2 2
[1] FALSE
D42V5, binary
                               cls
clus                              0   1
  DEL PEAK 14(6P25.1) MUTATED     0  27
  DEL PEAK 14(6P25.1) WILD-TYPE  13 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(6P25.1) MUTATED      0   27
  DEL PEAK 14(6P25.1) WILD-TYPE   13  323
                                        clus
vv                                       DEL PEAK 14(6P25.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             27
                                        clus
vv                                       DEL PEAK 14(6P25.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              323
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(6P25.1) MUTATED    15  10   0   1
  DEL PEAK 14(6P25.1) WILD-TYPE 228  80   5  10
D42V6, multiclass
    clus
vv   DEL PEAK 14(6P25.1) MUTATED DEL PEAK 14(6P25.1) WILD-TYPE
  R0                          15                           228
  R1                          10                            80
  R2                           0                             5
  RX                           1                            10
[1] 4 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, continuous
D42V8, continuous
D42V9, continuous
D42V10, continuous
D42V11, continuous
D42V12, continuous
D42V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(6P25.1) MUTATED       2                         1    11
  DEL PEAK 14(6P25.1) WILD-TYPE     0                         6   135
D42V14, multiclass
                           clus
vv                          DEL PEAK 14(6P25.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              11
                           clus
vv                          DEL PEAK 14(6P25.1) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               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(43) Variable = DEL PEAK 15(6Q14.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(6Q14.3) MUTATED   129   3
  DEL PEAK 15(6Q14.3) WILD-TYPE 226   3
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                          132                           229 
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                            3                             3 
$`DEL PEAK 15(6Q14.3) MUTATED`
TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 TCGA-CH-5748 TCGA-CH-5751 TCGA-CH-5753 
       33.96         3.68         2.99         1.02        35.01         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5788 TCGA-CH-5792 
        2.04         0.92         1.02        15.06        26.99         2.99 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 
       28.93        30.31        23.90        48.13        48.53        36.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5531 TCGA-EJ-7115 
       46.55        47.80        52.27        64.50        41.85        27.02 
TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7317 TCGA-EJ-7330 TCGA-EJ-7331 
       49.02        83.57        21.80         9.37         6.28         0.30 
TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-8468 
       38.37        25.68        14.53        14.14        18.15        64.47 
TCGA-EJ-8470 TCGA-EJ-A46F TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65J TCGA-EJ-A65M 
       26.99         9.83        12.92        13.71         2.99         7.56 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6351 
       15.42        13.45         8.98        81.04        66.67        46.16 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6379 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       46.52        47.44        45.80        56.75        52.87        50.73 
TCGA-G9-7510 TCGA-G9-A9S0 TCGA-H9-A6BY TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7210 
       38.96        26.01         3.68         5.33         2.01        28.54 
TCGA-HC-7213 TCGA-HC-7736 TCGA-HC-7747 TCGA-HC-7821 TCGA-HC-8256 TCGA-HC-8257 
        1.97         0.72        24.59         1.84         3.12        23.87 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 
       17.95        22.32         1.58        22.36         0.76         2.01 
TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AP TCGA-J4-A83J TCGA-J9-A52B TCGA-J9-A52E 
        2.20         5.49         2.33        10.19        13.87        10.62 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E1 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A8IB 
       56.28        61.78        54.54        49.25        58.19         2.73 
TCGA-M7-A71Z TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IO 
        6.87        13.15        27.02        15.88         3.19        47.21 
TCGA-TP-A8TV TCGA-VN-A88O TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 
        8.19        15.81        15.09       106.95        26.47        94.65 
TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-X4-A8KS 
       75.91        21.80        21.53        17.82        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJ3 
        3.91        38.04        48.03        31.96        31.50        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-Y6-A8TL TCGA-YL-A8HK 
       30.58        29.23        27.09        37.02        25.48        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SH TCGA-YL-A8SK 
       38.56        36.95        71.77        62.14        28.77        37.97 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       26.24       106.75        62.79         7.00        14.04        41.39 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9ND 
       60.99        62.37         1.64         4.93         1.12         6.02 

$`DEL PEAK 15(6Q14.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-CH-5738 TCGA-CH-5739 
       20.42        43.79        22.06        25.35         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5750 
        1.02        12.99        13.97         1.97        24.03        13.02 
TCGA-CH-5752 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5768 
       31.00        44.02        12.00         1.02        23.01        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
        2.04        13.02        15.98         9.99        32.02        33.01 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5506 TCGA-EJ-5508 
       46.52        44.88        26.30        45.73        27.19        38.93 
TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       36.69        38.53        60.23        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        38.76        39.75        60.23        47.87        29.06 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       61.15         9.70         9.50        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7791 
        5.75        27.68        23.90        25.87        20.55        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8474 
       17.29         3.75        23.05        19.92        63.98        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        5.33         4.24        17.49         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65F TCGA-EJ-A65G TCGA-FC-7708 TCGA-FC-A66V TCGA-FC-A6HD 
       17.62        18.41         9.14        28.41        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 
        1.78        41.62        87.35        67.99        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       18.21        68.68        49.81        50.70        49.35        47.15 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 
       38.01        40.31        26.66        31.50        37.97        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       27.29        58.22        38.27        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-HC-7075 
       28.18        32.68        21.14         6.08        30.94        19.76 
TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.93         2.37        14.47         0.79        28.60         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.37         2.93         1.71         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.48         1.68         2.07        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 
        3.22        30.51         1.48        17.85        24.56        19.36 
TCGA-HC-8216 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8265 TCGA-HC-8266 
       22.42         2.17         2.27         1.94        15.88         1.15 
TCGA-HC-A631 TCGA-HC-A6AN TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.78         1.61         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C 
        9.17         6.77        10.39        14.37        20.28         5.85 
TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       93.99        44.68       115.86        30.02       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       90.51       113.33        67.07        27.62        34.95        22.75 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A723 TCGA-M7-A725 
       26.43        20.65         5.19         9.93        25.08        18.84 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88K 
       41.00       114.64        86.14        11.90         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A943 
       12.95         6.02        15.52        30.15        32.91         4.34 
TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       84.69        23.93        55.56        60.92        66.97        48.85 
TCGA-WW-A8ZI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIW TCGA-XK-AAJU 
        5.79         9.04         2.99        25.97        31.96        39.65 
TCGA-YL-A8HJ TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       52.96        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SP TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       47.38        45.86        71.34        24.33        49.91        28.34 
TCGA-ZG-A8QZ 
        7.86 

  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                         0.30                          0.79 
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                       106.95                        151.36 
  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE 
                       25.845                        23.010 
[1] "0.3 - 107.0 (25.8)" "0.8 - 151.4 (23.0)"
[1] "hr=" "1.5"
D43V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 15(6Q14.3) MUTATED    44  86   2
  DEL PEAK 15(6Q14.3) WILD-TYPE 106 120   3
D43V3, multiclass
    clus
vv   DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE
  T2                          44                           106
  T3                          86                           120
  T4                           2                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                               cls
clus                              0   1
  DEL PEAK 15(6Q14.3) MUTATED    96  26
  DEL PEAK 15(6Q14.3) WILD-TYPE 167  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6Q14.3) MUTATED     96   26
  DEL PEAK 15(6Q14.3) WILD-TYPE  167   18
   clus
vv  DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE
  0                          96                           167
  1                          26                            18
[1] 2 2
[1] FALSE
D43V5, binary
                               cls
clus                              0   1
  DEL PEAK 15(6Q14.3) MUTATED     5 127
  DEL PEAK 15(6Q14.3) WILD-TYPE   8 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6Q14.3) MUTATED      5  127
  DEL PEAK 15(6Q14.3) WILD-TYPE    8  223
                                        clus
vv                                       DEL PEAK 15(6Q14.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            127
                                        clus
vv                                       DEL PEAK 15(6Q14.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             8
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              223
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(6Q14.3) MUTATED    71  45   2   7
  DEL PEAK 15(6Q14.3) WILD-TYPE 172  45   3   4
D43V6, multiclass
    clus
vv   DEL PEAK 15(6Q14.3) MUTATED DEL PEAK 15(6Q14.3) WILD-TYPE
  R0                          71                           172
  R1                          45                            45
  R2                           2                             3
  RX                           7                             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"
D43V7, continuous
D43V8, continuous
D43V9, continuous
D43V10, continuous
D43V11, continuous
D43V12, continuous
D43V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(6Q14.3) MUTATED       0                         3    43
  DEL PEAK 15(6Q14.3) WILD-TYPE     2                         4   103
D43V14, multiclass
                           clus
vv                          DEL PEAK 15(6Q14.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              43
                           clus
vv                          DEL PEAK 15(6Q14.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                               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(44) Variable = DEL PEAK 16(7Q31.33) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(7Q31.33) MUTATED    24   0
  DEL PEAK 16(7Q31.33) WILD-TYPE 331   6
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                            24                            337 
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                             0                              6 
$`DEL PEAK 16(7Q31.33) MUTATED`
TCGA-CH-5761 TCGA-CH-5788 TCGA-EJ-5521 TCGA-EJ-7123 TCGA-G9-6366 TCGA-HC-7080 
        0.92        26.99        51.88        49.02         3.32         2.01 
TCGA-HC-7821 TCGA-HC-A6AO TCGA-J4-A83I TCGA-J4-A83J TCGA-KK-A59V TCGA-KK-A6E4 
        1.84         5.49         9.17        10.19        93.99        90.51 
TCGA-KK-A8IB TCGA-QU-A6IO TCGA-VN-A88L TCGA-VP-A87B TCGA-VP-A87D TCGA-XK-AAIV 
        2.73        47.21        12.95        75.91        60.92        31.50 
TCGA-XK-AAJA TCGA-YL-A8S9 TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A9WI TCGA-ZG-A8QZ 
       30.58        60.56        26.24       106.75        41.39         7.86 

$`DEL PEAK 16(7Q31.33) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         2.04        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 
       60.23        46.55        47.80        52.27        64.50        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       47.87        29.06        27.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
        5.75        27.68         6.28         0.30        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
        9.83         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       44.81        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
        9.17         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        5.85        10.62        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E6 
       30.02        54.54       151.36        67.59        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF 
       67.07        58.19        27.62        34.95        22.75        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M 
       86.14        11.90         8.19         8.84        25.51         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C 
      106.95        26.47        84.69        94.65        23.93        55.56 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP 
        2.99        25.97        31.96        31.96        28.54        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       27.09        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB 
       38.56        36.95        71.77        62.14        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        47.38        45.86        37.97 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79         7.00        14.04        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A9ND 
        6.02 

  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                          0.92                           0.30 
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                        106.75                         151.36 
  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE 
                        28.785                         23.900 
[1] "0.9 - 106.8 (28.8)" "0.3 - 151.4 (23.9)"
[1] "hr="     "7.6e+07"
D44V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 16(7Q31.33) MUTATED     8  16   0
  DEL PEAK 16(7Q31.33) WILD-TYPE 142 190   5
D44V3, multiclass
    clus
vv   DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE
  T2                            8                            142
  T3                           16                            190
  T4                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                                cls
clus                               0   1
  DEL PEAK 16(7Q31.33) MUTATED    14   7
  DEL PEAK 16(7Q31.33) WILD-TYPE 249  37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(7Q31.33) MUTATED     14    7
  DEL PEAK 16(7Q31.33) WILD-TYPE  249   37
   clus
vv  DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE
  0                           14                            249
  1                            7                             37
[1] 2 2
[1] FALSE
D44V5, binary
                                cls
clus                               0   1
  DEL PEAK 16(7Q31.33) MUTATED     0  24
  DEL PEAK 16(7Q31.33) WILD-TYPE  13 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(7Q31.33) MUTATED      0   24
  DEL PEAK 16(7Q31.33) WILD-TYPE   13  326
                                        clus
vv                                       DEL PEAK 16(7Q31.33) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              24
                                        clus
vv                                       DEL PEAK 16(7Q31.33) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               326
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 16(7Q31.33) MUTATED    17   6   0   0
  DEL PEAK 16(7Q31.33) WILD-TYPE 226  84   5  11
D44V6, multiclass
    clus
vv   DEL PEAK 16(7Q31.33) MUTATED DEL PEAK 16(7Q31.33) WILD-TYPE
  R0                           17                            226
  R1                            6                             84
  R2                            0                              5
  RX                            0                             11
[1] 4 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, continuous
D44V8, continuous
D44V9, continuous
D44V10, continuous
D44V11, continuous
D44V12, continuous
D44V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(7Q31.33) MUTATED       0                         0     7
  DEL PEAK 16(7Q31.33) WILD-TYPE     2                         7   139
D44V14, multiclass
                           clus
vv                          DEL PEAK 16(7Q31.33) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                7
                           clus
vv                          DEL PEAK 16(7Q31.33) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                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(45) Variable = DEL PEAK 17(8P23.2) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(8P23.2) MUTATED   148   3
  DEL PEAK 17(8P23.2) WILD-TYPE 207   3
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                          151                           210 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                            3                             3 
$`DEL PEAK 17(8P23.2) MUTATED`
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5739 TCGA-CH-5744 
       22.06        33.96         3.68        25.35        22.06         1.97 
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5764 TCGA-CH-5765 
       35.01         1.02         2.04         0.92         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5499 
        1.02        15.06        13.02        26.99        33.01        46.52 
TCGA-EJ-5501 TCGA-EJ-5507 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-5519 
       44.88        23.90        36.69        48.53        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5532 
       51.88        43.07        36.66        38.76        60.23        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7314 TCGA-EJ-7321 TCGA-EJ-7325 
       29.06        27.02        49.02         9.70         7.66        17.52 
TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-8469 TCGA-EJ-8474 TCGA-EJ-A46F 
       27.68        23.90        25.87        63.98        10.32         9.83 
TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-FC-7708 TCGA-FC-7961 
       21.96        12.92        13.71        18.41        28.41        15.42 
TCGA-FC-A4JI TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       13.45        87.35        81.04        69.37        55.76        18.21 
TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6366 TCGA-G9-6369 
       49.35        46.52        45.30        39.39         3.32        39.95 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6496 
       40.31        26.66        31.50        25.15        58.22        56.75 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-A9S0 TCGA-G9-A9S7 
       38.27        38.96        30.97        35.34        26.01        21.14 
TCGA-H9-7775 TCGA-HC-7078 TCGA-HC-7081 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7742 
        6.08         5.33         2.37         1.97         2.37         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7752 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8216 
        1.68         2.07         3.22        17.85         1.84        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        3.12        23.87        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AQ 
       22.36         0.76         2.01         2.20         5.49         3.48 
TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 TCGA-J4-A67M TCGA-J4-A67N 
       78.61        82.92        43.69        12.30        16.04        16.54 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A83I TCGA-J4-A83L TCGA-J4-A83N TCGA-J9-A52E 
       17.19         6.02         9.17        10.39        20.28        10.62 
TCGA-KK-A59Y TCGA-KK-A6E1 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-M7-A71Z TCGA-M7-A725 
       44.68        54.54        58.19        27.62         6.87        18.84 
TCGA-QU-A6IL TCGA-QU-A6IO TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88K TCGA-VN-A88M 
        3.19        47.21        11.90         8.19        25.51         6.02 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VP-A875 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       15.81        30.15        26.47        75.91        55.56        60.92 
TCGA-VP-A87J TCGA-VP-A87K TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DQ TCGA-XK-AAIR 
       48.85        21.53        38.04        48.03         2.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-YL-A8HK 
       31.50        28.54        30.58        29.23        27.09        49.02 
TCGA-YL-A8S9 TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO 
       60.56        41.46        45.14        45.86        37.97       106.75 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       71.34         7.00        14.04        60.99        62.37        24.33 
TCGA-ZG-A9ND 
        6.02 

$`DEL PEAK 17(8P23.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 
       20.42        43.79         2.99         6.97         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5762 
       13.97        24.03         1.02        13.02        31.00        44.02 
TCGA-CH-5763 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 
       12.00        24.03         2.04        15.98         9.99        32.02 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       29.79        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       38.93        48.13        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5522 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7125 TCGA-EJ-7218 
       47.80        68.35        39.75        41.85        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7330 
       21.80         9.50         9.37        16.77         5.75         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
        0.30        38.37        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G 
       64.47        26.99         5.33         4.24        17.49         3.06 
TCGA-EJ-A46H TCGA-EJ-A65B TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-A5OB 
        7.53        17.62         9.14         2.99         7.56         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6338 
       17.23        16.24         1.78        41.62        67.99        66.67 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6362 
       68.68        49.81        46.16        50.70        47.15        47.44 
TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6385 
       44.81        40.18        38.01        37.97        45.80        27.29 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7519 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-A6BX 
       52.87        50.73        27.91        28.18        32.68        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7210 
        3.68        19.76         2.93         2.01        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
        0.79        28.60         1.68         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        2.10         2.66         1.74        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8258 
        1.12        30.51         1.48        24.56        19.36         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-A631 TCGA-HC-A6AN TCGA-HC-A6AP 
        2.27         1.94        17.95         1.78         1.61         2.33 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-J4-8198 TCGA-J4-A67K 
        1.45         1.25         4.41        88.24        20.19        21.76 
TCGA-J4-A67L TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A6G1 TCGA-J4-A6G3 
       17.03        16.14        20.52        14.93        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83M TCGA-J9-A52B TCGA-J9-A52C 
        9.17        10.19         6.77        14.37        13.87         5.85 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 
       93.99        56.28        61.78       115.86        30.02       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7B1 
       67.59        90.51        49.25       113.33        67.07        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 
       22.75         2.73        26.43        20.65         5.19         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IM TCGA-QU-A6IN 
       13.15        27.02        25.08        15.88        41.00       114.64 
TCGA-QU-A6IP TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88Q TCGA-VN-A88R 
       86.14         8.84        12.95        15.52        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87E 
        4.34       106.95        84.69        94.65        23.93        66.97 
TCGA-VP-A87H TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.80        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A9DK TCGA-XJ-A9DX TCGA-XK-AAIW TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
        9.04        25.97        31.96        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA 
       52.96        38.56        36.95        71.77        62.14        16.83 
TCGA-YL-A8SB TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WI 
       45.50        28.77        47.38        26.24        62.79        41.39 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 

  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                         0.76                          0.30 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                       106.75                        151.36 
  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE 
                       25.350                        22.275 
[1] "0.8 - 106.8 (25.4)" "0.3 - 151.4 (22.3)"
[1] "hr=" "1.4"
D45V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 17(8P23.2) MUTATED    44 105   4
  DEL PEAK 17(8P23.2) WILD-TYPE 106 101   1
D45V3, multiclass
    clus
vv   DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  T2                          44                           106
  T3                         105                           101
  T4                           4                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.2) MUTATED   109  24
  DEL PEAK 17(8P23.2) WILD-TYPE 154  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.2) MUTATED    109   24
  DEL PEAK 17(8P23.2) WILD-TYPE  154   20
   clus
vv  DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  0                         109                           154
  1                          24                            20
[1] 2 2
[1] FALSE
D45V5, binary
                               cls
clus                              0   1
  DEL PEAK 17(8P23.2) MUTATED     6 147
  DEL PEAK 17(8P23.2) WILD-TYPE   7 203
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(8P23.2) MUTATED      6  147
  DEL PEAK 17(8P23.2) WILD-TYPE    7  203
                                        clus
vv                                       DEL PEAK 17(8P23.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            147
                                        clus
vv                                       DEL PEAK 17(8P23.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             7
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              203
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(8P23.2) MUTATED   105  36   3   5
  DEL PEAK 17(8P23.2) WILD-TYPE 138  54   2   6
D45V6, multiclass
    clus
vv   DEL PEAK 17(8P23.2) MUTATED DEL PEAK 17(8P23.2) WILD-TYPE
  R0                         105                           138
  R1                          36                            54
  R2                           3                             2
  RX                           5                             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"
D45V7, continuous
D45V8, continuous
D45V9, continuous
D45V10, continuous
D45V11, continuous
D45V12, continuous
D45V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(8P23.2) MUTATED       2                         3    61
  DEL PEAK 17(8P23.2) WILD-TYPE     0                         4    85
D45V14, multiclass
                           clus
vv                          DEL PEAK 17(8P23.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              61
                           clus
vv                          DEL PEAK 17(8P23.2) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                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"

Clustering(46) Variable = DEL PEAK 18(8P21.3) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(8P21.3) MUTATED   201   4
  DEL PEAK 18(8P21.3) WILD-TYPE 154   2
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                          205                           156 
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                            4                             2 
$`DEL PEAK 18(8P21.3) MUTATED`
TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5739 
       43.79        22.06        33.96         3.68        25.35        22.06 
TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       12.99         1.97        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04         0.92        44.02         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5790 TCGA-CH-5791 
       15.06        24.03        13.02        26.99        32.02        33.01 
TCGA-CH-5792 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5499 TCGA-EJ-5501 
        2.99        33.11        19.56        13.32        46.52        44.88 
TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5517 
       28.93        23.90        36.69        48.53        38.53        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       52.27        64.50        51.88        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7314 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7328 
       49.02         9.70        16.77         7.66        17.52        27.68 
TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7797 
        6.28        23.90        25.87        14.14        18.15        19.92 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       63.98        26.99        10.32        12.92        13.71        18.41 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6332 TCGA-G9-6333 
        7.56        28.41        15.42        13.45        87.35        81.04 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6354 TCGA-G9-6361 
       66.67        69.37        55.76        18.21        49.35        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6366 TCGA-G9-6369 TCGA-G9-6371 
       47.44        45.30        39.39         3.32        39.95        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6496 
       26.66        31.50        45.80        25.15        58.22        56.75 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-A9S0 TCGA-G9-A9S7 
       38.27        38.96        30.97        35.34        26.01        21.14 
TCGA-H9-7775 TCGA-HC-7078 TCGA-HC-7081 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        6.08         5.33         2.37         0.79        28.60         1.97 
TCGA-HC-7231 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        2.37         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8216 
        1.97         3.22        17.85        24.56         1.84        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        3.12        23.87        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         0.76         2.01         2.20         1.61         5.49 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        3.48         1.45        78.61        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A83I 
       12.30        16.04        16.54        17.19         6.02         9.17 
TCGA-J4-A83L TCGA-J4-A83N TCGA-J9-A52E TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 
       10.39        20.28        10.62        44.68       115.86        54.54 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A8IF TCGA-M7-A71Z 
       90.51        49.25        58.19        27.62        26.43         6.87 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-TP-A8TT TCGA-TP-A8TV 
       18.84         3.19       114.64        47.21        11.90         8.19 
TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
       25.51         6.02        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
        4.34        26.47        94.65        75.91        55.56        60.92 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-XJ-A83G TCGA-XJ-A9DQ TCGA-XK-AAIR 
       48.85        21.53        17.82        38.04         2.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-YL-A8HK 
       31.50        28.54        29.23        27.09        37.02        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC 
       38.56        36.95        62.14        60.56        16.83        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       24.33        49.91        28.34         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

$`DEL PEAK 18(8P21.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5746 
       20.42         2.99         6.97         1.02        13.97        24.03 
TCGA-CH-5748 TCGA-CH-5763 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5794 
        1.02        12.00         2.04        15.98         9.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5498 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 
       27.16        29.79        26.30        45.73        30.31        27.19 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5522 
       38.93        48.13        36.23        60.23        46.55        68.35 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 
       61.15        83.57        21.80         9.50         9.37         5.75 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7791 
        0.30        38.37        25.68        20.55        14.53        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-A46B TCGA-EJ-A46D 
       17.29         3.75        23.05        64.47         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        9.14         2.99         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       41.62        67.99        68.68        49.81        46.16        50.70 
TCGA-G9-6356 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6378 TCGA-G9-6385 
       47.15        44.81        40.18        38.01        37.97        27.29 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7519 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-A6BX 
       52.87        50.73        27.91        28.18        32.68        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7210 
        3.68        19.76         2.93         2.01        14.47        28.54 
TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        1.68         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-8213 TCGA-HC-8258 
        1.74         1.12        30.51         1.48        19.36         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-A631 TCGA-HC-A6AP TCGA-HC-A6HX 
        2.27         1.94        17.95         1.78         2.33         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67O TCGA-J4-A67Q 
        4.41        88.24        21.76        17.03        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K 
       14.93        13.32        17.36         9.17        10.19         6.77 
TCGA-J4-A83M TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z 
       14.37        13.87         5.85        93.99        56.28        61.78 
TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7B1 
       30.02       151.36        67.59       113.33        67.07        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 
       22.75         2.73        20.65         5.19         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IM TCGA-QU-A6IP TCGA-VN-A88I 
       27.02        25.08        15.88        41.00        86.14         8.84 
TCGA-VN-A88L TCGA-VN-A88N TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87E 
       12.95        15.52       106.95        84.69        23.93        66.97 
TCGA-VP-A87H TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI 
       21.80         5.79        37.18        27.81         3.91        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DX TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJU TCGA-Y6-A8TL 
        9.04        25.97        31.96        30.58        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SI TCGA-YL-A8SQ TCGA-ZG-A8QW 
       52.96        71.77        45.50        47.38        62.79         1.64 

  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                         0.76                          0.30 
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                       115.86                        151.36 
  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE 
                       26.010                        20.535 
[1] "0.8 - 115.9 (26.0)" "0.3 - 151.4 (20.5)"
[1] "hr=" "1.4"
D46V2, continuous
                               vv
clus                             T2  T3  T4
  DEL PEAK 18(8P21.3) MUTATED    67 136   4
  DEL PEAK 18(8P21.3) WILD-TYPE  83  70   1
D46V3, multiclass
    clus
vv   DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE
  T2                          67                            83
  T3                         136                            70
  T4                           4                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P21.3) MUTATED   149  34
  DEL PEAK 18(8P21.3) WILD-TYPE 114  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P21.3) MUTATED    149   34
  DEL PEAK 18(8P21.3) WILD-TYPE  114   10
   clus
vv  DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE
  0                         149                           114
  1                          34                            10
[1] 2 2
[1] FALSE
D46V5, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P21.3) MUTATED     6 201
  DEL PEAK 18(8P21.3) WILD-TYPE   7 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P21.3) MUTATED      6  201
  DEL PEAK 18(8P21.3) WILD-TYPE    7  149
                                        clus
vv                                       DEL PEAK 18(8P21.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            201
                                        clus
vv                                       DEL PEAK 18(8P21.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             7
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              149
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(8P21.3) MUTATED   134  55   3   6
  DEL PEAK 18(8P21.3) WILD-TYPE 109  35   2   5
D46V6, multiclass
    clus
vv   DEL PEAK 18(8P21.3) MUTATED DEL PEAK 18(8P21.3) WILD-TYPE
  R0                         134                           109
  R1                          55                            35
  R2                           3                             2
  RX                           6                             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"
D46V7, continuous
D46V8, continuous
D46V9, continuous
D46V10, continuous
D46V11, continuous
D46V12, continuous
D46V13, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(8P21.3) MUTATED       2                         4    87
  DEL PEAK 18(8P21.3) WILD-TYPE     0                         3    59
D46V14, multiclass
                           clus
vv                          DEL PEAK 18(8P21.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              87
                           clus
vv                          DEL PEAK 18(8P21.3) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                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"

Clustering(47) Variable = DEL PEAK 19(9P23) MUTATION ANALYSIS
D47V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 19(9P23) MUTATED    32   0
  DEL PEAK 19(9P23) WILD-TYPE 323   6
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         32                         329 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                          0                           6 
$`DEL PEAK 19(9P23) MUTATED`
TCGA-2A-A8VX TCGA-CH-5746 TCGA-CH-5751 TCGA-CH-5766 TCGA-EJ-5507 TCGA-EJ-5509 
       33.96        24.03        35.01         1.02        23.90        48.13 
TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-7788 
       47.80        64.50        51.88        23.90        25.68        14.14 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6377 TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-8216 
       15.42        13.45        31.50        30.97         1.97        22.42 
TCGA-HC-A631 TCGA-HI-7168 TCGA-J4-A67L TCGA-J4-A83J TCGA-J9-A52E TCGA-KK-A6DY 
        1.78        78.61        17.03        10.19        10.62       115.86 
TCGA-M7-A725 TCGA-VP-A87D TCGA-XK-AAIV TCGA-XK-AAJA TCGA-YL-A8S8 TCGA-YL-A8SB 
       18.84        60.92        31.50        30.58        62.14        45.50 
TCGA-YL-A9WH TCGA-YL-A9WY 
       14.04        28.34 

$`DEL PEAK 19(9P23) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5737 
       20.42        43.79        22.06         3.68        25.35         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 
       44.02        12.00         1.02        23.01        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 
       28.93        30.31        27.19        38.93        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5522 
       38.53        36.23        60.23        46.55        52.27        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       17.52         5.75        27.68         6.28         0.30        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       25.87        20.55        14.53        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V 
        9.14         2.99         7.56        28.41         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       38.01        40.31        26.66        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        52.87        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       38.96        27.91        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       21.14         6.08        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       28.60         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 
        1.48        17.85        24.56         1.84        19.36         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 
        1.58        15.88         1.15        22.36         0.76         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        1.25         4.41        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       12.30        21.76        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
        9.17         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6E0 
        5.85        93.99        56.28        44.68        61.78        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
       67.07        58.19        27.62        34.95        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       27.02        25.08        15.88         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       15.09         4.34       106.95        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       23.93        75.91        55.56        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       31.96        28.54        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        41.39        60.99        62.37        24.33        49.91 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                       1.02                        0.30 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                     115.86                      151.36 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                      27.01                       23.05 
[1] "1.0 - 115.9 (27.0)" "0.3 - 151.4 (23.1)"
[1] "hr="     "7.8e+07"
D47V2, continuous
                             vv
clus                           T2  T3  T4
  DEL PEAK 19(9P23) MUTATED     9  22   1
  DEL PEAK 19(9P23) WILD-TYPE 141 184   4
D47V3, multiclass
    clus
vv   DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  T2                         9                         141
  T3                        22                         184
  T4                         1                           4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                             cls
clus                            0   1
  DEL PEAK 19(9P23) MUTATED    22   9
  DEL PEAK 19(9P23) WILD-TYPE 241  35
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(9P23) MUTATED     22    9
  DEL PEAK 19(9P23) WILD-TYPE  241   35
   clus
vv  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  0                        22                         241
  1                         9                          35
[1] 2 2
[1] FALSE
D47V5, binary
                             cls
clus                            0   1
  DEL PEAK 19(9P23) MUTATED     0  32
  DEL PEAK 19(9P23) WILD-TYPE  13 318
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(9P23) MUTATED      0   32
  DEL PEAK 19(9P23) WILD-TYPE   13  318
                                        clus
vv                                       DEL PEAK 19(9P23) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                         0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                           32
                                        clus
vv                                       DEL PEAK 19(9P23) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            318
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(9P23) MUTATED    19  12   0   0
  DEL PEAK 19(9P23) WILD-TYPE 224  78   5  11
D47V6, multiclass
    clus
vv   DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  R0                        19                         224
  R1                        12                          78
  R2                         0                           5
  RX                         0                          11
[1] 4 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, continuous
D47V8, continuous
D47V9, continuous
D47V10, continuous
D47V11, continuous
D47V12, continuous
D47V13, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(9P23) MUTATED       0                         0    15
  DEL PEAK 19(9P23) WILD-TYPE     2                         7   131
D47V14, multiclass
                           clus
vv                          DEL PEAK 19(9P23) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            15
                           clus
vv                          DEL PEAK 19(9P23) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 20(10Q23.31) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 20(10Q23.31) MUTATED   107   1
  DEL PEAK 20(10Q23.31) WILD-TYPE 248   5
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            108                             253 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                              1                               5 
$`DEL PEAK 20(10Q23.31) MUTATED`
TCGA-CH-5737 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5751 TCGA-CH-5754 
        2.99         1.02        12.99         1.97        35.01         2.04 
TCGA-CH-5766 TCGA-CH-5769 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5495 
        1.02         2.04        32.02        33.01        29.00        33.11 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5510 TCGA-EJ-5514 
       46.52        44.88        28.93        23.90        36.69        36.23 
TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       46.55        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5527 TCGA-EJ-5542 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7327 
       39.75        29.06        21.80         9.70         9.50         5.75 
TCGA-EJ-7784 TCGA-EJ-7788 TCGA-EJ-8469 TCGA-EJ-A46F TCGA-EJ-A65J TCGA-FC-7708 
       25.68        14.14        63.98         9.83         2.99        28.41 
TCGA-FC-7961 TCGA-G9-6332 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6356 
       15.42        87.35        69.37        55.76        49.81        47.15 
TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6499 
       46.52        45.30        39.39        26.66        31.50        50.73 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-HC-7081 TCGA-HC-7209 
       30.97        35.34        32.68        21.14         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       28.54        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7737 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-8265 
        2.10         1.48         1.68        26.04         1.97        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HI-7168 
        1.15        22.36         1.78         2.20         1.61        78.61 
TCGA-HI-7171 TCGA-J4-A67N TCGA-J4-A67S TCGA-J4-A83I TCGA-J4-A83J TCGA-J9-A52B 
       43.69        16.54        17.19         9.17        10.19        13.87 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E6 
       44.68        61.78       115.86        30.02        54.54       113.33 
TCGA-KK-A6E7 TCGA-M7-A721 TCGA-TP-A8TT TCGA-VN-A88L TCGA-VN-A88Q TCGA-VP-A872 
       67.07        13.15        11.90        12.95        32.91       106.95 
TCGA-VP-A875 TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-XJ-A9DI TCGA-XK-AAIV 
       26.47        48.85        21.53        17.82        48.03        31.50 
TCGA-XK-AAJT TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SF TCGA-YL-A8SJ 
       37.02        49.02        38.56        16.83        45.14        45.86 
TCGA-YL-A8SL TCGA-YL-A9WH TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QZ 
       26.24        14.04        62.37        24.33        28.34         7.86 

$`DEL PEAK 20(10Q23.31) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
        6.97        22.06        13.97        24.03         1.02        13.02 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
       31.00         1.02         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       23.01        15.06        24.03        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
        9.99         2.99        27.16        19.56        13.32        29.79 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 
       26.30        45.73        30.31        27.19        38.93        48.13 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5525 TCGA-EJ-5526 
       48.53        38.53        60.23        47.80        36.66        38.76 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       60.23        41.85        47.87        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7328 
       83.57         9.37        16.77         7.66        17.52        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
        6.28         0.30        23.90        38.37        25.87        20.55 
TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.53        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       19.92        64.47        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.49         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-FC-A4JI TCGA-FC-A5OB 
       13.71        18.41         9.14         7.56        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 
       17.23        16.24         1.78        41.62        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       66.67        18.21        68.68        46.16        50.70        49.35 
TCGA-G9-6362 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       47.44        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       40.31        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7523 
       56.75        52.87        38.27        38.96        27.91        28.18 
TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       26.01         6.08        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7211 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7738 
        2.93         2.01         0.79         1.71         0.72         2.66 
TCGA-HC-7740 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
        1.74         2.07        24.59         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AO TCGA-HC-A6AP 
       22.32         1.58         0.76         2.01         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 
        3.48         1.45         1.25         4.41        88.24        82.92 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O 
       20.19        12.30        21.76        17.03        16.04        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       20.52        14.93         6.02        13.32        17.36         9.17 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E 
        6.77        10.39        14.37        20.28         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       93.99        56.28       151.36        67.59        90.51        49.25 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       58.19        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 
       20.65         5.19         6.87         9.93        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N 
       86.14         8.19         8.84        25.51         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 
       15.81        30.15        15.09         4.34        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        75.91        55.56        60.92        66.97        21.80 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DK 
        5.79        37.18        27.81         3.91        38.04         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        25.97        31.96        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HM 
       29.23        27.09        39.65        25.48        52.96        36.95 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SH 
       71.77        62.14        60.56        45.50        41.46        28.77 
TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       47.38        37.97       106.75        71.34        62.79         7.00 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       41.39        60.99        49.91         1.64         4.93         1.12 
TCGA-ZG-A9ND 
        6.02 

  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                           1.02                            0.30 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                         115.86                          151.36 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                         28.475                          22.060 
[1] "1.0 - 115.9 (28.5)" "0.3 - 151.4 (22.1)"
[1] "hr=" "2.7"
D48V2, continuous
                                 vv
clus                               T2  T3  T4
  DEL PEAK 20(10Q23.31) MUTATED    29  77   3
  DEL PEAK 20(10Q23.31) WILD-TYPE 121 129   2
D48V3, multiclass
    clus
vv   DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  T2                            29                             121
  T3                            77                             129
  T4                             3                               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED    80  22
  DEL PEAK 20(10Q23.31) WILD-TYPE 183  22
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED     80   22
  DEL PEAK 20(10Q23.31) WILD-TYPE  183   22
   clus
vv  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  0                            80                             183
  1                            22                              22
[1] 2 2
[1] FALSE
D48V5, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED     4 105
  DEL PEAK 20(10Q23.31) WILD-TYPE   9 245
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED      4  105
  DEL PEAK 20(10Q23.31) WILD-TYPE    9  245
                                        clus
vv                                       DEL PEAK 20(10Q23.31) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              105
                                        clus
vv                                       DEL PEAK 20(10Q23.31) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                               9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                245
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 20(10Q23.31) MUTATED    67  34   2   4
  DEL PEAK 20(10Q23.31) WILD-TYPE 176  56   3   7
D48V6, multiclass
    clus
vv   DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  R0                            67                             176
  R1                            34                              56
  R2                             2                               3
  RX                             4                               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"
D48V7, continuous
D48V8, continuous
D48V9, continuous
D48V10, continuous
D48V11, continuous
D48V12, continuous
D48V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10Q23.31) MUTATED       2                         2    55
  DEL PEAK 20(10Q23.31) WILD-TYPE     0                         5    91
D48V14, multiclass
                           clus
vv                          DEL PEAK 20(10Q23.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                55
                           clus
vv                          DEL PEAK 20(10Q23.31) WILD-TYPE
  ASIAN                                                   0
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                  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(49) Variable = DEL PEAK 21(11P11.2) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(11P11.2) MUTATED    22   1
  DEL PEAK 21(11P11.2) WILD-TYPE 333   5
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                            23                            338 
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                             1                              5 
$`DEL PEAK 21(11P11.2) MUTATED`
TCGA-2A-A8W1 TCGA-CH-5788 TCGA-EJ-5531 TCGA-EJ-7789 TCGA-FC-7708 TCGA-G9-6379 
        3.68        26.99        41.85        18.15        28.41        45.80 
TCGA-HC-7737 TCGA-HI-7171 TCGA-J4-A83J TCGA-J9-A52C TCGA-KK-A59X TCGA-KK-A8IB 
        2.10        43.69        10.19         5.85        56.28         2.73 
TCGA-QU-A6IM TCGA-VN-A88O TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XK-AAJP 
       41.00        15.81        17.82        37.18        38.04        29.23 
TCGA-YL-A8S8 TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WI TCGA-YL-A9WK 
       62.14        26.24        62.79        41.39        62.37 

$`DEL PEAK 21(11P11.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W3 TCGA-CH-5737 
       20.42        43.79        22.06        33.96        25.35         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
        9.83         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 
       13.71        18.41         9.14         2.99         7.56        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       31.50        37.97        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7738 
        1.68         2.37         2.93         1.71         0.72         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
        1.25         4.41        78.61        88.24        82.92        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17         9.17         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       13.87        10.62        93.99        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN 
       27.02        25.08        15.88        18.84         3.19       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
       12.95         6.02        15.52        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
        4.34       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK 
       21.53         5.79        27.81         3.91        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       30.58        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        38.56        36.95        71.77        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       45.50        41.46        45.14        28.77        47.38        45.86 
TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ 
       37.97       106.75        71.34         7.00        14.04        60.99 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                           2.1                            0.3 
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                         62.79                         151.36 
  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE 
                         29.23                          23.46 
[1] "2.1 - 62.8 (29.2)"  "0.3 - 151.4 (23.5)"
[1] "hr=" "2.3"
D49V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 21(11P11.2) MUTATED     4  20   0
  DEL PEAK 21(11P11.2) WILD-TYPE 146 186   5
D49V3, multiclass
    clus
vv   DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE
  T2                            4                            146
  T3                           20                            186
  T4                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P11.2) MUTATED    18   5
  DEL PEAK 21(11P11.2) WILD-TYPE 245  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P11.2) MUTATED     18    5
  DEL PEAK 21(11P11.2) WILD-TYPE  245   39
   clus
vv  DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE
  0                           18                            245
  1                            5                             39
[1] 2 2
[1] FALSE
D49V5, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P11.2) MUTATED     0  24
  DEL PEAK 21(11P11.2) WILD-TYPE  13 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P11.2) MUTATED      0   24
  DEL PEAK 21(11P11.2) WILD-TYPE   13  326
                                        clus
vv                                       DEL PEAK 21(11P11.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              24
                                        clus
vv                                       DEL PEAK 21(11P11.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               326
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 21(11P11.2) MUTATED    12   9   0   2
  DEL PEAK 21(11P11.2) WILD-TYPE 231  81   5   9
D49V6, multiclass
    clus
vv   DEL PEAK 21(11P11.2) MUTATED DEL PEAK 21(11P11.2) WILD-TYPE
  R0                           12                            231
  R1                            9                             81
  R2                            0                              5
  RX                            2                              9
[1] 4 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, continuous
D49V8, continuous
D49V9, continuous
D49V10, continuous
D49V11, continuous
D49V12, continuous
D49V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11P11.2) MUTATED       1                         2     3
  DEL PEAK 21(11P11.2) WILD-TYPE     1                         5   143
D49V14, multiclass
                           clus
vv                          DEL PEAK 21(11P11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                                3
                           clus
vv                          DEL PEAK 21(11P11.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                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(50) Variable = DEL PEAK 22(11Q22.3) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(11Q22.3) MUTATED    29   0
  DEL PEAK 22(11Q22.3) WILD-TYPE 326   6
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                            29                            332 
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                             0                              6 
$`DEL PEAK 22(11Q22.3) MUTATED`
TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5769 TCGA-CH-5792 TCGA-EJ-5509 TCGA-EJ-5518 
        1.02         0.92         2.04         2.99        48.13        52.27 
TCGA-EJ-5527 TCGA-EJ-7312 TCGA-EJ-7330 TCGA-EJ-7783 TCGA-EJ-7789 TCGA-EJ-A65B 
       39.75        21.80         6.28        25.87        18.15        17.62 
TCGA-FC-A4JI TCGA-G9-6494 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7232 TCGA-HC-7736 
       13.45        58.22        28.54        28.60         2.93         0.72 
TCGA-HC-7745 TCGA-J9-A52C TCGA-KK-A59X TCGA-VP-AA1N TCGA-XJ-A9DX TCGA-XK-AAJR 
        2.07         5.85        56.28        17.82        25.97        27.09 
TCGA-XK-AAJT TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       37.02        37.97       106.75        71.34        62.79 

$`DEL PEAK 22(11Q22.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       32.02        33.01        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 
       28.93        30.31        27.19        23.90        38.93        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       61.15        83.57         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 
        7.66        17.52         5.75        27.68         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 
       38.37        25.68        20.55        14.53        14.14        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        3.06         7.53        21.96        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB 
        9.14         2.99         7.56        28.41        15.42         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       45.80        25.15        27.29        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7737 
        0.79         1.97         1.68         2.37         1.71         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 
        2.66         1.74         1.48         1.68        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         4.41        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59Y 
       14.37        20.28        13.87        10.62        93.99        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       30.58        29.23        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       38.56        36.95        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       45.50        41.46        45.14        28.77        47.38        45.86 
TCGA-YL-A8SL TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       26.24         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                          0.72                           0.30 
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                        106.75                         151.36 
  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE 
                        25.870                         23.915 
[1] "0.7 - 106.8 (25.9)" "0.3 - 151.4 (23.9)"
[1] "hr="     "7.5e+07"
D50V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 22(11Q22.3) MUTATED     4  23   2
  DEL PEAK 22(11Q22.3) WILD-TYPE 146 183   3
D50V3, multiclass
    clus
vv   DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE
  T2                            4                            146
  T3                           23                            183
  T4                            2                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q22.3) MUTATED    20   4
  DEL PEAK 22(11Q22.3) WILD-TYPE 243  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q22.3) MUTATED     20    4
  DEL PEAK 22(11Q22.3) WILD-TYPE  243   40
   clus
vv  DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE
  0                           20                            243
  1                            4                             40
[1] 2 2
[1] FALSE
D50V5, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q22.3) MUTATED     2  27
  DEL PEAK 22(11Q22.3) WILD-TYPE  11 323
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q22.3) MUTATED      2   27
  DEL PEAK 22(11Q22.3) WILD-TYPE   11  323
                                        clus
vv                                       DEL PEAK 22(11Q22.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              27
                                        clus
vv                                       DEL PEAK 22(11Q22.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               323
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 22(11Q22.3) MUTATED    14  13   0   0
  DEL PEAK 22(11Q22.3) WILD-TYPE 229  77   5  11
D50V6, multiclass
    clus
vv   DEL PEAK 22(11Q22.3) MUTATED DEL PEAK 22(11Q22.3) WILD-TYPE
  R0                           14                            229
  R1                           13                             77
  R2                            0                              5
  RX                            0                             11
[1] 4 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, continuous
D50V8, continuous
D50V9, continuous
D50V10, continuous
D50V11, continuous
D50V12, continuous
D50V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11Q22.3) MUTATED       0                         1    15
  DEL PEAK 22(11Q22.3) WILD-TYPE     2                         6   131
D50V14, multiclass
                           clus
vv                          DEL PEAK 22(11Q22.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               15
                           clus
vv                          DEL PEAK 22(11Q22.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DEL PEAK 23(11Q23.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(11Q23.2) MUTATED    34   0
  DEL PEAK 23(11Q23.2) WILD-TYPE 321   6
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                            34                            327 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                             0                              6 
$`DEL PEAK 23(11Q23.2) MUTATED`
TCGA-CH-5761 TCGA-CH-5769 TCGA-CH-5790 TCGA-CH-5792 TCGA-EJ-5504 TCGA-EJ-5518 
        0.92         2.04        32.02         2.99        28.93        52.27 
TCGA-EJ-5527 TCGA-EJ-7312 TCGA-EJ-7330 TCGA-EJ-A65B TCGA-EJ-A65J TCGA-FC-A4JI 
       39.75        21.80         6.28        17.62         2.99        13.45 
TCGA-G9-6363 TCGA-G9-6377 TCGA-G9-6494 TCGA-G9-7522 TCGA-HC-7210 TCGA-HC-7212 
       45.30        31.50        58.22        35.34        28.54        28.60 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7745 TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59X 
        2.93         0.72         2.07         5.85        10.62        56.28 
TCGA-KK-A59Y TCGA-KK-A6E8 TCGA-KK-A8IB TCGA-VP-AA1N TCGA-XJ-A9DX TCGA-XK-AAJR 
       44.68        58.19         2.73        17.82        25.97        27.09 
TCGA-XK-AAJT TCGA-YL-A8SK TCGA-YL-A8SP TCGA-YL-A8SQ 
       37.02        37.97        71.34        62.79 

$`DEL PEAK 23(11Q23.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         2.04        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
        1.02        15.06        24.03        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
        9.99        33.01        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       61.15        83.57         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 
        7.66        17.52         5.75        27.68         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D 
       17.49         9.83         3.06         7.53        21.96        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
       13.71        18.41         9.14         7.56        28.41        15.42 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        47.44        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 
       39.95        38.01        40.31        26.66        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       25.15        27.29        56.75        52.87        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       38.96        27.91        30.97        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       21.14         6.08        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7213 
        2.93         2.01         2.37        14.47         0.79         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        1.68         2.37         1.71         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.48         1.68        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-KK-A59V TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       13.87        93.99        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       27.62        34.95        22.75        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       30.58        29.23        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       38.56        36.95        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       45.50        41.46        45.14        28.77        47.38        45.86 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       26.24       106.75         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                          0.72                           0.30 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                         71.34                         151.36 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                        27.815                         23.900 
[1] "0.7 - 71.3 (27.8)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "7.7e+07"
D51V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 23(11Q23.2) MUTATED     7  25   3
  DEL PEAK 23(11Q23.2) WILD-TYPE 143 181   2
D51V3, multiclass
    clus
vv   DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  T2                            7                            143
  T3                           25                            181
  T4                            3                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.2) MUTATED    25   5
  DEL PEAK 23(11Q23.2) WILD-TYPE 238  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED     25    5
  DEL PEAK 23(11Q23.2) WILD-TYPE  238   39
   clus
vv  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  0                           25                            238
  1                            5                             39
[1] 2 2
[1] FALSE
D51V5, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.2) MUTATED     2  33
  DEL PEAK 23(11Q23.2) WILD-TYPE  11 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED      2   33
  DEL PEAK 23(11Q23.2) WILD-TYPE   11  317
                                        clus
vv                                       DEL PEAK 23(11Q23.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              33
                                        clus
vv                                       DEL PEAK 23(11Q23.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               317
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(11Q23.2) MUTATED    17  14   0   2
  DEL PEAK 23(11Q23.2) WILD-TYPE 226  76   5   9
D51V6, multiclass
    clus
vv   DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  R0                           17                            226
  R1                           14                             76
  R2                            0                              5
  RX                            2                              9
[1] 4 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, continuous
D51V8, continuous
D51V9, continuous
D51V10, continuous
D51V11, continuous
D51V12, continuous
D51V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11Q23.2) MUTATED       0                         1    16
  DEL PEAK 23(11Q23.2) WILD-TYPE     2                         6   130
D51V14, multiclass
                           clus
vv                          DEL PEAK 23(11Q23.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               16
                           clus
vv                          DEL PEAK 23(11Q23.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 24(12P13.1) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(12P13.1) MUTATED    79   2
  DEL PEAK 24(12P13.1) WILD-TYPE 276   4
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            81                            280 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                             2                              4 
$`DEL PEAK 24(12P13.1) MUTATED`
TCGA-2A-A8W3 TCGA-CH-5744 TCGA-CH-5748 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5761 
       25.35         1.97         1.02        35.01        31.00         0.92 
TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5792 TCGA-EJ-5501 TCGA-EJ-5507 TCGA-EJ-5510 
        1.02        24.03         2.99        44.88        23.90        36.69 
TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-7314 
       36.23        52.27        64.50        68.35        38.76         9.70 
TCGA-EJ-7315 TCGA-EJ-7781 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-8468 TCGA-EJ-8470 
        9.50        23.90        14.14        18.15        64.47        26.99 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-G9-6333 TCGA-G9-6354 TCGA-G9-6362 
       12.92        13.71        18.41        81.04        49.35        47.44 
TCGA-G9-6364 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-7525 
       39.39        45.80        25.15        50.73        30.97        32.68 
TCGA-G9-A9S0 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7230 TCGA-HC-7736 TCGA-HC-7817 
       26.01         2.37        14.47         1.68         0.72        30.51 
TCGA-HC-8216 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL 
       22.42        22.32         1.58        22.36         2.01         2.20 
TCGA-HI-7168 TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A83J TCGA-J9-A52B TCGA-KK-A59X 
       78.61        16.04        16.54        10.19        13.87        56.28 
TCGA-KK-A6E1 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-M7-A725 
       54.54        49.25       113.33        27.62        34.95        18.84 
TCGA-QU-A6IO TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A87D TCGA-VP-A87J TCGA-VP-A87K 
       47.21        15.09       106.95        60.92        48.85        21.53 
TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       17.82        37.18        31.50        28.54        30.58        29.23 
TCGA-XK-AAJT TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SJ 
       37.02        38.56        36.95        16.83        41.46        45.86 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WY 
       60.99        62.37        28.34 

$`DEL PEAK 24(12P13.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 
       20.42        43.79        22.06        33.96         3.68         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 
        6.97        22.06         1.02        12.99        13.97        24.03 
TCGA-CH-5750 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
       13.02         1.02         2.04        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       23.01        15.06         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
        9.99        32.02        33.01        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5502 TCGA-EJ-5503 
       19.56        13.32        29.79        46.52        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 
       28.93        30.31        27.19        38.93        48.13        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5521 TCGA-EJ-5524 
       38.53        60.23        46.55        47.80        51.88        43.07 
TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7317 
       27.02        49.02        61.15        83.57        21.80         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 
       19.59        17.29         3.75        23.05        19.92        63.98 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
        7.53        21.96        17.62         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
        1.78        41.62        87.35        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.15        46.52        45.30        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        56.75        52.87        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       27.91        35.34        28.18        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7210 
        3.68        19.76         5.33         2.93         2.01        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
        0.79        28.60         1.97         2.37         2.93         1.71 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7818 
       24.59        26.04         1.97         1.12         3.22         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56         1.84        19.36         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-8266 
        2.17         2.27         1.94        17.95        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        0.76         1.78         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67O TCGA-J4-A67Q 
       20.19        12.30        21.76        17.03        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C 
        9.17         6.77        10.39        14.37        20.28         5.85 
TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       10.62        93.99        44.68        61.78       115.86        30.02 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7B2 
      151.36        67.59        90.51        67.07        58.19        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM 
       13.15        27.02        25.08        15.88         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
      114.64        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR 
       55.56        66.97        21.80         5.79        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIW TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       31.96        27.09        39.65        25.48        52.96        49.02 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH 
       71.77        62.14        60.56        45.50        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       47.38        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW 
        7.00        14.04        41.39        24.33        49.91         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                          0.72                           0.30 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                        113.33                         151.36 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                         28.54                          21.88 
[1] "0.7 - 113.3 (28.5)" "0.3 - 151.4 (21.9)"
[1] "hr=" "1.4"
D52V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 24(12P13.1) MUTATED    18  62   2
  DEL PEAK 24(12P13.1) WILD-TYPE 132 144   3
D52V3, multiclass
    clus
vv   DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  T2                           18                            132
  T3                           62                            144
  T4                            2                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED    62  17
  DEL PEAK 24(12P13.1) WILD-TYPE 201  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED     62   17
  DEL PEAK 24(12P13.1) WILD-TYPE  201   27
   clus
vv  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  0                           62                            201
  1                           17                             27
[1] 2 2
[1] FALSE
D52V5, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED     5  77
  DEL PEAK 24(12P13.1) WILD-TYPE   8 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED      5   77
  DEL PEAK 24(12P13.1) WILD-TYPE    8  273
                                        clus
vv                                       DEL PEAK 24(12P13.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              77
                                        clus
vv                                       DEL PEAK 24(12P13.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              8
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               273
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(12P13.1) MUTATED    51  24   2   2
  DEL PEAK 24(12P13.1) WILD-TYPE 192  66   3   9
D52V6, multiclass
    clus
vv   DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  R0                           51                            192
  R1                           24                             66
  R2                            2                              3
  RX                            2                              9
[1] 4 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, continuous
D52V8, continuous
D52V9, continuous
D52V10, continuous
D52V11, continuous
D52V12, continuous
D52V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(12P13.1) MUTATED       0                         1    30
  DEL PEAK 24(12P13.1) WILD-TYPE     2                         6   116
D52V14, multiclass
                           clus
vv                          DEL PEAK 24(12P13.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               30
                           clus
vv                          DEL PEAK 24(12P13.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 25(12Q24.32) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(12Q24.32) MUTATED    30   1
  DEL PEAK 25(12Q24.32) WILD-TYPE 325   5
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                             31                             330 
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                              1                               5 
$`DEL PEAK 25(12Q24.32) MUTATED`
TCGA-2A-A8W3 TCGA-EJ-5495 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5521 TCGA-EJ-5526 
       25.35        33.11        38.93        36.69        51.88        38.76 
TCGA-EJ-7781 TCGA-EJ-7784 TCGA-G9-6347 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-7521 
       23.90        25.68        68.68        58.22        56.75        30.97 
TCGA-HC-7213 TCGA-HC-7736 TCGA-HC-7742 TCGA-HC-8216 TCGA-HC-8265 TCGA-HC-A4ZV 
        1.97         0.72         1.48        22.42        15.88         0.76 
TCGA-HI-7168 TCGA-J9-A52B TCGA-KK-A6E1 TCGA-KK-A8IF TCGA-VN-A88K TCGA-VP-A872 
       78.61        13.87        54.54        26.43        25.51       106.95 
TCGA-VP-A875 TCGA-VP-AA1N TCGA-XJ-A83G TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A9WJ 
       26.47        17.82        38.04        49.02        38.56        60.99 
TCGA-ZG-A8QY 
        1.12 

$`DEL PEAK 25(12Q24.32) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 
       20.42        43.79        22.06        33.96         3.68         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       27.16        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       47.80        52.27        64.50        68.35        43.07        36.66 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 
        6.28         0.30        38.37        25.87        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 
       66.67        69.37        55.76        18.21        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       27.29        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.37        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.37         2.93         1.71         2.10         2.66         1.74 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       19.36         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 
       17.95        22.32         1.58         1.15        22.36         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       14.37        20.28         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       44.68        61.78       115.86        30.02       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       34.95        22.75         2.73        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.19         8.84        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 
       30.15        32.91        15.09         4.34        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        75.91        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       48.85        21.53         5.79        37.18        27.81         3.91 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       39.65        25.48        52.96        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK TCGA-YL-A9WL 
       62.79         7.00        14.04        41.39        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       49.91        28.34         1.64         4.93         7.86         6.02 

  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                           0.72                            0.30 
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                         106.95                          151.36 
  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE 
                         30.970                          22.555 
[1] "0.7 - 107.0 (31.0)" "0.3 - 151.4 (22.6)"
[1] "hr=" "1.6"
D53V2, continuous
                                 vv
clus                               T2  T3  T4
  DEL PEAK 25(12Q24.32) MUTATED     6  24   1
  DEL PEAK 25(12Q24.32) WILD-TYPE 144 182   4
D53V3, multiclass
    clus
vv   DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE
  T2                             6                             144
  T3                            24                             182
  T4                             1                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.32) MUTATED    22   8
  DEL PEAK 25(12Q24.32) WILD-TYPE 241  36
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.32) MUTATED     22    8
  DEL PEAK 25(12Q24.32) WILD-TYPE  241   36
   clus
vv  DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE
  0                            22                             241
  1                             8                              36
[1] 2 2
[1] FALSE
D53V5, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.32) MUTATED     1  30
  DEL PEAK 25(12Q24.32) WILD-TYPE  12 320
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.32) MUTATED      1   30
  DEL PEAK 25(12Q24.32) WILD-TYPE   12  320
                                        clus
vv                                       DEL PEAK 25(12Q24.32) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               30
                                        clus
vv                                       DEL PEAK 25(12Q24.32) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                320
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 25(12Q24.32) MUTATED    19   8   0   2
  DEL PEAK 25(12Q24.32) WILD-TYPE 224  82   5   9
D53V6, multiclass
    clus
vv   DEL PEAK 25(12Q24.32) MUTATED DEL PEAK 25(12Q24.32) WILD-TYPE
  R0                            19                             224
  R1                             8                              82
  R2                             0                               5
  RX                             2                               9
[1] 4 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, continuous
D53V8, continuous
D53V9, continuous
D53V10, continuous
D53V11, continuous
D53V12, continuous
D53V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(12Q24.32) MUTATED       0                         0    13
  DEL PEAK 25(12Q24.32) WILD-TYPE     2                         7   133
D53V14, multiclass
                           clus
vv                          DEL PEAK 25(12Q24.32) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                13
                           clus
vv                          DEL PEAK 25(12Q24.32) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               7
  WHITE                                                 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(54) Variable = DEL PEAK 26(13Q14.13) MUTATION ANALYSIS
D54V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 26(13Q14.13) MUTATED   164   2
  DEL PEAK 26(13Q14.13) WILD-TYPE 191   4
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                            166                             195 
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                              2                               4 
$`DEL PEAK 26(13Q14.13) MUTATED`
TCGA-CH-5737 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5748 TCGA-CH-5752 
        2.99        22.06         1.02        12.99         1.02        31.00 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5768 TCGA-CH-5771 
        2.04        44.02         1.02        23.01        24.03        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 
       15.98        26.99         2.99        29.00        33.11        19.56 
TCGA-EJ-5499 TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       46.52        28.93        23.90        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5525 
       38.53        36.23        46.55        52.27        51.88        36.66 
TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7315 
       39.75        41.85        27.02        49.02        83.57         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7782 
        9.37        16.77         7.66         6.28        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-EJ-7794 TCGA-EJ-8469 
       25.87        25.68        14.53        18.15        23.05        63.98 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A65F TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A5OB 
       10.32         4.24        18.41         7.56        15.42         8.98 
TCGA-G9-6329 TCGA-G9-6348 TCGA-G9-6361 TCGA-G9-6365 TCGA-G9-6369 TCGA-G9-6378 
       41.62        49.81        46.52        44.81        39.95        37.97 
TCGA-G9-6379 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       45.80        58.22        38.27        38.96        27.91        30.97 
TCGA-H9-7775 TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 
        6.08         5.33         2.01        14.47        28.54        28.60 
TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7744 
        1.97         2.37         2.93         2.10         2.66         1.68 
TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8261 TCGA-HC-8264 
       24.59         1.12        17.85         1.84        17.95         1.58 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AO 
        1.15        22.36         0.76         2.01         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67K 
        2.33         1.45        78.61        43.69        20.19        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67S TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83M 
       17.03        16.04        17.19         9.17        10.19        14.37 
TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       13.87        10.62        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       30.02        54.54       151.36        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7B1 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A721 
       67.07        58.19        34.95         2.73        26.43        13.15 
TCGA-M7-A722 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO TCGA-TP-A8TT 
       27.02        18.84         3.19        41.00        47.21        11.90 
TCGA-TP-A8TV TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87B 
        8.19        15.09         4.34        26.47        84.69        75.91 
TCGA-VP-A87D TCGA-VP-AA1N TCGA-XJ-A9DI TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA 
       60.92        17.82        48.03        31.50        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-Y6-A8TL TCGA-YL-A8HK TCGA-YL-A8HM 
       29.23        27.09        37.02        25.48        49.02        36.95 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        45.50        41.46 
TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       62.79        14.04        41.39        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       49.91         1.12         7.86         6.02 

$`DEL PEAK 26(13Q14.13) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5738 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5751 
        6.97        13.97         1.97        24.03        13.02        35.01 
TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 
        1.02         0.92        12.00         1.02        15.06         2.04 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5494 TCGA-EJ-5497 TCGA-EJ-5498 
        9.99        32.02        33.01        27.16        13.32        29.79 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       44.88        26.30        45.73        30.31        27.19        38.93 
TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 
       60.23        47.80        64.50        68.35        43.07        38.76 
TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7125 TCGA-EJ-7312 TCGA-EJ-7314 
       60.23        47.87        29.06        61.15        21.80         9.70 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7785 TCGA-EJ-7788 
       17.52         5.75        27.68         0.30        20.55        14.14 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 
       19.59        17.29         3.75        19.92        64.47        26.99 
TCGA-EJ-A46B TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        5.33        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7708 
       17.62        12.92        13.71         9.14         2.99        28.41 
TCGA-FC-A4JI TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 
       13.45        17.23        16.24         1.78        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 
       46.16        50.70        49.35        47.15        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       39.39         3.32        40.18        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       31.50        25.15        27.29        56.75        52.87        50.73 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-A6BX 
       35.34        28.18        32.68        26.01        21.14        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7211 TCGA-HC-7230 
        3.68        19.76         2.93         2.37         0.79         1.68 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7748 
        1.71         0.72         1.74         1.48         2.07        26.04 
TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8213 
        1.97         3.22        30.51         1.48        24.56        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AQ TCGA-HC-A6HX 
       22.32        15.88         1.78         2.20         3.48         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8200 TCGA-J4-A67N TCGA-J4-A67O 
        4.41        88.24        82.92        12.30        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       20.52        14.93         6.02        13.32        17.36         9.17 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83N TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A6E3 
        6.77        10.39        20.28         5.85        93.99        67.59 
TCGA-KK-A7AZ TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       27.62        22.75        20.65         5.19         6.87         9.93 
TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IN TCGA-QU-A6IP TCGA-VN-A88I TCGA-VN-A88K 
       25.08        15.88       114.64        86.14         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VP-A872 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H 
      106.95        94.65        23.93        55.56        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       48.85        21.53         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       38.04         9.04         2.99        25.97        31.96        31.96 
TCGA-XK-AAJU TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8SH TCGA-YL-A8SP TCGA-YL-A8SR 
       39.65        52.96        38.56        28.77        71.34         7.00 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       28.34         1.64         4.93 

  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                           0.76                            0.30 
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                         151.36                          114.64 
  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE 
                          26.45                           21.80 
[1] "0.8 - 151.4 (26.4)" "0.3 - 114.6 (21.8)"
[1] "hr=" "2"  
D54V2, continuous
                                 vv
clus                               T2  T3  T4
  DEL PEAK 26(13Q14.13) MUTATED    59 106   3
  DEL PEAK 26(13Q14.13) WILD-TYPE  91 100   2
D54V3, multiclass
    clus
vv   DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE
  T2                            59                              91
  T3                           106                             100
  T4                             3                               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                                 cls
clus                                0   1
  DEL PEAK 26(13Q14.13) MUTATED   125  25
  DEL PEAK 26(13Q14.13) WILD-TYPE 138  19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(13Q14.13) MUTATED    125   25
  DEL PEAK 26(13Q14.13) WILD-TYPE  138   19
   clus
vv  DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE
  0                           125                             138
  1                            25                              19
[1] 2 2
[1] FALSE
D54V5, binary
                                 cls
clus                                0   1
  DEL PEAK 26(13Q14.13) MUTATED     2 166
  DEL PEAK 26(13Q14.13) WILD-TYPE  11 184
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(13Q14.13) MUTATED      2  166
  DEL PEAK 26(13Q14.13) WILD-TYPE   11  184
                                        clus
vv                                       DEL PEAK 26(13Q14.13) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              166
                                        clus
vv                                       DEL PEAK 26(13Q14.13) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                184
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 26(13Q14.13) MUTATED    99  54   1   6
  DEL PEAK 26(13Q14.13) WILD-TYPE 144  36   4   5
D54V6, multiclass
    clus
vv   DEL PEAK 26(13Q14.13) MUTATED DEL PEAK 26(13Q14.13) WILD-TYPE
  R0                            99                             144
  R1                            54                              36
  R2                             1                               4
  RX                             6                               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"
D54V7, continuous
D54V8, continuous
D54V9, continuous
D54V10, continuous
D54V11, continuous
D54V12, continuous
D54V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(13Q14.13) MUTATED       1                         7    64
  DEL PEAK 26(13Q14.13) WILD-TYPE     1                         0    82
D54V14, multiclass
                           clus
vv                          DEL PEAK 26(13Q14.13) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                64
                           clus
vv                          DEL PEAK 26(13Q14.13) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                  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"

Clustering(55) Variable = DEL PEAK 27(13Q22.1) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(13Q22.1) MUTATED   122   0
  DEL PEAK 27(13Q22.1) WILD-TYPE 233   6
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                           122                            239 
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                             0                              6 
$`DEL PEAK 27(13Q22.1) MUTATED`
TCGA-CH-5737 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 
        2.99         1.02        12.99        35.01        31.00         2.04 
TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5794 
       44.02        23.01        24.03        13.02        26.99        29.00 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       33.11        19.56        23.90        48.13        36.69        48.53 
TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5524 TCGA-EJ-5525 
       36.23        46.55        52.27        51.88        43.07        36.66 
TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       49.02        83.57         9.50         9.37        16.77         7.66 
TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7786 
        6.28        23.90        38.37        25.87        25.68        14.53 
TCGA-EJ-7789 TCGA-EJ-7794 TCGA-EJ-8469 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A65J 
       18.15        23.05        63.98        10.32         4.24         2.99 
TCGA-FC-7961 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6348 TCGA-G9-6365 
       15.42        41.62        81.04        66.67        49.81        44.81 
TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       37.97        25.15        58.22        38.96        27.91        30.97 
TCGA-HC-7078 TCGA-HC-7080 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7232 
        5.33         2.01        28.60         1.97         2.37         2.93 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7747 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8266 
        2.10         2.66        24.59        17.85         1.84         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AS 
       22.36         0.76         2.01         1.61         2.33         1.45 
TCGA-HI-7168 TCGA-J4-8198 TCGA-J4-A67M TCGA-J4-A67S TCGA-J4-A83J TCGA-J9-A52B 
       78.61        20.19        16.04        17.19        10.19        13.87 
TCGA-J9-A52E TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E4 
       10.62        56.28        61.78       115.86        54.54        90.51 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A721 
      113.33        67.07        58.19         2.73        26.43        13.15 
TCGA-M7-A722 TCGA-M7-A724 TCGA-QU-A6IM TCGA-TP-A8TV TCGA-VN-A88L TCGA-VP-A875 
       27.02        15.88        41.00         8.19        12.95        26.47 
TCGA-VP-A876 TCGA-VP-A87B TCGA-VP-A87D TCGA-VP-AA1N TCGA-XJ-A9DI TCGA-XK-AAIV 
       84.69        75.91        60.92        17.82        48.03        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJT TCGA-YL-A8HK TCGA-YL-A8HM 
       31.96        28.54        29.23        37.02        49.02        36.95 
TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SI TCGA-YL-A8SJ 
       60.56        45.50        41.46        45.14        47.38        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI 
       37.97        26.24       106.75        62.79        14.04        41.39 
TCGA-YL-A9WK TCGA-YL-A9WY 
       62.37        28.34 

$`DEL PEAK 27(13Q22.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        6.97        22.06        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5766 
       13.02         1.02         0.92        12.00         1.02         1.02 
TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       15.06         2.04        15.98         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
        2.99        27.16        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       26.30        45.73        28.93        30.31        27.19        38.93 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5526 
       38.53        60.23        47.80        64.50        68.35        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7125 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       61.15        21.80         9.70        17.52         5.75        27.68 
TCGA-EJ-7331 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
        0.30        20.55        14.14        19.59        17.29         3.75 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-A46B TCGA-EJ-A46E TCGA-EJ-A46F 
       19.92        64.47        26.99         5.33        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        3.06         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB 
       18.41         9.14         7.56        28.41        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6336 TCGA-G9-6339 
       17.23        16.24         1.78        87.35        67.99        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       55.76        18.21        68.68        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        39.39         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       45.80        27.29        56.75        52.87        50.73        38.27 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 
       30.94         3.68        19.76         2.93         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7230 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7740 
       28.54         0.79         1.68         1.71         0.72         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.48         1.68         2.07        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 
        3.22        30.51         1.48        24.56        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AO 
       22.32         1.58        15.88         1.78         2.20         5.49 
TCGA-HC-A6AQ TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        3.48         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       12.30        21.76        17.03        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       14.93         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-KK-A59V 
        6.77        10.39        14.37        20.28         5.85        93.99 
TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A7AZ 
       44.68        30.02       151.36        67.59        49.25        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       34.95        22.75        20.65         5.19         6.87         9.93 
TCGA-M7-A723 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       25.08        18.84         3.19       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
       11.90         8.84        25.51         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A878 
       30.15        32.91        15.09         4.34       106.95        94.65 
TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       23.93        55.56        66.97        21.80        48.85        21.53 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DK 
        5.79        37.18        27.81         3.91        38.04         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJU 
        2.99        25.97        31.96        30.58        27.09        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA 
       25.48        52.96        38.56        71.77        62.14        16.83 
TCGA-YL-A8SH TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
       28.77        71.34         7.00        60.99        24.33        49.91 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                          0.76                           0.30 
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                        115.86                         151.36 
  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE 
                        28.125                         21.530 
[1] "0.8 - 115.9 (28.1)" "0.3 - 151.4 (21.5)"
[1] "hr="     "4.2e+08"
D55V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 27(13Q22.1) MUTATED    44  76   4
  DEL PEAK 27(13Q22.1) WILD-TYPE 106 130   1
D55V3, multiclass
    clus
vv   DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE
  T2                           44                            106
  T3                           76                            130
  T4                            4                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                                cls
clus                               0   1
  DEL PEAK 27(13Q22.1) MUTATED    92  20
  DEL PEAK 27(13Q22.1) WILD-TYPE 171  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(13Q22.1) MUTATED     92   20
  DEL PEAK 27(13Q22.1) WILD-TYPE  171   24
   clus
vv  DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE
  0                           92                            171
  1                           20                             24
[1] 2 2
[1] FALSE
D55V5, binary
                                cls
clus                               0   1
  DEL PEAK 27(13Q22.1) MUTATED     1 123
  DEL PEAK 27(13Q22.1) WILD-TYPE  12 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(13Q22.1) MUTATED      1  123
  DEL PEAK 27(13Q22.1) WILD-TYPE   12  227
                                        clus
vv                                       DEL PEAK 27(13Q22.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            1
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             123
                                        clus
vv                                       DEL PEAK 27(13Q22.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               227
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(13Q22.1) MUTATED    73  40   1   4
  DEL PEAK 27(13Q22.1) WILD-TYPE 170  50   4   7
D55V6, multiclass
    clus
vv   DEL PEAK 27(13Q22.1) MUTATED DEL PEAK 27(13Q22.1) WILD-TYPE
  R0                           73                            170
  R1                           40                             50
  R2                            1                              4
  RX                            4                              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"
D55V7, continuous
D55V8, continuous
D55V9, continuous
D55V10, continuous
D55V11, continuous
D55V12, continuous
D55V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(13Q22.1) MUTATED       0                         7    51
  DEL PEAK 27(13Q22.1) WILD-TYPE     2                         0    95
D55V14, multiclass
                           clus
vv                          DEL PEAK 27(13Q22.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               51
                           clus
vv                          DEL PEAK 27(13Q22.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 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 = DEL PEAK 28(15Q21.3) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(15Q21.3) MUTATED    44   1
  DEL PEAK 28(15Q21.3) WILD-TYPE 311   5
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                            45                            316 
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                             1                              5 
$`DEL PEAK 28(15Q21.3) MUTATED`
TCGA-2A-A8VO TCGA-CH-5740 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5761 
       43.79         1.02        35.01        31.00         1.02         0.92 
TCGA-EJ-5507 TCGA-EJ-5524 TCGA-EJ-7783 TCGA-FC-A4JI TCGA-G9-6369 TCGA-G9-7521 
       23.90        43.07        25.87        13.45        39.95        30.97 
TCGA-G9-A9S7 TCGA-HC-7081 TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7749 TCGA-HC-7752 
       21.14         2.37         1.97         2.37         1.97         3.22 
TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A631 
        1.84        22.42         3.12         1.58         1.15         1.78 
TCGA-HC-A6AO TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-A67N TCGA-J9-A52E TCGA-KK-A59X 
        5.49        78.61        43.69        16.54        10.62        56.28 
TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E6 TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 
       61.78        30.02       113.33        32.91       106.95        26.47 
TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJT TCGA-YL-A8HO TCGA-YL-A8SB 
       31.50        28.54        30.58        37.02        71.77        45.50 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WL 
       62.79        14.04        24.33 

$`DEL PEAK 28(15Q21.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5737 
       20.42        22.06        33.96         3.68        25.35         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
        6.97        22.06        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02        13.02         2.04        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       27.19        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       51.88        68.35        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       23.90        38.37        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        15.42         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       44.81         3.32        40.18        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX 
       35.34        28.18        32.68        26.01         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7209 
        3.68        19.76         5.33         2.93         2.01        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 
       28.54         0.79        28.60         1.68         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 
        2.07        24.59        26.04         1.12        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       17.85        24.56        19.36        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A4ZV 
        1.94        17.95        22.32        15.88        22.36         0.76 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.01         2.20         1.61         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 
        1.25         4.41        88.24        82.92        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       21.76        17.03        16.04        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 
        5.85        93.99        44.68       115.86        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       67.59        90.51        49.25        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 
       15.52        15.81        30.15        15.09         4.34        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       94.65        23.93        75.91        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        48.85        21.53        17.82         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       25.97        31.96        31.96        29.23        27.09        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        36.95        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR 
       45.86        37.97        26.24       106.75        71.34         7.00 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       41.39        60.99        62.37        49.91        28.34         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                          0.92                           0.30 
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                        113.33                         151.36 
  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE 
                        25.870                         23.885 
[1] "0.9 - 113.3 (25.9)" "0.3 - 151.4 (23.9)"
[1] "hr=" "1.3"
D56V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 28(15Q21.3) MUTATED     9  35   1
  DEL PEAK 28(15Q21.3) WILD-TYPE 141 171   4
D56V3, multiclass
    clus
vv   DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE
  T2                            9                            141
  T3                           35                            171
  T4                            1                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q21.3) MUTATED    30   9
  DEL PEAK 28(15Q21.3) WILD-TYPE 233  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q21.3) MUTATED     30    9
  DEL PEAK 28(15Q21.3) WILD-TYPE  233   35
   clus
vv  DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE
  0                           30                            233
  1                            9                             35
[1] 2 2
[1] FALSE
D56V5, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q21.3) MUTATED     2  43
  DEL PEAK 28(15Q21.3) WILD-TYPE  11 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q21.3) MUTATED      2   43
  DEL PEAK 28(15Q21.3) WILD-TYPE   11  307
                                        clus
vv                                       DEL PEAK 28(15Q21.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              43
                                        clus
vv                                       DEL PEAK 28(15Q21.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               307
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 28(15Q21.3) MUTATED    29  14   1   0
  DEL PEAK 28(15Q21.3) WILD-TYPE 214  76   4  11
D56V6, multiclass
    clus
vv   DEL PEAK 28(15Q21.3) MUTATED DEL PEAK 28(15Q21.3) WILD-TYPE
  R0                           29                            214
  R1                           14                             76
  R2                            1                              4
  RX                            0                             11
[1] 4 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, continuous
D56V8, continuous
D56V9, continuous
D56V10, continuous
D56V11, continuous
D56V12, continuous
D56V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(15Q21.3) MUTATED       0                         0    17
  DEL PEAK 28(15Q21.3) WILD-TYPE     2                         7   129
D56V14, multiclass
                           clus
vv                          DEL PEAK 28(15Q21.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               17
                           clus
vv                          DEL PEAK 28(15Q21.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                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(57) Variable = DEL PEAK 29(16Q22.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16Q22.3) MUTATED   127   2
  DEL PEAK 29(16Q22.3) WILD-TYPE 228   4
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                           129                            232 
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                             2                              4 
$`DEL PEAK 29(16Q22.3) MUTATED`
TCGA-2A-A8W3 TCGA-CH-5739 TCGA-CH-5744 TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 
       25.35        22.06         1.97        35.01         1.02         2.04 
TCGA-CH-5764 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5498 
        1.02        26.99        33.01        33.11        19.56        29.79 
TCGA-EJ-5508 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5521 TCGA-EJ-5525 
       38.93        48.53        36.23        46.55        51.88        36.66 
TCGA-EJ-5527 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       39.75        49.02        21.80        16.77         7.66         5.75 
TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7789 
       27.68        23.90        25.87        25.68        20.55        18.15 
TCGA-EJ-7794 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-A46F TCGA-EJ-A65D TCGA-EJ-A65F 
       23.05        63.98        26.99         9.83        12.92        18.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A6HD TCGA-G9-6329 TCGA-G9-6342 
       15.42        13.45         8.98        16.24        41.62        55.76 
TCGA-G9-6343 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6373 TCGA-G9-6379 
       18.21        49.35        46.52        47.44        26.66        45.80 
TCGA-G9-6384 TCGA-G9-6496 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S7 
       25.15        56.75        50.73        30.97        28.18        21.14 
TCGA-H9-A6BY TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7232 
        3.68        14.47         0.79        28.60         1.97         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7742 TCGA-HC-7749 TCGA-HC-7819 TCGA-HC-7821 
        1.71         0.72         1.48         1.97        17.85         1.84 
TCGA-HC-8216 TCGA-HC-8257 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
       22.42        23.87         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AO TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7171 
        2.01         5.49         1.25         4.41        78.61        43.69 
TCGA-J4-A67N TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83N TCGA-J9-A52B TCGA-KK-A59V 
       16.54         9.17        10.19        20.28        13.87        93.99 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E5 
       56.28        61.78       115.86       151.36        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A8IF TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IO 
      113.33        67.07        26.43        15.88         3.19        47.21 
TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88Q TCGA-VP-A875 TCGA-VP-A876 
       25.51         6.02        15.52        32.91        26.47        84.69 
TCGA-VP-A879 TCGA-VP-A87D TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       23.93        60.92        21.53        17.82         5.79        37.18 
TCGA-XJ-A83G TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAJP TCGA-XK-AAJR TCGA-YL-A8HK 
       38.04        25.97        31.96        29.23        27.09        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SC TCGA-YL-A8SJ 
       38.56        36.95        71.77        60.56        41.46        45.86 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WK 
       26.24       106.75        71.34        62.79         7.00        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A9ND 
       24.33        49.91         6.02 

$`DEL PEAK 29(16Q22.3) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 
       20.42        43.79        22.06        33.96         3.68         2.99 
TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 
        6.97         1.02        12.99        13.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5765 
       13.02        31.00         0.92        44.02        12.00        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5497 
        9.99        32.02         2.99        29.00        27.16        13.32 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 
       27.19        23.90        48.13        36.69        38.53        60.23 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 
       47.80        52.27        64.50        68.35        43.07        38.76 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 
       60.23        41.85        47.87        29.06        27.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7325 TCGA-EJ-7330 
       83.57         9.70         9.50         9.37        17.52         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
        0.30        38.37        14.53        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
        3.75        19.92        64.47        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E 
       17.49         3.06         7.53        21.96        17.62        13.71 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A66V TCGA-FC-A8O0 
        9.14         2.99         7.56        28.41        17.23         1.78 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6347 
       87.35        81.04        67.99        66.67        69.37        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6363 TCGA-G9-6364 
       49.81        46.16        50.70        47.15        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6498 TCGA-G9-7509 
       31.50        37.97        27.29        58.22        52.87        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-H9-7775 
       38.96        27.91        35.34        32.68        26.01         6.08 
TCGA-H9-A6BX TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       30.94        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7210 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       28.54         1.68         2.37         2.10         2.66         1.74 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 
        1.68         2.07        24.59        26.04         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8258 
       30.51         1.48        24.56        19.36         3.12         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HI-7169 
        2.20         1.61         2.33         3.48         1.45        88.24 
TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       82.92        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J9-A52C 
       17.36         9.17         6.77        10.39        14.37         5.85 
TCGA-J9-A52E TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E3 TCGA-KK-A6E8 
       10.62        44.68        30.02        54.54        67.59        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y 
       27.62        34.95        22.75         2.73        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 
        6.87         9.93        13.15        27.02        25.08        18.84 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
       41.00       114.64        86.14        11.90         8.19         8.84 
TCGA-VN-A88L TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       12.95        15.81        30.15        15.09         4.34       106.95 
TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       94.65        75.91        55.56        66.97        21.80        48.85 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIV 
       27.81         3.91        48.03         9.04         2.99        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       31.96        28.54        30.58        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH 
       52.96        62.14        16.83        45.50        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WY 
       47.38        37.97        14.04        41.39        60.99        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        1.64         4.93         1.12         7.86 

  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                          0.72                           0.30 
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                        151.36                         114.64 
  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE 
                         25.87                          21.88 
[1] "0.7 - 151.4 (25.9)" "0.3 - 114.6 (21.9)"
[1] "hr=" "1.3"
D57V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 29(16Q22.3) MUTATED    40  89   1
  DEL PEAK 29(16Q22.3) WILD-TYPE 110 117   4
D57V3, multiclass
    clus
vv   DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE
  T2                           40                            110
  T3                           89                            117
  T4                            1                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q22.3) MUTATED    99  18
  DEL PEAK 29(16Q22.3) WILD-TYPE 164  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q22.3) MUTATED     99   18
  DEL PEAK 29(16Q22.3) WILD-TYPE  164   26
   clus
vv  DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE
  0                           99                            164
  1                           18                             26
[1] 2 2
[1] FALSE
D57V5, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q22.3) MUTATED     5 125
  DEL PEAK 29(16Q22.3) WILD-TYPE   8 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q22.3) MUTATED      5  125
  DEL PEAK 29(16Q22.3) WILD-TYPE    8  225
                                        clus
vv                                       DEL PEAK 29(16Q22.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            5
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             125
                                        clus
vv                                       DEL PEAK 29(16Q22.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              8
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               225
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(16Q22.3) MUTATED    84  36   1   3
  DEL PEAK 29(16Q22.3) WILD-TYPE 159  54   4   8
D57V6, multiclass
    clus
vv   DEL PEAK 29(16Q22.3) MUTATED DEL PEAK 29(16Q22.3) WILD-TYPE
  R0                           84                            159
  R1                           36                             54
  R2                            1                              4
  RX                            3                              8
[1] 4 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, continuous
D57V8, continuous
D57V9, continuous
D57V10, continuous
D57V11, continuous
D57V12, continuous
D57V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(16Q22.3) MUTATED       0                         3    48
  DEL PEAK 29(16Q22.3) WILD-TYPE     2                         4    98
D57V14, multiclass
                           clus
vv                          DEL PEAK 29(16Q22.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               48
                           clus
vv                          DEL PEAK 29(16Q22.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 30(16Q24.1) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(16Q24.1) MUTATED   144   2
  DEL PEAK 30(16Q24.1) WILD-TYPE 211   4
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                           146                            215 
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                             2                              4 
$`DEL PEAK 30(16Q24.1) MUTATED`
TCGA-2A-A8W3 TCGA-CH-5739 TCGA-CH-5744 TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 
       25.35        22.06         1.97        35.01         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5771 TCGA-CH-5788 
        0.92        44.02         1.02         1.02        13.02        26.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5498 
       32.02        33.01         2.99        33.11        19.56        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5514 
       46.52        44.88        38.93        36.69        48.53        36.23 
TCGA-EJ-5516 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-7123 
       46.55        43.07        36.66        38.76        39.75        49.02 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       21.80         9.70        16.77         7.66        17.52         5.75 
TCGA-EJ-7328 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7789 
       27.68        23.90        25.87        25.68        20.55        18.15 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-A46F TCGA-EJ-A65D TCGA-EJ-A65F TCGA-FC-7961 
       63.98        26.99         9.83        12.92        18.41        15.42 
TCGA-FC-A4JI TCGA-FC-A6HD TCGA-G9-6329 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6354 
       13.45        16.24        41.62        55.76        18.21        49.35 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6384 TCGA-G9-6496 
       46.52        47.44        26.66        31.50        25.15        56.75 
TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S7 TCGA-H9-A6BY TCGA-HC-7078 
       50.73        30.97        28.18        21.14         3.68         5.33 
TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7232 TCGA-HC-7233 
       14.47         0.79        28.60         1.97         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7742 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7819 TCGA-HC-7821 
        0.72         1.48        26.04         1.97        17.85         1.84 
TCGA-HC-8216 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 
       22.42        15.88         1.15        22.36         0.76         2.01 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7171 
        1.61         5.49         1.25         4.41        78.61        43.69 
TCGA-J4-A67N TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83N TCGA-J9-A52B TCGA-KK-A59V 
       16.54         9.17        10.19        20.28        13.87        93.99 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 
       56.28        61.78       115.86       151.36        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A8IF TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IO 
       67.07        27.62        26.43        15.88         3.19        47.21 
TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A88Q TCGA-VP-A875 
       25.51         6.02        15.52        30.15        32.91        26.47 
TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87D TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       84.69        23.93        60.92        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XJ-A83G TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAJP 
        5.79        37.18        38.04        25.97        31.96        29.23 
TCGA-XK-AAJR TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       27.09        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO 
       60.56        16.83        41.46        45.86        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       71.34        62.79         7.00        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A9ND 
       28.34         6.02 

$`DEL PEAK 30(16Q24.1) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 
       20.42        43.79        22.06        33.96         3.68         2.99 
TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 
        6.97         1.02        12.99        13.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 
       13.02        31.00        12.00        23.01        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5497 
        2.04        15.98         9.99        29.00        27.16        13.32 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5509 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       48.13        38.53        60.23        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       51.88        68.35        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7330 
       27.02        61.15        83.57         9.50         9.37         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
        0.30        38.37        14.53        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8474 TCGA-EJ-A46B 
        3.75        23.05        19.92        64.47        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
        4.24        17.49         3.06         7.53        21.96        17.62 
TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A5OB 
       13.71         9.14         2.99         7.56        28.41         8.98 
TCGA-FC-A66V TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       17.23         1.78        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 
       69.37        68.68        49.81        46.16        50.70        47.15 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6494 
       38.01        40.31        37.97        45.80        27.29        58.22 
TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 
       52.87        38.27        38.96        27.91        35.34        32.68 
TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 
       26.01         6.08        30.94        19.76         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7210 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7737 TCGA-HC-7738 
        2.37        28.54         1.68         2.37         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 
        1.74         1.68         2.07        24.59         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       30.51         1.48        24.56        19.36         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HI-7169 
        1.78         2.20         2.33         3.48         1.45        88.24 
TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       82.92        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J9-A52C 
       17.36         9.17         6.77        10.39        14.37         5.85 
TCGA-J9-A52E TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E3 TCGA-KK-A6E4 
       10.62        44.68        30.02        54.54        67.59        90.51 
TCGA-KK-A6E8 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y 
       58.19        34.95        22.75         2.73        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 
        6.87         9.93        13.15        27.02        25.08        18.84 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
       41.00       114.64        86.14        11.90         8.19         8.84 
TCGA-VN-A88L TCGA-VN-A88O TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A878 
       12.95        15.81        15.09         4.34       106.95        94.65 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-X4-A8KS TCGA-XA-A8JR 
       75.91        55.56        66.97        21.80        27.81         3.91 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
       48.03         9.04         2.99        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8S8 TCGA-YL-A8SB 
       30.58        37.02        39.65        25.48        62.14        45.50 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A9WH TCGA-YL-A9WI 
       45.14        28.77        47.38        37.97        14.04        41.39 
TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99         1.64         4.93         1.12         7.86 

  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                          0.72                           0.30 
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                        151.36                         114.64 
  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE 
                         26.14                          21.80 
[1] "0.7 - 151.4 (26.1)" "0.3 - 114.6 (21.8)"
[1] "hr=" "1.5"
D58V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 30(16Q24.1) MUTATED    43 103   1
  DEL PEAK 30(16Q24.1) WILD-TYPE 107 103   4
D58V3, multiclass
    clus
vv   DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE
  T2                           43                            107
  T3                          103                            103
  T4                            1                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q24.1) MUTATED   112  21
  DEL PEAK 30(16Q24.1) WILD-TYPE 151  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.1) MUTATED    112   21
  DEL PEAK 30(16Q24.1) WILD-TYPE  151   23
   clus
vv  DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE
  0                          112                            151
  1                           21                             23
[1] 2 2
[1] FALSE
D58V5, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q24.1) MUTATED     6 141
  DEL PEAK 30(16Q24.1) WILD-TYPE   7 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q24.1) MUTATED      6  141
  DEL PEAK 30(16Q24.1) WILD-TYPE    7  209
                                        clus
vv                                       DEL PEAK 30(16Q24.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            6
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             141
                                        clus
vv                                       DEL PEAK 30(16Q24.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              7
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               209
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(16Q24.1) MUTATED    98  38   2   3
  DEL PEAK 30(16Q24.1) WILD-TYPE 145  52   3   8
D58V6, multiclass
    clus
vv   DEL PEAK 30(16Q24.1) MUTATED DEL PEAK 30(16Q24.1) WILD-TYPE
  R0                           98                            145
  R1                           38                             52
  R2                            2                              3
  RX                            3                              8
[1] 4 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, continuous
D58V8, continuous
D58V9, continuous
D58V10, continuous
D58V11, continuous
D58V12, continuous
D58V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(16Q24.1) MUTATED       1                         3    60
  DEL PEAK 30(16Q24.1) WILD-TYPE     1                         4    86
D58V14, multiclass
                           clus
vv                          DEL PEAK 30(16Q24.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               60
                           clus
vv                          DEL PEAK 30(16Q24.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 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"

Clustering(59) Variable = DEL PEAK 31(17P13.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(17P13.1) MUTATED   106   2
  DEL PEAK 31(17P13.1) WILD-TYPE 249   4
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                           108                            253 
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                             2                              4 
$`DEL PEAK 31(17P13.1) MUTATED`
TCGA-2A-A8VL TCGA-2A-A8W3 TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       20.42        25.35        35.01         2.04         0.92        44.02 
TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5507 
        1.02         1.02        32.02        33.01        29.00        23.90 
TCGA-EJ-5514 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       36.23        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-7315 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7328 
       38.76        39.75         9.50        16.77         7.66        27.68 
TCGA-EJ-7781 TCGA-EJ-7797 TCGA-EJ-8474 TCGA-EJ-A46F TCGA-EJ-A65J TCGA-FC-A4JI 
       23.90        19.92        10.32         9.83         2.99        13.45 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6354 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6384 
       69.37        55.76        49.35        26.66        31.50        25.15 
TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S0 
       58.22        50.73        38.27        38.96        30.97        26.01 
TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       21.14         5.33        28.60         1.97         1.68         2.37 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7821 TCGA-HC-8216 
        1.48         1.68         2.07        24.59         1.84        22.42 
TCGA-HC-8257 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       23.87         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A83I TCGA-J9-A52B 
        4.41        78.61        21.76        17.03         9.17        13.87 
TCGA-J9-A52E TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 
       10.62        44.68        61.78       115.86        54.54       151.36 
TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A8IL TCGA-M7-A71Z TCGA-M7-A725 TCGA-QU-A6IN 
       90.51       113.33        20.65         6.87        18.84       114.64 
TCGA-VN-A88L TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87C 
       12.95        32.91       106.95        26.47        84.69        55.56 
TCGA-VP-A87D TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XK-AAIV 
       60.92        21.53        17.82         5.79        37.18        31.50 
TCGA-XK-AAJA TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8SA 
       30.58        52.96        49.02        38.56        71.77        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.50        41.46        45.14        45.86        37.97        26.24 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WY 
       71.34        62.79        14.04        62.37        24.33        28.34 

$`DEL PEAK 31(17P13.1) WILD-TYPE`
TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 TCGA-CH-5738 
       43.79        22.06        33.96         3.68         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
       22.06         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5765 
        1.02        13.02        31.00         1.02        12.00        23.01 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        9.99         2.99        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       30.31        27.19        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5530 
       38.53        60.23        46.55        47.80        52.27        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7325 TCGA-EJ-7327 
       83.57        21.80         9.70         9.37        17.52         5.75 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        6.28         0.30        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-A46B TCGA-EJ-A46D 
       23.05        64.47        63.98        26.99         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.49         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
       13.71        18.41         9.14         7.56        28.41        15.42 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       81.04        67.99        66.67        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       46.16        50.70        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 
       40.31        37.97        45.80        27.29        56.75        52.87 
TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       27.91        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
        3.68        19.76         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
       28.54         0.79         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.66         1.74        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 
       30.51         1.48        17.85        24.56        19.36         3.12 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
       15.88         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        1.45         1.25        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       12.30        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J 
       17.19         6.02        13.32        17.36         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-KK-A59V 
        6.77        10.39        14.37        20.28         5.85        93.99 
TCGA-KK-A59X TCGA-KK-A6E0 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 
       56.28        30.02        67.59        49.25        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A71Y 
       27.62        34.95        22.75         2.73        26.43         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL 
        9.93        13.15        27.02        25.08        15.88         3.19 
TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
       41.00        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R 
       25.51         6.02        15.52        15.81        30.15        15.09 
TCGA-VN-A943 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87E TCGA-VP-A87H 
        4.34        94.65        23.93        75.91        66.97        21.80 
TCGA-VP-A87J TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       48.85        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP 
        2.99        25.97        31.96        31.96        28.54        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HM TCGA-YL-A8S8 
       27.09        37.02        39.65        25.48        36.95        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SO TCGA-YL-A8SR TCGA-YL-A9WI 
       60.56        28.77        47.38       106.75         7.00        41.39 
TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        49.91         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                          0.76                           0.30 
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                        151.36                         106.75 
  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE 
                         27.17                          21.80 
[1] "0.8 - 151.4 (27.2)" "0.3 - 106.8 (21.8)"
[1] "hr=" "1.2"
D59V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 31(17P13.1) MUTATED    29  77   2
  DEL PEAK 31(17P13.1) WILD-TYPE 121 129   3
D59V3, multiclass
    clus
vv   DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE
  T2                           29                            121
  T3                           77                            129
  T4                            2                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                                cls
clus                               0   1
  DEL PEAK 31(17P13.1) MUTATED    75  22
  DEL PEAK 31(17P13.1) WILD-TYPE 188  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17P13.1) MUTATED     75   22
  DEL PEAK 31(17P13.1) WILD-TYPE  188   22
   clus
vv  DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE
  0                           75                            188
  1                           22                             22
[1] 2 2
[1] FALSE
D59V5, binary
                                cls
clus                               0   1
  DEL PEAK 31(17P13.1) MUTATED     4 104
  DEL PEAK 31(17P13.1) WILD-TYPE   9 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17P13.1) MUTATED      4  104
  DEL PEAK 31(17P13.1) WILD-TYPE    9  246
                                        clus
vv                                       DEL PEAK 31(17P13.1) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             104
                                        clus
vv                                       DEL PEAK 31(17P13.1) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               246
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(17P13.1) MUTATED    68  34   0   3
  DEL PEAK 31(17P13.1) WILD-TYPE 175  56   5   8
D59V6, multiclass
    clus
vv   DEL PEAK 31(17P13.1) MUTATED DEL PEAK 31(17P13.1) WILD-TYPE
  R0                           68                            175
  R1                           34                             56
  R2                            0                              5
  RX                            3                              8
[1] 4 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, continuous
D59V8, continuous
D59V9, continuous
D59V10, continuous
D59V11, continuous
D59V12, continuous
D59V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(17P13.1) MUTATED       0                         1    39
  DEL PEAK 31(17P13.1) WILD-TYPE     2                         6   107
D59V14, multiclass
                           clus
vv                          DEL PEAK 31(17P13.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               39
                           clus
vv                          DEL PEAK 31(17P13.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                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(60) Variable = DEL PEAK 32(17Q21.31) MUTATION ANALYSIS
D60V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(17Q21.31) MUTATED    69   1
  DEL PEAK 32(17Q21.31) WILD-TYPE 286   5
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                             70                             291 
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                              1                               5 
$`DEL PEAK 32(17Q21.31) MUTATED`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5744 TCGA-CH-5750 
       20.42        43.79        22.06         1.02         1.97        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5768 TCGA-CH-5771 TCGA-EJ-5507 TCGA-EJ-5511 
       35.01        31.00        24.03        13.02        23.90        48.53 
TCGA-EJ-5516 TCGA-EJ-5521 TCGA-EJ-5524 TCGA-EJ-5542 TCGA-EJ-7314 TCGA-EJ-7318 
       46.55        51.88        43.07        29.06         9.70        16.77 
TCGA-EJ-7325 TCGA-EJ-7781 TCGA-EJ-7788 TCGA-EJ-7793 TCGA-EJ-8474 TCGA-EJ-A46F 
       17.52        23.90        14.14         3.75        10.32         9.83 
TCGA-G9-6339 TCGA-G9-6348 TCGA-G9-6377 TCGA-G9-6499 TCGA-HC-7075 TCGA-HC-7081 
       69.37        49.81        31.50        50.73        19.76         2.37 
TCGA-HC-7209 TCGA-HC-7213 TCGA-HC-7744 TCGA-HC-7748 TCGA-HC-7820 TCGA-HC-8213 
       14.47         1.97         1.68        26.04        24.56        19.36 
TCGA-HC-8216 TCGA-HC-8262 TCGA-HC-A48F TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HI-7168 
       22.42        22.32        22.36         3.48         1.45        78.61 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67S TCGA-J4-A67T 
       43.69        20.19        21.76        17.03        17.19         6.02 
TCGA-J4-A83M TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-M7-A725 
       14.37        13.87        10.62        90.51       113.33        18.84 
TCGA-QU-A6IP TCGA-VN-A88M TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87C TCGA-VP-AA1N 
       86.14         6.02       106.95        26.47        55.56        17.82 
TCGA-X4-A8KQ TCGA-XK-AAJA TCGA-XK-AAJT TCGA-YL-A8HJ TCGA-YL-A8HO TCGA-YL-A8SA 
       37.18        30.58        37.02        52.96        71.77        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SK TCGA-YL-A8SQ 
       45.50        41.46        37.97        62.79 

$`DEL PEAK 32(17Q21.31) WILD-TYPE`
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 
       22.06        33.96         3.68        25.35         2.99         6.97 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5753 TCGA-CH-5754 
       12.99        13.97        24.03         1.02         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
       15.06         2.04        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       28.93        30.31        27.19        38.93        48.13        36.69 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       38.53        36.23        60.23        47.80        52.27        64.50 
TCGA-EJ-5522 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       47.87        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
        9.50         9.37         7.66         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       18.15        19.59        17.29        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G 
       63.98        26.99         5.33         4.24        17.49         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       81.04        67.99        66.67        55.76        18.21        68.68 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       38.01        40.31        26.66        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        56.75        52.87        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7078 TCGA-HC-7079 
       21.14         6.08        30.94         3.68         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
        2.01        28.54         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        1.48         2.07        24.59         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8256 TCGA-HC-8257 
       30.51         1.48        17.85         1.84         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 
        2.17         2.27         1.94        17.95         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.15         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 
        5.49         2.33         1.25         4.41        88.24        82.92 
TCGA-J4-8200 TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       12.30        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83N TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       10.39        20.28         5.85        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       49.25        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM 
       13.15        27.02        25.08        15.88         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
      114.64        47.21        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
       12.95        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87D 
        4.34        84.69        94.65        23.93        75.91        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS 
       66.97        21.80        48.85        21.53         5.79        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.50        31.96        28.54        29.23        27.09 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
       39.65        25.48        49.02        38.56        36.95        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL 
       60.56        45.14        28.77        47.38        45.86        26.24 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      106.75        71.34         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                           1.02                            0.30 
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                         113.33                          151.36 
  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE 
                          22.39                           24.59 
[1] "1.0 - 113.3 (22.4)" "0.3 - 151.4 (24.6)"
[1] "hr=" "1.2"
D60V2, continuous
                                 vv
clus                               T2  T3  T4
  DEL PEAK 32(17Q21.31) MUTATED    25  46   1
  DEL PEAK 32(17Q21.31) WILD-TYPE 125 160   4
D60V3, multiclass
    clus
vv   DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE
  T2                            25                             125
  T3                            46                             160
  T4                             1                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                                 cls
clus                                0   1
  DEL PEAK 32(17Q21.31) MUTATED    54   5
  DEL PEAK 32(17Q21.31) WILD-TYPE 209  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(17Q21.31) MUTATED     54    5
  DEL PEAK 32(17Q21.31) WILD-TYPE  209   39
   clus
vv  DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE
  0                            54                             209
  1                             5                              39
[1] 2 2
[1] FALSE
D60V5, binary
                                 cls
clus                                0   1
  DEL PEAK 32(17Q21.31) MUTATED     2  70
  DEL PEAK 32(17Q21.31) WILD-TYPE  11 280
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(17Q21.31) MUTATED      2   70
  DEL PEAK 32(17Q21.31) WILD-TYPE   11  280
                                        clus
vv                                       DEL PEAK 32(17Q21.31) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               70
                                        clus
vv                                       DEL PEAK 32(17Q21.31) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                280
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(17Q21.31) MUTATED    51  18   1   1
  DEL PEAK 32(17Q21.31) WILD-TYPE 192  72   4  10
D60V6, multiclass
    clus
vv   DEL PEAK 32(17Q21.31) MUTATED DEL PEAK 32(17Q21.31) WILD-TYPE
  R0                            51                             192
  R1                            18                              72
  R2                             1                               4
  RX                             1                              10
[1] 4 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, continuous
D60V8, continuous
D60V9, continuous
D60V10, continuous
D60V11, continuous
D60V12, continuous
D60V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(17Q21.31) MUTATED       0                         2    29
  DEL PEAK 32(17Q21.31) WILD-TYPE     2                         5   117
D60V14, multiclass
                           clus
vv                          DEL PEAK 32(17Q21.31) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                29
                           clus
vv                          DEL PEAK 32(17Q21.31) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                 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(61) Variable = DEL PEAK 33(18Q21.31) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(18Q21.31) MUTATED    91   2
  DEL PEAK 33(18Q21.31) WILD-TYPE 264   4
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                             93                             268 
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                              2                               4 
$`DEL PEAK 33(18Q21.31) MUTATED`
TCGA-2A-A8W1 TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5769 
        3.68        22.06        35.01         2.04         0.92         2.04 
TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5514 
       15.98        33.01        28.93        23.90        48.53        36.23 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-7218 TCGA-EJ-7312 
       47.80        52.27        43.07        36.66        83.57        21.80 
TCGA-EJ-7315 TCGA-EJ-7781 TCGA-EJ-7794 TCGA-EJ-A46I TCGA-EJ-A65B TCGA-G9-6329 
        9.50        23.90        23.05        21.96        17.62        41.62 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6354 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       49.81        46.16        49.35        26.66        31.50        37.97 
TCGA-G9-6384 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7078 TCGA-HC-7211 
       25.15        30.97        28.18        26.01         5.33         0.79 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7820 
        1.97         1.68         1.48        26.04         1.97        24.56 
TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6HY 
        1.84        22.42        22.36         0.76         1.78         4.41 
TCGA-HI-7168 TCGA-HI-7170 TCGA-J4-A67L TCGA-J4-A67N TCGA-J4-A83I TCGA-J4-A83N 
       78.61        82.92        17.03        16.54         9.17        20.28 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E5 
       56.28        61.78       115.86        30.02        54.54        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A724 TCGA-M7-A725 
      113.33        67.07         2.73        20.65        15.88        18.84 
TCGA-TP-A8TV TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A872 
        8.19        25.51        15.52        30.15         4.34       106.95 
TCGA-VP-A87B TCGA-VP-A87C TCGA-WW-A8ZI TCGA-XJ-A83G TCGA-XK-AAIV TCGA-XK-AAJ3 
       75.91        55.56         5.79        38.04        31.50        28.54 
TCGA-XK-AAJA TCGA-XK-AAJT TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       30.58        37.02        49.02        36.95        71.77        62.14 
TCGA-YL-A8SA TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       16.83        45.86       106.75        62.79         7.00        14.04 
TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY 
       62.37        49.91        28.34 

$`DEL PEAK 33(18Q21.31) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W3 TCGA-CH-5737 
       20.42        43.79        22.06        33.96        25.35         2.99 
TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 
        6.97         1.02        12.99        13.97         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5762 TCGA-CH-5763 
        1.02        13.02        31.00         1.02        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5771 
        1.02        23.01         1.02        15.06        24.03        13.02 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       26.99         9.99        32.02         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 
       26.30        45.73        30.31        27.19        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5521 
       36.69        38.53        60.23        46.55        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       68.35        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7317 
       29.06        27.02        49.02        61.15         9.70         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7797 
       14.14        18.15        19.59        17.29         3.75        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A65D TCGA-EJ-A65E 
       17.49         9.83         3.06         7.53        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
       18.41         9.14         2.99         7.56        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 
       13.45         8.98        17.23        16.24         1.78        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       68.68        50.70        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       40.31        45.80        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 
       50.73        38.27        38.96        27.91        35.34        32.68 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 
       21.14         6.08        30.94         3.68        19.76         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7231 
        2.01         2.37        14.47        28.54        28.60         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
        1.68         2.07        24.59         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.48        17.85        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.15         2.01         2.20         1.61         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HI-7169 TCGA-HI-7171 TCGA-J4-8198 
        3.48         1.45         1.25        88.24        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       12.30        21.76        16.04        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J 
       17.19         6.02        13.32        17.36         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
        6.77        10.39        14.37        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 
       93.99        44.68       151.36        67.59        90.51        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF TCGA-M7-A71Y TCGA-M7-A71Z 
       27.62        34.95        22.75        26.43         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-QU-A6IL TCGA-QU-A6IM 
        9.93        13.15        27.02        25.08         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88L 
      114.64        47.21        86.14        11.90         8.84        12.95 
TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A875 TCGA-VP-A876 
        6.02        15.81        32.91        15.09        26.47        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       94.65        23.93        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI 
       21.53        17.82        37.18        27.81         3.91        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJP 
        9.04         2.99        25.97        31.96        31.96        29.23 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8S9 
       27.09        39.65        25.48        52.96        38.56        60.56 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       45.50        41.46        45.14        28.77        47.38        37.97 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-ZG-A8QW 
       26.24        71.34        41.39        60.99        24.33         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                           0.76                            0.30 
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                         115.86                          151.36 
  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE 
                          28.18                           21.78 
[1] "0.8 - 115.9 (28.2)" "0.3 - 151.4 (21.8)"
[1] "hr=" "1.1"
D61V2, continuous
                                 vv
clus                               T2  T3  T4
  DEL PEAK 33(18Q21.31) MUTATED    30  63   2
  DEL PEAK 33(18Q21.31) WILD-TYPE 120 143   3
D61V3, multiclass
    clus
vv   DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE
  T2                            30                             120
  T3                            63                             143
  T4                             2                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                                 cls
clus                                0   1
  DEL PEAK 33(18Q21.31) MUTATED    68  17
  DEL PEAK 33(18Q21.31) WILD-TYPE 195  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(18Q21.31) MUTATED     68   17
  DEL PEAK 33(18Q21.31) WILD-TYPE  195   27
   clus
vv  DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE
  0                            68                             195
  1                            17                              27
[1] 2 2
[1] FALSE
D61V5, binary
                                 cls
clus                                0   1
  DEL PEAK 33(18Q21.31) MUTATED     2  93
  DEL PEAK 33(18Q21.31) WILD-TYPE  11 257
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(18Q21.31) MUTATED      2   93
  DEL PEAK 33(18Q21.31) WILD-TYPE   11  257
                                        clus
vv                                       DEL PEAK 33(18Q21.31) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             2
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               93
                                        clus
vv                                       DEL PEAK 33(18Q21.31) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                                257
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(18Q21.31) MUTATED    56  36   0   1
  DEL PEAK 33(18Q21.31) WILD-TYPE 187  54   5  10
D61V6, multiclass
    clus
vv   DEL PEAK 33(18Q21.31) MUTATED DEL PEAK 33(18Q21.31) WILD-TYPE
  R0                            56                             187
  R1                            36                              54
  R2                             0                               5
  RX                             1                              10
[1] 4 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, continuous
D61V8, continuous
D61V9, continuous
D61V10, continuous
D61V11, continuous
D61V12, continuous
D61V13, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(18Q21.31) MUTATED       0                         3    34
  DEL PEAK 33(18Q21.31) WILD-TYPE     2                         4   112
D61V14, multiclass
                           clus
vv                          DEL PEAK 33(18Q21.31) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                34
                           clus
vv                          DEL PEAK 33(18Q21.31) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               4
  WHITE                                                 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(62) Variable = DEL PEAK 34(18Q23) MUTATION ANALYSIS
D62V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 34(18Q23) MUTATED    96   2
  DEL PEAK 34(18Q23) WILD-TYPE 259   4
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                          98                          263 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                           2                            4 
$`DEL PEAK 34(18Q23) MUTATED`
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5772 
       35.01         1.02         2.04         0.92        44.02        15.98 
TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5514 
       33.01        33.11        28.93        23.90        48.53        36.23 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-7218 
       47.80        52.27        43.07        36.66        39.75        83.57 
TCGA-EJ-7315 TCGA-EJ-7781 TCGA-EJ-7794 TCGA-EJ-8470 TCGA-EJ-A46D TCGA-EJ-A46I 
        9.50        23.90        23.05        26.99         4.24        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-G9-6329 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 
       17.62        12.92        41.62        55.76        49.81        46.16 
TCGA-G9-6354 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6499 
       49.35        26.66        31.50        37.97        25.15        50.73 
TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7078 TCGA-HC-7211 TCGA-HC-7213 
       30.97        28.18        26.01         5.33         0.79         1.97 
TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7820 
        1.68         1.48         2.07        26.04         1.97        24.56 
TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AN 
        1.84        22.42        22.36         0.76         1.78         1.61 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-A67L TCGA-J4-A67N 
        4.41        78.61        82.92        43.69        17.03        16.54 
TCGA-J4-A83I TCGA-J4-A83N TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
        9.17        20.28        61.78       115.86        30.02        54.54 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A8IB TCGA-M7-A71Z TCGA-M7-A724 
       49.25       113.33        67.07         2.73         6.87        15.88 
TCGA-M7-A725 TCGA-TP-A8TV TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A943 
       18.84         8.19        25.51        15.52        30.15         4.34 
TCGA-VP-A872 TCGA-VP-A87B TCGA-VP-A87C TCGA-WW-A8ZI TCGA-XK-AAIV TCGA-XK-AAJ3 
      106.95        75.91        55.56         5.79        31.50        28.54 
TCGA-XK-AAJT TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8SA TCGA-YL-A8SJ 
       37.02        49.02        36.95        71.77        16.83        45.86 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WK 
      106.75        71.34        62.79         7.00        14.04        62.37 
TCGA-YL-A9WX TCGA-YL-A9WY 
       49.91        28.34 

$`DEL PEAK 34(18Q23) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5763 
        1.97        24.03         1.02        13.02        31.00        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 
       13.02        26.99         9.99        32.02         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       27.16        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 
       26.30        45.73        30.31        27.19        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-5521 
       36.69        38.53        60.23        46.55        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       68.35        38.76        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7317 
       27.02        49.02        61.15        21.80         9.70         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7797 
       14.14        18.15        19.59        17.29         3.75        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46E TCGA-EJ-A46F 
       64.47        63.98        10.32         5.33        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
        3.06         7.53        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       16.24         1.78        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       69.37        18.21        68.68        50.70        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6494 
       39.95        38.01        40.31        45.80        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 
       56.75        52.87        38.27        38.96        27.91        35.34 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 
        2.93         2.01         2.37        14.47        28.54        28.60 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
        1.74         1.68        24.59         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.48        17.85        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        1.15         2.01         2.20         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HI-7169 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
        1.45         1.25        88.24        20.19        12.30        21.76 
TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.04        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       13.32        17.36         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       14.37        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       44.68       151.36        67.59        90.51        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 
       34.95        22.75        26.43        20.65         5.19         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       13.15        27.02        25.08         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M 
       47.21        86.14        11.90         8.84        12.95         6.02 
TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       15.81        32.91        15.09        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       23.93        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
       17.82        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA 
        9.04         2.99        25.97        31.96        31.96        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HL 
       29.23        27.09        39.65        25.48        52.96        38.56 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       62.14        60.56        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL 
       47.38        37.97        26.24        41.39        60.99        24.33 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                        0.76                         0.30 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                      115.86                       151.36 
  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE 
                       28.26                        21.80 
[1] "0.8 - 115.9 (28.3)" "0.3 - 151.4 (21.8)"
[1] "hr=" "1"  
D62V2, continuous
                              vv
clus                            T2  T3  T4
  DEL PEAK 34(18Q23) MUTATED    32  66   2
  DEL PEAK 34(18Q23) WILD-TYPE 118 140   3
D62V3, multiclass
    clus
vv   DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE
  T2                         32                          118
  T3                         66                          140
  T4                          2                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                              cls
clus                             0   1
  DEL PEAK 34(18Q23) MUTATED    71  17
  DEL PEAK 34(18Q23) WILD-TYPE 192  27
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 34(18Q23) MUTATED     71   17
  DEL PEAK 34(18Q23) WILD-TYPE  192   27
   clus
vv  DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE
  0                         71                          192
  1                         17                           27
[1] 2 2
[1] FALSE
D62V5, binary
                              cls
clus                             0   1
  DEL PEAK 34(18Q23) MUTATED     3  97
  DEL PEAK 34(18Q23) WILD-TYPE  10 253
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 34(18Q23) MUTATED      3   97
  DEL PEAK 34(18Q23) WILD-TYPE   10  253
                                        clus
vv                                       DEL PEAK 34(18Q23) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                          3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                            97
                                        clus
vv                                       DEL PEAK 34(18Q23) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                           10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             253
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 34(18Q23) MUTATED    61  35   0   1
  DEL PEAK 34(18Q23) WILD-TYPE 182  55   5  10
D62V6, multiclass
    clus
vv   DEL PEAK 34(18Q23) MUTATED DEL PEAK 34(18Q23) WILD-TYPE
  R0                         61                          182
  R1                         35                           55
  R2                          0                            5
  RX                          1                           10
[1] 4 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, continuous
D62V8, continuous
D62V9, continuous
D62V10, continuous
D62V11, continuous
D62V12, continuous
D62V13, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(18Q23) MUTATED       0                         3    40
  DEL PEAK 34(18Q23) WILD-TYPE     2                         4   106
D62V14, multiclass
                           clus
vv                          DEL PEAK 34(18Q23) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             40
                           clus
vv                          DEL PEAK 34(18Q23) WILD-TYPE
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                              106
[1] 3 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 = DEL PEAK 35(19Q13.2) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(19Q13.2) MUTATED    32   1
  DEL PEAK 35(19Q13.2) WILD-TYPE 323   5
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                            33                            328 
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                             1                              5 
$`DEL PEAK 35(19Q13.2) MUTATED`
TCGA-CH-5741 TCGA-CH-5751 TCGA-CH-5753 TCGA-EJ-5542 TCGA-EJ-7327 TCGA-EJ-7328 
       12.99        35.01         1.02        29.06         5.75        27.68 
TCGA-EJ-7781 TCGA-EJ-8474 TCGA-G9-6379 TCGA-G9-7525 TCGA-HC-7078 TCGA-HC-7080 
       23.90        10.32        45.80        32.68         5.33         2.01 
TCGA-HC-7752 TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HI-7171 TCGA-J4-A83M 
        3.22        22.42        22.36         0.76        43.69        14.37 
TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-TP-A8TV 
       13.87        10.62        49.25       113.33        67.07         8.19 
TCGA-VN-A88P TCGA-WW-A8ZI TCGA-XK-AAJA TCGA-YL-A8HM TCGA-YL-A8SB TCGA-YL-A8SJ 
       30.15         5.79        30.58        36.95        45.50        45.86 
TCGA-YL-A8SL TCGA-YL-A9WK TCGA-YL-A9WL 
       26.24        62.37        24.33 

$`DEL PEAK 35(19Q13.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 
       24.03         1.02        13.02        31.00         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       47.87        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        6.28         0.30        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-A46B 
       23.05        19.92        64.47        63.98        26.99         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 
       38.01        40.31        26.66        31.50        37.97        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        52.87        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-A9S0 
       38.96        27.91        30.97        35.34        28.18        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 
       21.14         6.08        30.94         3.68        19.76         2.93 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       26.04         1.97         1.12        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56         1.84        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        1.15         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       88.24        82.92        20.19        12.30        21.76        17.03 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       16.04        16.54        16.14        20.52        14.93        17.19 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        13.32        17.36         9.17         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83N TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X 
        6.77        10.39        20.28         5.85        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       67.59        90.51        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I 
       41.00       114.64        47.21        86.14        11.90         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q 
       25.51        12.95         6.02        15.52        15.81        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       15.09         4.34       106.95        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        75.91        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       48.85        21.53        17.82        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.50        31.96        28.54        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       39.65        25.48        52.96        49.02        38.56        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       62.14        60.56        16.83        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       47.38        37.97       106.75        71.34        62.79         7.00 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       14.04        41.39        60.99        49.91        28.34         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                          0.76                           0.30 
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                        113.33                         151.36 
  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE 
                        24.330                         23.915 
[1] "0.8 - 113.3 (24.3)" "0.3 - 151.4 (23.9)"
[1] "hr=" "1.9"
D63V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 35(19Q13.2) MUTATED     9  23   1
  DEL PEAK 35(19Q13.2) WILD-TYPE 141 183   4
D63V3, multiclass
    clus
vv   DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE
  T2                            9                            141
  T3                           23                            183
  T4                            1                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, binary
                                cls
clus                               0   1
  DEL PEAK 35(19Q13.2) MUTATED    27   6
  DEL PEAK 35(19Q13.2) WILD-TYPE 236  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(19Q13.2) MUTATED     27    6
  DEL PEAK 35(19Q13.2) WILD-TYPE  236   38
   clus
vv  DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE
  0                           27                            236
  1                            6                             38
[1] 2 2
[1] FALSE
D63V5, binary
                                cls
clus                               0   1
  DEL PEAK 35(19Q13.2) MUTATED     0  33
  DEL PEAK 35(19Q13.2) WILD-TYPE  13 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(19Q13.2) MUTATED      0   33
  DEL PEAK 35(19Q13.2) WILD-TYPE   13  317
                                        clus
vv                                       DEL PEAK 35(19Q13.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            0
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              33
                                        clus
vv                                       DEL PEAK 35(19Q13.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               317
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(19Q13.2) MUTATED    20  13   0   0
  DEL PEAK 35(19Q13.2) WILD-TYPE 223  77   5  11
D63V6, multiclass
    clus
vv   DEL PEAK 35(19Q13.2) MUTATED DEL PEAK 35(19Q13.2) WILD-TYPE
  R0                           20                            223
  R1                           13                             77
  R2                            0                              5
  RX                            0                             11
[1] 4 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, continuous
D63V8, continuous
D63V9, continuous
D63V10, continuous
D63V11, continuous
D63V12, continuous
D63V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(19Q13.2) MUTATED       0                         0    11
  DEL PEAK 35(19Q13.2) WILD-TYPE     2                         7   135
D63V14, multiclass
                           clus
vv                          DEL PEAK 35(19Q13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               11
                           clus
vv                          DEL PEAK 35(19Q13.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                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(64) Variable = DEL PEAK 36(21Q22.2) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(21Q22.2) MUTATED    36   0
  DEL PEAK 36(21Q22.2) WILD-TYPE 319   6
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                            36                            325 
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                             0                              6 
$`DEL PEAK 36(21Q22.2) MUTATED`
TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5765 
       12.99        24.03        35.01         1.02         0.92        23.01 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5516 TCGA-EJ-5519 TCGA-EJ-7321 TCGA-EJ-7325 
       29.79        46.52        46.55        64.50         7.66        17.52 
TCGA-EJ-7785 TCGA-G9-6329 TCGA-G9-6342 TCGA-G9-7521 TCGA-G9-A9S7 TCGA-H9-A6BY 
       20.55        41.62        55.76        30.97        21.14         3.68 
TCGA-HC-7744 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-8259 TCGA-J4-A67T TCGA-J4-A6G1 
        1.68        26.04         1.84         2.27         6.02        13.32 
TCGA-J4-A83K TCGA-J9-A52B TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A87D TCGA-VP-A87K 
        6.77        13.87        32.91       106.95        60.92        21.53 
TCGA-X4-A8KQ TCGA-XK-AAIW TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A9WL TCGA-YL-A9WY 
       37.18        31.96        45.14        45.86        24.33        28.34 

$`DEL PEAK 36(21Q22.2) WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        13.97         1.97 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 
        1.02        13.02        31.00         2.04        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
        1.02         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5501 
       29.00        27.16        33.11        19.56        13.32        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       60.23        47.80        52.27        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7328 
        9.70         9.50         9.37        16.77         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       17.23        16.24         1.78        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       66.67        69.37        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        52.87        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       38.96        27.91        35.34        28.18        32.68        26.01 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        6.08        30.94        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
        2.66         1.74         1.48         2.07        24.59         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 
       19.36        22.42         3.12        23.87         2.17         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83L 
       17.19        17.36         9.17         9.17        10.19        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       14.37        20.28         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 
        6.02        15.52        15.81        30.15        15.09         4.34 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       26.47        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KS 
       66.97        21.80        48.85        17.82         5.79        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.50        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       36.95        71.77        62.14        60.56        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       41.46        28.77        47.38        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       62.37        49.91         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                          0.92                           0.30 
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                        106.95                         151.36 
  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE 
                         24.18                          23.90 
[1] "0.9 - 107.0 (24.2)" "0.3 - 151.4 (23.9)"
[1] "hr="     "7.8e+07"
D64V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 36(21Q22.2) MUTATED     8  28   1
  DEL PEAK 36(21Q22.2) WILD-TYPE 142 178   4
D64V3, multiclass
    clus
vv   DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE
  T2                            8                            142
  T3                           28                            178
  T4                            1                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q22.2) MUTATED    23   8
  DEL PEAK 36(21Q22.2) WILD-TYPE 240  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q22.2) MUTATED     23    8
  DEL PEAK 36(21Q22.2) WILD-TYPE  240   36
   clus
vv  DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE
  0                           23                            240
  1                            8                             36
[1] 2 2
[1] FALSE
D64V5, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q22.2) MUTATED     3  34
  DEL PEAK 36(21Q22.2) WILD-TYPE  10 316
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q22.2) MUTATED      3   34
  DEL PEAK 36(21Q22.2) WILD-TYPE   10  316
                                        clus
vv                                       DEL PEAK 36(21Q22.2) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            3
  PROSTATE ADENOCARCINOMA ACINAR TYPE                              34
                                        clus
vv                                       DEL PEAK 36(21Q22.2) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                             10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               316
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(21Q22.2) MUTATED    25   9   0   2
  DEL PEAK 36(21Q22.2) WILD-TYPE 218  81   5   9
D64V6, multiclass
    clus
vv   DEL PEAK 36(21Q22.2) MUTATED DEL PEAK 36(21Q22.2) WILD-TYPE
  R0                           25                            218
  R1                            9                             81
  R2                            0                              5
  RX                            2                              9
[1] 4 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, continuous
D64V8, continuous
D64V9, continuous
D64V10, continuous
D64V11, continuous
D64V12, continuous
D64V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(21Q22.2) MUTATED       1                         2    15
  DEL PEAK 36(21Q22.2) WILD-TYPE     1                         5   131
D64V14, multiclass
                           clus
vv                          DEL PEAK 36(21Q22.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               15
                           clus
vv                          DEL PEAK 36(21Q22.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = DEL PEAK 37(21Q22.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(21Q22.3) MUTATED   110   0
  DEL PEAK 37(21Q22.3) WILD-TYPE 245   6
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                           110                            251 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                             0                              6 
$`DEL PEAK 37(21Q22.3) MUTATED`
TCGA-2A-A8VL TCGA-2A-A8VV TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5746 TCGA-CH-5751 
       20.42        22.06         1.02        12.99        24.03        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5764 TCGA-CH-5765 
       31.00         1.02         2.04         0.92         1.02        23.01 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5794 TCGA-EJ-5495 
       24.03         2.04        32.02        33.01        29.00        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5499 TCGA-EJ-5508 TCGA-EJ-5512 TCGA-EJ-5516 
       19.56        13.32        46.52        38.93        38.53        46.55 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5542 
       64.50        51.88        68.35        43.07        38.76        29.06 
TCGA-EJ-7315 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-8469 
        9.50        16.77         7.66        25.87        25.68        63.98 
TCGA-EJ-A46F TCGA-EJ-A65F TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6342 
        9.83        18.41        28.41        41.62        67.99        55.76 
TCGA-G9-6354 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6371 
       49.35        47.44        45.30        39.39        44.81        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-7509 TCGA-G9-7521 TCGA-G9-7525 TCGA-G9-A9S7 
       26.66        31.50        38.27        30.97        32.68        21.14 
TCGA-H9-A6BY TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
        3.68         2.37        14.47         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8213 
        2.93         2.07        26.04        17.85         1.84        19.36 
TCGA-HC-8257 TCGA-HC-8259 TCGA-HC-8262 TCGA-HC-A48F TCGA-J4-8198 TCGA-J4-A67K 
       23.87         2.27        22.32        22.36        20.19        21.76 
TCGA-J4-A67L TCGA-J4-A67S TCGA-J4-A6M7 TCGA-J4-A83K TCGA-J9-A52B TCGA-J9-A52E 
       17.03        17.19         9.17         6.77        13.87        10.62 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A7B1 
       44.68       115.86        54.54        90.51       113.33        34.95 
TCGA-M7-A71Z TCGA-M7-A725 TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88K 
        6.87        18.84       114.64        86.14        11.90        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       12.95         6.02        32.91       106.95        26.47        84.69 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87K TCGA-X4-A8KQ TCGA-XK-AAIV TCGA-XK-AAIW 
       55.56        60.92        21.53        37.18        31.50        31.96 
TCGA-YL-A8HK TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WL 
       49.02        45.14        45.86        26.24        71.34        24.33 
TCGA-YL-A9WY TCGA-ZG-A8QZ 
       28.34         7.86 

$`DEL PEAK 37(21Q22.3) WILD-TYPE`
TCGA-2A-A8VO TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 
       43.79        33.96         3.68        25.35         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5762 
       22.06        13.97         1.97         1.02        13.02        44.02 
TCGA-CH-5763 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       12.00         1.02        15.06        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5498 TCGA-EJ-5501 TCGA-EJ-5502 
        9.99         2.99        27.16        29.79        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5509 
       45.73        28.93        30.31        27.19        23.90        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 
       36.69        48.53        36.23        60.23        47.80        52.27 
TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       36.66        39.75        60.23        41.85        47.87        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7317 
       49.02        61.15        83.57        21.80         9.70         9.37 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       38.37        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 
       17.29         3.75        23.05        19.92        64.47        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H 
       10.32         5.33         4.24        17.49         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        17.62        12.92        13.71         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        7.56        15.42        13.45         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6343 
        1.78        87.35        81.04        66.67        69.37        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       68.68        49.81        46.16        50.70        47.15        46.52 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6378 TCGA-G9-6379 
        3.32        40.18        39.95        38.01        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-H9-7775 
       38.96        27.91        35.34        28.18        26.01         6.08 
TCGA-H9-A6BX TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7210 
       30.94        19.76         5.33         2.93         2.01        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        0.79        28.60         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
        1.74         1.48         1.68        24.59         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-8216 TCGA-HC-8256 
        3.22        30.51         1.48        24.56        22.42         3.12 
TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        2.17         1.94        17.95         1.58        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 TCGA-J4-A67M TCGA-J4-A67N 
       88.24        82.92        43.69        12.30        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       16.14        20.52        14.93         6.02        13.32        17.36 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C 
        9.17        10.19        10.39        14.37        20.28         5.85 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       93.99        56.28        61.78        30.02       151.36        67.59 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B2 TCGA-KK-A8IB 
       49.25        67.07        58.19        27.62        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       26.43        20.65         5.19         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO TCGA-TP-A8TV 
       25.08        15.88         3.19        41.00        47.21         8.19 
TCGA-VN-A88I TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VN-A943 
        8.84        15.52        15.81        30.15        15.09         4.34 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       94.65        23.93        75.91        66.97        21.80        48.85 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
       17.82         5.79        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAJ3 TCGA-XK-AAJA 
        9.04         2.99        25.97        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       38.56        36.95        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO 
       45.50        41.46        28.77        47.38        37.97       106.75 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9ND 
       49.91         1.64         4.93         1.12         6.02 

  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                          0.92                           0.30 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                        115.86                         151.36 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                         26.14                          21.96 
[1] "0.9 - 115.9 (26.1)" "0.3 - 151.4 (22.0)"
[1] "hr="     "3.5e+08"
D65V2, continuous
                                vv
clus                              T2  T3  T4
  DEL PEAK 37(21Q22.3) MUTATED    38  69   3
  DEL PEAK 37(21Q22.3) WILD-TYPE 112 137   2
D65V3, multiclass
    clus
vv   DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE
  T2                           38                            112
  T3                           69                            137
  T4                            3                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V4, binary
                                cls
clus                               0   1
  DEL PEAK 37(21Q22.3) MUTATED    74  20
  DEL PEAK 37(21Q22.3) WILD-TYPE 189  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(21Q22.3) MUTATED     74   20
  DEL PEAK 37(21Q22.3) WILD-TYPE  189   24
   clus
vv  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE
  0                           74                            189
  1                           20                             24
[1] 2 2
[1] FALSE
D65V5, binary
                                cls
clus                               0   1
  DEL PEAK 37(21Q22.3) MUTATED     4 107
  DEL PEAK 37(21Q22.3) WILD-TYPE   9 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(21Q22.3) MUTATED      4  107
  DEL PEAK 37(21Q22.3) WILD-TYPE    9  243
                                        clus
vv                                       DEL PEAK 37(21Q22.3) MUTATED
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                            4
  PROSTATE ADENOCARCINOMA ACINAR TYPE                             107
                                        clus
vv                                       DEL PEAK 37(21Q22.3) WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                              9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                               243
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(21Q22.3) MUTATED    76  25   2   6
  DEL PEAK 37(21Q22.3) WILD-TYPE 167  65   3   5
D65V6, multiclass
    clus
vv   DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE
  R0                           76                            167
  R1                           25                             65
  R2                            2                              3
  RX                            6                              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"
D65V7, continuous
D65V8, continuous
D65V9, continuous
D65V10, continuous
D65V11, continuous
D65V12, continuous
D65V13, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(21Q22.3) MUTATED       2                         1    50
  DEL PEAK 37(21Q22.3) WILD-TYPE     0                         6    96
D65V14, multiclass
                           clus
vv                          DEL PEAK 37(21Q22.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               50
                           clus
vv                          DEL PEAK 37(21Q22.3) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 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"
